Extract mutations in VGSC

In [1]:

    

%run setup.ipynb


    

In [2]:

    

# download gene annotations from vectorbase
!wget \
    --no-clobber \
    -O ../data/Anopheles-gambiae-PEST_BASEFEATURES_AgamP4.4.gff3.gz \
    https://www.vectorbase.org/download/anopheles-gambiae-pestbasefeaturesagamp44gff3gz


    

    




--2018-08-01 15:06:26--  https://www.vectorbase.org/download/anopheles-gambiae-pestbasefeaturesagamp44gff3gz
Resolving www.vectorbase.org (www.vectorbase.org)... 129.74.255.228
Connecting to www.vectorbase.org (www.vectorbase.org)|129.74.255.228|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://www.vectorbase.org/sites/default/files/ftp/downloads/Anopheles-gambiae-PEST_BASEFEATURES_AgamP4.4.gff3.gz [following]
--2018-08-01 15:06:27--  https://www.vectorbase.org/sites/default/files/ftp/downloads/Anopheles-gambiae-PEST_BASEFEATURES_AgamP4.4.gff3.gz
Reusing existing connection to www.vectorbase.org:443.
HTTP request sent, awaiting response... 200 OK
Length: 2688173 (2.6M) [application/x-gzip]
Saving to: ‘../data/Anopheles-gambiae-PEST_BASEFEATURES_AgamP4.4.gff3.gz’

100%[======================================>] 2,688,173   2.78MB/s   in 0.9s   

2018-08-01 15:06:28 (2.78 MB/s) - ‘../data/Anopheles-gambiae-PEST_BASEFEATURES_AgamP4.4.gff3.gz’ saved [2688173/2688173]

In [3]:

    

# download the Davies et al. (2007) gene models
!wget \
    --no-clobber \
    -O ../data/davies_vgsc_model_20170125.gff3 \
    http://alimanfoo.github.io/assets/davies_vgsc_model_20170125.gff3


    

    




--2018-08-01 15:06:33--  http://alimanfoo.github.io/assets/davies_vgsc_model_20170125.gff3
Resolving alimanfoo.github.io (alimanfoo.github.io)... 185.199.108.153, 185.199.109.153, 185.199.110.153, ...
Connecting to alimanfoo.github.io (alimanfoo.github.io)|185.199.108.153|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 48092 (47K) [application/octet-stream]
Saving to: ‘../data/davies_vgsc_model_20170125.gff3’

100%[======================================>] 48,092      --.-K/s   in 0.009s  

2018-08-01 15:06:34 (4.84 MB/s) - ‘../data/davies_vgsc_model_20170125.gff3’ saved [48092/48092]

In [4]:

    

# load the vectorbase geneset
geneset_agamp44 = allel.FeatureTable.from_gff3('../data/Anopheles-gambiae-PEST_BASEFEATURES_AgamP4.4.gff3.gz',
                                               attributes=['ID', 'Parent'])
geneset_agamp44 = geneset_to_pandas(geneset_agamp44)
geneset_agamp44.head()


    

    
Out[4]:







  

    

      

      
seqid
      
source
      
type
      
start
      
end
      
score
      
strand
      
phase
      
ID
      
Parent
    
  
  

    

      
0
      
2L
      
VectorBase
      
chromosome
      
1
      
49364325
      
-1.0
      
.
      
-1
      
2L
      
b'.'
    
    

      
1
      
2L
      
VectorBase
      
gene
      
157348
      
186936
      
-1.0
      
-
      
-1
      
AGAP004677
      
b'.'
    
    

      
2
      
2L
      
VectorBase
      
mRNA
      
157348
      
181305
      
-1.0
      
-
      
-1
      
AGAP004677-RA
      
AGAP004677
    
    

      
3
      
2L
      
VectorBase
      
three_prime_UTR
      
157348
      
157495
      
-1.0
      
-
      
-1
      
b'.'
      
AGAP004677-RA
    
    

      
4
      
2L
      
VectorBase
      
exon
      
157348
      
157623
      
-1.0
      
-
      
-1
      
b'.'
      
AGAP004677-RA
    
  

In [5]:

    

# subset to VGSC
geneset_agamp44_vgsc = geneset_agamp44.query(region_vgsc.query_str).copy()
# replace CDS IDs as not informative
geneset_agamp44_vgsc['ID'].values[(geneset_agamp44_vgsc.type == 'CDS').values] = ''
geneset_agamp44_vgsc.type.value_counts()


    

    
Out[5]:





exon    93
CDS     93
mRNA     3
gene     1
Name: type, dtype: int64

In [6]:

    

# load the Davies geneset
geneset_davies = allel.FeatureTable.from_gff3('../data/davies_vgsc_model_20170125.gff3',
                                              attributes=['ID', 'Parent'])
geneset_davies = geneset_to_pandas(geneset_davies)
geneset_davies.head()


    

    
Out[6]:







  

    

      

      
seqid
      
source
      
type
      
start
      
end
      
score
      
strand
      
phase
      
ID
      
Parent
    
  
  

    

      
0
      
2L
      
Davies et al. (2007)
      
mRNA
      
2358158
      
2431617
      
-1.0
      
+
      
-1
      
Davies-C1N2
      
AGAP004707
    
    

      
1
      
2L
      
Davies et al. (2007)
      
mRNA
      
2358158
      
2431617
      
-1.0
      
+
      
-1
      
Davies-C3N2
      
AGAP004707
    
    

      
2
      
2L
      
Davies et al. (2007)
      
mRNA
      
2358158
      
2431617
      
-1.0
      
+
      
-1
      
Davies-C5N2
      
AGAP004707
    
    

      
3
      
2L
      
Davies et al. (2007)
      
mRNA
      
2358158
      
2431617
      
-1.0
      
+
      
-1
      
Davies-C7N2
      
AGAP004707
    
    

      
4
      
2L
      
Davies et al. (2007)
      
mRNA
      
2358158
      
2431617
      
-1.0
      
+
      
-1
      
Davies-C8N2
      
AGAP004707
    
  

In [7]:

    

# make a combined geneset
geneset_vgsc_combined = pandas.concat([geneset_agamp44_vgsc, geneset_davies])
geneset_vgsc_combined.query("type == 'mRNA'")


    

    
Out[7]:







  

    

      

      
seqid
      
source
      
type
      
start
      
end
      
score
      
strand
      
phase
      
ID
      
Parent
    
  
  

    

      
666
      
2L
      
VectorBase
      
mRNA
      
2358158
      
2431617
      
-1.0
      
+
      
-1
      
AGAP004707-RA
      
AGAP004707
    
    

      
729
      
2L
      
VectorBase
      
mRNA
      
2358158
      
2431617
      
-1.0
      
+
      
-1
      
AGAP004707-RB
      
AGAP004707
    
    

      
792
      
2L
      
VectorBase
      
mRNA
      
2358158
      
2431617
      
-1.0
      
+
      
-1
      
AGAP004707-RC
      
AGAP004707
    
    

      
0
      
2L
      
Davies et al. (2007)
      
mRNA
      
2358158
      
2431617
      
-1.0
      
+
      
-1
      
Davies-C1N2
      
AGAP004707
    
    

      
1
      
2L
      
Davies et al. (2007)
      
mRNA
      
2358158
      
2431617
      
-1.0
      
+
      
-1
      
Davies-C3N2
      
AGAP004707
    
    

      
2
      
2L
      
Davies et al. (2007)
      
mRNA
      
2358158
      
2431617
      
-1.0
      
+
      
-1
      
Davies-C5N2
      
AGAP004707
    
    

      
3
      
2L
      
Davies et al. (2007)
      
mRNA
      
2358158
      
2431617
      
-1.0
      
+
      
-1
      
Davies-C7N2
      
AGAP004707
    
    

      
4
      
2L
      
Davies et al. (2007)
      
mRNA
      
2358158
      
2431617
      
-1.0
      
+
      
-1
      
Davies-C8N2
      
AGAP004707
    
    

      
5
      
2L
      
Davies et al. (2007)
      
mRNA
      
2358158
      
2431617
      
-1.0
      
+
      
-1
      
Davies-C10N2
      
AGAP004707
    
    

      
6
      
2L
      
Davies et al. (2007)
      
mRNA
      
2358158
      
2431617
      
-1.0
      
+
      
-1
      
Davies-C11N2
      
AGAP004707
    
    

      
7
      
2L
      
Davies et al. (2007)
      
mRNA
      
2358158
      
2431617
      
-1.0
      
+
      
-1
      
Davies-C1N9
      
AGAP004707
    
    

      
8
      
2L
      
Davies et al. (2007)
      
mRNA
      
2358158
      
2431617
      
-1.0
      
+
      
-1
      
Davies-C8N9
      
AGAP004707
    
    

      
9
      
2L
      
Davies et al. (2007)
      
mRNA
      
2358158
      
2431617
      
-1.0
      
+
      
-1
      
Davies-C1N9ck
      
AGAP004707
    
  

In [8]:

    

# setup a variant annotator
annotator = veff.Annotator(
    fasta_path='../ngs.sanger.ac.uk/production/ag1000g/phase1/AR3/genome/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP3.fa', 
    gff3_path=['../data/Anopheles-gambiae-PEST_BASEFEATURES_AgamP4.4.gff3.gz',
               '../data/davies_vgsc_model_20170125.gff3'],
    seqid='2L'
)


    

In [9]:

    

# identify VGSC transcripts
transcript_ids = [f.feature_id for f in annotator.get_children('AGAP004707')]
transcript_ids


    

    
Out[9]:





['AGAP004707-RA',
 'AGAP004707-RB',
 'AGAP004707-RC',
 'Davies-C1N2',
 'Davies-C3N2',
 'Davies-C5N2',
 'Davies-C7N2',
 'Davies-C8N2',
 'Davies-C10N2',
 'Davies-C11N2',
 'Davies-C1N9',
 'Davies-C8N9',
 'Davies-C1N9ck']

In [10]:

    

# tabulate Davies exons
tbl_davies_exons = (
    etl
    .fromdataframe(geneset_davies)
    .eq('type', 'CDS')
    .cutout('Parent', 'source', 'type', 'score', 'strand', 'phase')
    .merge(key=('start', 'end'))
    .rename('seqid', 'exon_seqid')
    .rename('ID', 'exon')
    .rename('start', 'exon_start')
    .rename('end', 'exon_end')
    .movefield('exon_seqid', 0)
)
tbl_davies_exons.displayall()


    

    








0|exon_seqid
1|exon_start
2|exon_end
3|exon




2L
2358158
2358304
1


2L
2359640
2359672
2j


2L
2361989
2362144
3


2L
2381065
2381270
4


2L
2382270
2382398
5


2L
2385694
2385785
6


2L
2390129
2390341
7


2L
2390425
2390485
8


2L
2390594
2390738
9


2L
2391156
2391320
10


2L
2399898
2400173
11i+


2L
2401549
2401569
12


2L
2402447
2402509
13a


2L
2403086
2403269
14


2L
2407622
2407818
15


2L
2407894
2407993
16


2L
2408071
2408139
17


2L
2416794
2417071
18b+


2L
2417185
2417358
19


2L
2417637
2417799
20c


2L
2421385
2421547
20d


2L
2422468
2422655
21


2L
2422713
2422920
22


2L
2424207
2424418
23f+


2L
2424237
2424418
23f-


2L
2424651
2424870
24h+


2L
2424729
2424870
24h-


2L
2424946
2425211
25


2L
2425278
2425451
26


2L
2425770
2425892
27k


2L
2427988
2428110
27l


2L
2429097
2429219
28


2L
2429282
2429476
29


2L
2429556
2429801
30


2L
2429872
2430142
31


2L
2430224
2430528
32


2L
2430601
2431617
33

In [11]:

    

callset = phase1_ar31.callset
callset


    

    
Out[11]:





<zarr.hierarchy.Group '/' read-only>

In [12]:

    

# what fields are available?
print(', '.join(callset['2L/variants']))


    

    




ABHet, ABHom, AC, AF, ALT, AN, ANN, Accessible, BaseCounts, BaseQRankSum, CHROM, Coverage, CoverageMQ0, DP, DS, Dels, FILTER_FS, FILTER_HRun, FILTER_HighCoverage, FILTER_HighMQ0, FILTER_LowCoverage, FILTER_LowMQ, FILTER_LowQual, FILTER_NoCoverage, FILTER_PASS, FILTER_QD, FILTER_ReadPosRankSum, FILTER_RefN, FILTER_RepeatDUST, FS, HRun, HW, HaplotypeScore, HighCoverage, HighMQ0, InbreedingCoeff, LOF, LowCoverage, LowMQ, LowPairing, MLEAC, MLEAF, MQ, MQ0, MQRankSum, NDA, NMD, NoCoverage, OND, POS, QD, QUAL, REF, RPA, RU, ReadPosRankSum, RefMasked, RefN, RepeatDUST, RepeatMasker, RepeatTRF, STR, VariantType, is_snp, num_alleles, svlen

In [13]:

    

# what SNPEFF fields are available?
print(', '.join(callset['2L/variants/ANN'].dtype.names))


    

    




Allele, Annotation, Annotation_Impact, Gene_Name, Gene_ID, Feature_Type, Feature_ID, Transcript_BioType, Rank, HGVS_c, HGVS_p, cDNA_pos, cDNA_length, CDS_pos, CDS_length, AA_pos, AA_length, Distance

In [14]:

    

samples = phase1_ar3.df_samples
samples.head()


    

    
Out[14]:







  

    

      

      
ox_code
      
src_code
      
sra_sample_accession
      
population
      
country
      
region
      
contributor
      
contact
      
year
      
m_s
      
...
      
pca_3L_free_pc3
      
pca_3L_free_pc4
      
pca_2La_pc1
      
pca_2La_pc2
      
pca_2La_pc3
      
pca_2La_pc4
      
pca_2Rb_pc1
      
pca_2Rb_pc2
      
pca_2Rb_pc3
      
pca_2Rb_pc4
    
    

      
index
      

      

      

      

      

      

      

      

      

      

      

      

      

      

      

      

      

      

      

      

      

    
  
  

    

      
0
      
AB0085-C
      
BF2-4
      
ERS223996
      
BFS
      
Burkina Faso
      
Pala
      
Austin Burt
      
Sam O'Loughlin
      
2012
      
S
      
...
      
-8.290940
      
-18.542768
      
-55.511389
      
32.682143
      
-1.833739
      
-0.381984
      
-38.934301
      
31.939383
      
19.345606
      
7.362004
    
    

      
1
      
AB0087-C
      
BF3-3
      
ERS224013
      
BFM
      
Burkina Faso
      
Bana
      
Austin Burt
      
Sam O'Loughlin
      
2012
      
M
      
...
      
-38.603076
      
76.915617
      
-51.856633
      
27.401249
      
2.586488
      
0.643100
      
-10.072879
      
29.007266
      
-21.736087
      
-30.309562
    
    

      
2
      
AB0088-C
      
BF3-5
      
ERS223991
      
BFM
      
Burkina Faso
      
Bana
      
Austin Burt
      
Sam O'Loughlin
      
2012
      
M
      
...
      
-35.553340
      
73.985488
      
-50.942456
      
28.572207
      
3.072583
      
-0.643137
      
12.281744
      
22.288417
      
-43.661301
      
-51.557140
    
    

      
3
      
AB0089-C
      
BF3-8
      
ERS224031
      
BFM
      
Burkina Faso
      
Bana
      
Austin Burt
      
Sam O'Loughlin
      
2012
      
M
      
...
      
-36.621568
      
76.453993
      
-51.169247
      
29.414975
      
2.198434
      
0.013562
      
-10.664072
      
29.601333
      
-16.831559
      
-25.452854
    
    

      
4
      
AB0090-C
      
BF3-10
      
ERS223936
      
BFM
      
Burkina Faso
      
Bana
      
Austin Burt
      
Sam O'Loughlin
      
2012
      
M
      
...
      
-36.097756
      
72.036309
      
-48.607416
      
26.407532
      
1.643226
      
0.102582
      
12.897113
      
22.194444
      
-48.882378
      
-52.420487
    
  

5 rows × 38 columns

In [15]:

    

def tabulate_variants(callset, snpeff, seqid, start, end, pop_ids, subpops):
    """Build a table of variants for a given callset and genome region."""
    
    variants = callset[seqid]['variants']
    ann = snpeff[seqid]['variants']['ANN']
    pos = allel.SortedIndex(variants['POS'])
    loc = pos.locate_range(start, end)
    genotype = allel.GenotypeArray(callset[seqid]['calldata/genotype'][loc])
    acs = genotype.count_alleles_subpops(max_allele=3, subpops=subpops)
    
    # extract columns
    variants_fields = [
        'CHROM',
        'POS',
        'num_alleles',
        'REF',
        'ALT',
        'AC',
        'FILTER_PASS',
        'NoCoverage',
        'LowCoverage',
        'HighCoverage',
        'LowMQ',
        'HighMQ0',
        'RepeatDUST',
        'RepeatMasker',
        'RepeatTRF',
        'FS',
        'HRun',
        'QD',
        'ReadPosRankSum',
    ]
    ann_fields = ['Allele', 'Annotation', 'HGVS_c', 'HGVS_p', 'Feature_ID', 'CDS_pos']
    cols = (
        [variants[f][loc] for f in variants_fields] + 
        [ann[loc][f] for f in ann_fields] + 
        [acs[p].to_frequencies() for p in pop_ids]
    )

    def split_alleles(row):
        for i in range(row.num_alleles - 1):
            # break down alleles
            out = [
                row['CHROM'], 
                row['POS'], 
                row['num_alleles'], 
                row['REF'], 
                row['ALT'][i], 
                row['AC'][i], 
                i, 
            ]
            # add in remaining variant annotations
            out += [row[f] for f in variants_fields[6:]]
            # SNPEFF annotation only applies to first allele
            if i == 0:
                out += [row[f] for f in ann_fields]
            else:
                out += [None for f in ann_fields]
            # add in population allele frequencies
            out += [row[p][i+1] for p in pop_ids]
            yield out
        
    tbl = (
        etl
        .fromcolumns(cols, header=variants_fields + ann_fields + list(pop_ids))
        .rowmapmany(split_alleles, header=variants_fields[:6] + ['ALTIX'] + variants_fields[6:] + ann_fields + list(pop_ids), failonerror=True)
        .convert('CHROM REF ALT Allele Annotation HGVS_c HGVS_p Feature_ID'.split(), lambda v: str(v, 'ascii'))
        .rename({f: 'SNPEFF_' + f for f in ann_fields})
        .rename({p: 'AF_%s' % p for p in pop_ids})
        .addfield('check_allele', lambda row: row['SNPEFF_Allele'] is None or row['SNPEFF_Allele'] == row['ALT'])
    )
    
    return tbl


    

In [16]:

    

pop_ids = 'AOM BFM GWA GNS BFS CMS GAS UGS KES'.split()


    

In [17]:

    

subpops = {p: samples[samples.population == p].index.values.tolist() for p in pop_ids}


    

In [18]:

    

# build a table of variants from phase 1
tbl_variants_phase1 = tabulate_variants(callset, callset, 
                                        seqid=region_vgsc.seqid, start=region_vgsc.start, end=region_vgsc.end, 
                                        pop_ids=pop_ids, subpops=subpops)
tbl_variants_phase1


    

    
Out[18]:







0|CHROM
1|POS
2|num_alleles
3|REF
4|ALT
5|AC
6|ALTIX
7|FILTER_PASS
8|NoCoverage
9|LowCoverage
10|HighCoverage
11|LowMQ
12|HighMQ0
13|RepeatDUST
14|RepeatMasker
15|RepeatTRF
16|FS
17|HRun
18|QD
19|ReadPosRankSum
20|SNPEFF_Allele
21|SNPEFF_Annotation
22|SNPEFF_HGVS_c
23|SNPEFF_HGVS_p
24|SNPEFF_Feature_ID
25|SNPEFF_CDS_pos
26|AF_AOM
27|AF_BFM
28|AF_GWA
29|AF_GNS
30|AF_BFS
31|AF_CMS
32|AF_GAS
33|AF_UGS
34|AF_KES
35|check_allele




2L
2358254
2
G
A
1
0
True
0
0
10
0
0
False
False
False
9.8672
1
17.547
-0.049988
A
missense_variant
n.97G>A
p.Asp33Asn
AGAP004707-RA
97
0.0
0.0
0.0
0.0
0.0
0.00181818181818
0.0
0.0
0.0
True


2L
2358316
2
T
G
73
0
True
0
0
15
0
0
False
False
False
2.4844
0
16.438
1.4219
G
intron_variant
n.147+12T>G
.
AGAP004707-RA
-1
0.0
0.0
0.0
0.0
0.0
0.132727272727
0.0
0.0
0.0
True


2L
2358328
2
T
C
2
0
True
0
0
14
0
0
False
False
False
2.7363
0
16.062
-0.646
C
intron_variant
n.147+24T>C
.
AGAP004707-RA
-1
0.0
0.00724637681159
0.0108695652174
0.0
0.0
0.0
0.0
0.0
0.0
True


2L
2358353
2
C
T
1
0
True
0
1
15
0
0
False
False
False
1.9512
0
9.8594
1.1582
T
intron_variant
n.147+49C>T
.
AGAP004707-RA
-1
0.0
0.0
0.0108695652174
0.0
0.0
0.0
0.0
0.0
0.0
True


2L
2358405
2
T
A
1
0
True
0
6
14
0
0
False
False
False
20.844
1
10.859
1.1562
A
intron_variant
n.147+101T>A
.
AGAP004707-RA
-1
0.0
0.0
0.0108695652174
0.0
0.0
0.0
0.0
0.0
0.0
True



...

In [19]:

    

cds_effects = [
    'NON_SYNONYMOUS_CODING', 
    'SYNONYMOUS_CODING',    
]
intron_effects = [
    'INTRONIC', 
    'SPLICE_CORE',
    'SPLICE_REGION',        
]
selected_effects = cds_effects + intron_effects


    

In [20]:

    

def lpop(l, default=None):
    """Pop the first item from a list if not empty."""
    try:
        return l[0]
    except IndexError:
        return default


    

In [21]:

    

def transcript_effect(transcript_id):
    def f(row):
        e = lpop([e for e in row.VEFF if e.transcript_id == transcript_id])
        if e and e.effect in cds_effects:
            return (e.effect, e.aa_change)
        elif e and e.effect in intron_effects:
            return (e.effect, e.intron_cds_5prime, e.intron_5prime_dist, e.intron_cds_3prime, e.intron_3prime_dist)
        else:
            return None
    return f


    

In [22]:

    

tbl_variants_phase1_eff = (
    tbl_variants_phase1
    # join in Davies exon information
    .intervalleftjoin(
        # don't include shorter exon alternatives
        tbl_davies_exons.select('exon', lambda v: v[-1] != '-'),
        lkey='CHROM', rkey='exon_seqid', lstart='POS', rstart='exon_start', lstop='POS', rstop='exon_end', include_stop=True)
    .cutout('exon_seqid')
    .addfield('VEFF', lambda row: [e for e in annotator.get_effects(chrom=row.CHROM, pos=row.POS, ref=row.REF, alt=row.ALT) 
                                   if e.effect in selected_effects])
    .addfield(transcript_ids[0], transcript_effect(transcript_ids[0]))
    .addfield(transcript_ids[1], transcript_effect(transcript_ids[1]))
    .addfield(transcript_ids[2], transcript_effect(transcript_ids[2]))
    .addfield(transcript_ids[3], transcript_effect(transcript_ids[3]))
    .addfield(transcript_ids[4], transcript_effect(transcript_ids[4]))
    .addfield(transcript_ids[5], transcript_effect(transcript_ids[5]))
    .addfield(transcript_ids[6], transcript_effect(transcript_ids[6]))
    .addfield(transcript_ids[7], transcript_effect(transcript_ids[7]))
    .addfield(transcript_ids[8], transcript_effect(transcript_ids[8]))
    .addfield(transcript_ids[9], transcript_effect(transcript_ids[9]))
    .addfield(transcript_ids[10], transcript_effect(transcript_ids[10]))
    .addfield(transcript_ids[11], transcript_effect(transcript_ids[11]))
    .addfield(transcript_ids[12], transcript_effect(transcript_ids[12]))
    .cutout('VEFF')
    .replaceall('.', None)
    .replaceall('', None)
    .cache()
)


    

In [23]:

    

tbl_variants_phase1_eff.display(20)


    

    








0|CHROM
1|POS
2|num_alleles
3|REF
4|ALT
5|AC
6|ALTIX
7|FILTER_PASS
8|NoCoverage
9|LowCoverage
10|HighCoverage
11|LowMQ
12|HighMQ0
13|RepeatDUST
14|RepeatMasker
15|RepeatTRF
16|FS
17|HRun
18|QD
19|ReadPosRankSum
20|SNPEFF_Allele
21|SNPEFF_Annotation
22|SNPEFF_HGVS_c
23|SNPEFF_HGVS_p
24|SNPEFF_Feature_ID
25|SNPEFF_CDS_pos
26|AF_AOM
27|AF_BFM
28|AF_GWA
29|AF_GNS
30|AF_BFS
31|AF_CMS
32|AF_GAS
33|AF_UGS
34|AF_KES
35|check_allele
36|exon_start
37|exon_end
38|exon
39|AGAP004707-RA
40|AGAP004707-RB
41|AGAP004707-RC
42|Davies-C1N2
43|Davies-C3N2
44|Davies-C5N2
45|Davies-C7N2
46|Davies-C8N2
47|Davies-C10N2
48|Davies-C11N2
49|Davies-C1N9
50|Davies-C8N9
51|Davies-C1N9ck




2L
2358254
2
G
A
1
0
True
0
0
10
0
0
False
False
False
9.8672
1
17.547
-0.049988
A
missense_variant
n.97G>A
p.Asp33Asn
AGAP004707-RA
97
0.0
0.0
0.0
0.0
0.0
0.00181818181818
0.0
0.0
0.0
True
2358158
2358304
1
('NON_SYNONYMOUS_CODING', 'D33N')
('NON_SYNONYMOUS_CODING', 'D33N')
('NON_SYNONYMOUS_CODING', 'D33N')
('NON_SYNONYMOUS_CODING', 'D33N')
('NON_SYNONYMOUS_CODING', 'D33N')
('NON_SYNONYMOUS_CODING', 'D33N')
('NON_SYNONYMOUS_CODING', 'D33N')
('NON_SYNONYMOUS_CODING', 'D33N')
('NON_SYNONYMOUS_CODING', 'D33N')
('NON_SYNONYMOUS_CODING', 'D33N')
('NON_SYNONYMOUS_CODING', 'D33N')
('NON_SYNONYMOUS_CODING', 'D33N')
('NON_SYNONYMOUS_CODING', 'D33N')


2L
2358316
2
T
G
73
0
True
0
0
15
0
0
False
False
False
2.4844
0
16.438
1.4219
G
intron_variant
n.147+12T>G
None
AGAP004707-RA
-1
0.0
0.0
0.0
0.0
0.0
0.132727272727
0.0
0.0
0.0
True
None
None
None
('INTRONIC', 'AGAP004707-PA', 12, 'AGAP004707-PA', -3691)
('INTRONIC', 'AGAP004707-PB', 12, 'AGAP004707-PB', -3691)
('INTRONIC', 'AGAP004707-PC', 12, 'AGAP004707-PC', -3691)
('INTRONIC', '1', 12, '3', -3673)
('INTRONIC', '1', 12, '3', -3673)
('INTRONIC', '1', 12, '3', -3673)
('INTRONIC', '1', 12, '3', -3673)
('INTRONIC', '1', 12, '2j', -1324)
('INTRONIC', '1', 12, '3', -3673)
('INTRONIC', '1', 12, '3', -3673)
('INTRONIC', '1', 12, '3', -3673)
('INTRONIC', '1', 12, '2j', -1324)
('INTRONIC', '1', 12, '3', -3673)


2L
2358328
2
T
C
2
0
True
0
0
14
0
0
False
False
False
2.7363
0
16.062
-0.646
C
intron_variant
n.147+24T>C
None
AGAP004707-RA
-1
0.0
0.00724637681159
0.0108695652174
0.0
0.0
0.0
0.0
0.0
0.0
True
None
None
None
('INTRONIC', 'AGAP004707-PA', 24, 'AGAP004707-PA', -3679)
('INTRONIC', 'AGAP004707-PB', 24, 'AGAP004707-PB', -3679)
('INTRONIC', 'AGAP004707-PC', 24, 'AGAP004707-PC', -3679)
('INTRONIC', '1', 24, '3', -3661)
('INTRONIC', '1', 24, '3', -3661)
('INTRONIC', '1', 24, '3', -3661)
('INTRONIC', '1', 24, '3', -3661)
('INTRONIC', '1', 24, '2j', -1312)
('INTRONIC', '1', 24, '3', -3661)
('INTRONIC', '1', 24, '3', -3661)
('INTRONIC', '1', 24, '3', -3661)
('INTRONIC', '1', 24, '2j', -1312)
('INTRONIC', '1', 24, '3', -3661)


2L
2358353
2
C
T
1
0
True
0
1
15
0
0
False
False
False
1.9512
0
9.8594
1.1582
T
intron_variant
n.147+49C>T
None
AGAP004707-RA
-1
0.0
0.0
0.0108695652174
0.0
0.0
0.0
0.0
0.0
0.0
True
None
None
None
('INTRONIC', 'AGAP004707-PA', 49, 'AGAP004707-PA', -3654)
('INTRONIC', 'AGAP004707-PB', 49, 'AGAP004707-PB', -3654)
('INTRONIC', 'AGAP004707-PC', 49, 'AGAP004707-PC', -3654)
('INTRONIC', '1', 49, '3', -3636)
('INTRONIC', '1', 49, '3', -3636)
('INTRONIC', '1', 49, '3', -3636)
('INTRONIC', '1', 49, '3', -3636)
('INTRONIC', '1', 49, '2j', -1287)
('INTRONIC', '1', 49, '3', -3636)
('INTRONIC', '1', 49, '3', -3636)
('INTRONIC', '1', 49, '3', -3636)
('INTRONIC', '1', 49, '2j', -1287)
('INTRONIC', '1', 49, '3', -3636)


2L
2358405
2
T
A
1
0
True
0
6
14
0
0
False
False
False
20.844
1
10.859
1.1562
A
intron_variant
n.147+101T>A
None
AGAP004707-RA
-1
0.0
0.0
0.0108695652174
0.0
0.0
0.0
0.0
0.0
0.0
True
None
None
None
('INTRONIC', 'AGAP004707-PA', 101, 'AGAP004707-PA', -3602)
('INTRONIC', 'AGAP004707-PB', 101, 'AGAP004707-PB', -3602)
('INTRONIC', 'AGAP004707-PC', 101, 'AGAP004707-PC', -3602)
('INTRONIC', '1', 101, '3', -3584)
('INTRONIC', '1', 101, '3', -3584)
('INTRONIC', '1', 101, '3', -3584)
('INTRONIC', '1', 101, '3', -3584)
('INTRONIC', '1', 101, '2j', -1235)
('INTRONIC', '1', 101, '3', -3584)
('INTRONIC', '1', 101, '3', -3584)
('INTRONIC', '1', 101, '3', -3584)
('INTRONIC', '1', 101, '2j', -1235)
('INTRONIC', '1', 101, '3', -3584)


2L
2358441
2
A
T
78
0
False
0
6
17
0
0
False
False
False
2.4805
1
21.703
0.94385
T
intron_variant
n.147+137A>T
None
AGAP004707-RA
-1
0.0
0.0
0.0
0.0
0.0
0.0145454545455
0.625
0.0
0.0
True
None
None
None
('INTRONIC', 'AGAP004707-PA', 137, 'AGAP004707-PA', -3566)
('INTRONIC', 'AGAP004707-PB', 137, 'AGAP004707-PB', -3566)
('INTRONIC', 'AGAP004707-PC', 137, 'AGAP004707-PC', -3566)
('INTRONIC', '1', 137, '3', -3548)
('INTRONIC', '1', 137, '3', -3548)
('INTRONIC', '1', 137, '3', -3548)
('INTRONIC', '1', 137, '3', -3548)
('INTRONIC', '1', 137, '2j', -1199)
('INTRONIC', '1', 137, '3', -3548)
('INTRONIC', '1', 137, '3', -3548)
('INTRONIC', '1', 137, '3', -3548)
('INTRONIC', '1', 137, '2j', -1199)
('INTRONIC', '1', 137, '3', -3548)


2L
2358463
2
G
T
5
0
False
0
4
16
0
0
False
False
False
22.0
0
15.211
-0.42798
T
intron_variant
n.147+159G>T
None
AGAP004707-RA
-1
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0568181818182
True
None
None
None
('INTRONIC', 'AGAP004707-PA', 159, 'AGAP004707-PA', -3544)
('INTRONIC', 'AGAP004707-PB', 159, 'AGAP004707-PB', -3544)
('INTRONIC', 'AGAP004707-PC', 159, 'AGAP004707-PC', -3544)
('INTRONIC', '1', 159, '3', -3526)
('INTRONIC', '1', 159, '3', -3526)
('INTRONIC', '1', 159, '3', -3526)
('INTRONIC', '1', 159, '3', -3526)
('INTRONIC', '1', 159, '2j', -1177)
('INTRONIC', '1', 159, '3', -3526)
('INTRONIC', '1', 159, '3', -3526)
('INTRONIC', '1', 159, '3', -3526)
('INTRONIC', '1', 159, '2j', -1177)
('INTRONIC', '1', 159, '3', -3526)


2L
2358468
2
A
C
150
0
False
0
4
17
0
0
False
False
False
1.668
0
19.812
-0.198
C
intron_variant
n.147+164A>C
None
AGAP004707-RA
-1
0.0
0.0
0.0978260869565
0.0
0.0
0.0509090909091
0.0
0.52427184466
0.0568181818182
True
None
None
None
('INTRONIC', 'AGAP004707-PA', 164, 'AGAP004707-PA', -3539)
('INTRONIC', 'AGAP004707-PB', 164, 'AGAP004707-PB', -3539)
('INTRONIC', 'AGAP004707-PC', 164, 'AGAP004707-PC', -3539)
('INTRONIC', '1', 164, '3', -3521)
('INTRONIC', '1', 164, '3', -3521)
('INTRONIC', '1', 164, '3', -3521)
('INTRONIC', '1', 164, '3', -3521)
('INTRONIC', '1', 164, '2j', -1172)
('INTRONIC', '1', 164, '3', -3521)
('INTRONIC', '1', 164, '3', -3521)
('INTRONIC', '1', 164, '3', -3521)
('INTRONIC', '1', 164, '2j', -1172)
('INTRONIC', '1', 164, '3', -3521)


2L
2358501
2
A
T
5
0
False
0
4
22
0
0
False
False
False
11.672
0
14.359
-1.2432
T
intron_variant
n.147+197A>T
None
AGAP004707-RA
-1
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0568181818182
True
None
None
None
('INTRONIC', 'AGAP004707-PA', 197, 'AGAP004707-PA', -3506)
('INTRONIC', 'AGAP004707-PB', 197, 'AGAP004707-PB', -3506)
('INTRONIC', 'AGAP004707-PC', 197, 'AGAP004707-PC', -3506)
('INTRONIC', '1', 197, '3', -3488)
('INTRONIC', '1', 197, '3', -3488)
('INTRONIC', '1', 197, '3', -3488)
('INTRONIC', '1', 197, '3', -3488)
('INTRONIC', '1', 197, '2j', -1139)
('INTRONIC', '1', 197, '3', -3488)
('INTRONIC', '1', 197, '3', -3488)
('INTRONIC', '1', 197, '3', -3488)
('INTRONIC', '1', 197, '2j', -1139)
('INTRONIC', '1', 197, '3', -3488)


2L
2358536
2
T
G
4
0
False
0
3
25
0
0
False
False
False
4.3203
1
17.234
2.2852
G
intron_variant
n.147+232T>G
None
AGAP004707-RA
-1
0.0
0.0
0.0
0.0
0.0
0.00727272727273
0.0
0.0
0.0
True
None
None
None
('INTRONIC', 'AGAP004707-PA', 232, 'AGAP004707-PA', -3471)
('INTRONIC', 'AGAP004707-PB', 232, 'AGAP004707-PB', -3471)
('INTRONIC', 'AGAP004707-PC', 232, 'AGAP004707-PC', -3471)
('INTRONIC', '1', 232, '3', -3453)
('INTRONIC', '1', 232, '3', -3453)
('INTRONIC', '1', 232, '3', -3453)
('INTRONIC', '1', 232, '3', -3453)
('INTRONIC', '1', 232, '2j', -1104)
('INTRONIC', '1', 232, '3', -3453)
('INTRONIC', '1', 232, '3', -3453)
('INTRONIC', '1', 232, '3', -3453)
('INTRONIC', '1', 232, '2j', -1104)
('INTRONIC', '1', 232, '3', -3453)


2L
2358560
2
C
T
1
0
False
0
2
21
0
0
False
False
False
0.0
0
16.109
0.40991
T
intron_variant
n.147+256C>T
None
AGAP004707-RA
-1
0.0
0.0
0.0108695652174
0.0
0.0
0.0
0.0
0.0
0.0
True
None
None
None
('INTRONIC', 'AGAP004707-PA', 256, 'AGAP004707-PA', -3447)
('INTRONIC', 'AGAP004707-PB', 256, 'AGAP004707-PB', -3447)
('INTRONIC', 'AGAP004707-PC', 256, 'AGAP004707-PC', -3447)
('INTRONIC', '1', 256, '3', -3429)
('INTRONIC', '1', 256, '3', -3429)
('INTRONIC', '1', 256, '3', -3429)
('INTRONIC', '1', 256, '3', -3429)
('INTRONIC', '1', 256, '2j', -1080)
('INTRONIC', '1', 256, '3', -3429)
('INTRONIC', '1', 256, '3', -3429)
('INTRONIC', '1', 256, '3', -3429)
('INTRONIC', '1', 256, '2j', -1080)
('INTRONIC', '1', 256, '3', -3429)


2L
2358581
2
T
A
330
0
False
0
2
20
0
0
False
False
False
0.20801
1
21.109
-0.3811
A
intron_variant
n.147+277T>A
None
AGAP004707-RA
-1
0.0
0.0
0.0
0.0
0.0
0.525454545455
0.366071428571
0.0
0.0
True
None
None
None
('INTRONIC', 'AGAP004707-PA', 277, 'AGAP004707-PA', -3426)
('INTRONIC', 'AGAP004707-PB', 277, 'AGAP004707-PB', -3426)
('INTRONIC', 'AGAP004707-PC', 277, 'AGAP004707-PC', -3426)
('INTRONIC', '1', 277, '3', -3408)
('INTRONIC', '1', 277, '3', -3408)
('INTRONIC', '1', 277, '3', -3408)
('INTRONIC', '1', 277, '3', -3408)
('INTRONIC', '1', 277, '2j', -1059)
('INTRONIC', '1', 277, '3', -3408)
('INTRONIC', '1', 277, '3', -3408)
('INTRONIC', '1', 277, '3', -3408)
('INTRONIC', '1', 277, '2j', -1059)
('INTRONIC', '1', 277, '3', -3408)


2L
2358591
2
G
T
4
0
False
0
4
18
0
0
False
False
False
1.9912
1
15.461
-0.50586
T
intron_variant
n.147+287G>T
None
AGAP004707-RA
-1
0.0
0.0
0.0326086956522
0.0
0.0
0.00181818181818
0.0
0.0
0.0
True
None
None
None
('INTRONIC', 'AGAP004707-PA', 287, 'AGAP004707-PA', -3416)
('INTRONIC', 'AGAP004707-PB', 287, 'AGAP004707-PB', -3416)
('INTRONIC', 'AGAP004707-PC', 287, 'AGAP004707-PC', -3416)
('INTRONIC', '1', 287, '3', -3398)
('INTRONIC', '1', 287, '3', -3398)
('INTRONIC', '1', 287, '3', -3398)
('INTRONIC', '1', 287, '3', -3398)
('INTRONIC', '1', 287, '2j', -1049)
('INTRONIC', '1', 287, '3', -3398)
('INTRONIC', '1', 287, '3', -3398)
('INTRONIC', '1', 287, '3', -3398)
('INTRONIC', '1', 287, '2j', -1049)
('INTRONIC', '1', 287, '3', -3398)


2L
2358621
2
G
C
2
0
True
0
8
13
0
0
False
False
False
7.3477
1
14.0
-1.6348
C
intron_variant
n.147+317G>C
None
AGAP004707-RA
-1
0.0
0.0
0.0217391304348
0.0
0.0
0.0
0.0
0.0
0.0
True
None
None
None
('INTRONIC', 'AGAP004707-PA', 317, 'AGAP004707-PA', -3386)
('INTRONIC', 'AGAP004707-PB', 317, 'AGAP004707-PB', -3386)
('INTRONIC', 'AGAP004707-PC', 317, 'AGAP004707-PC', -3386)
('INTRONIC', '1', 317, '3', -3368)
('INTRONIC', '1', 317, '3', -3368)
('INTRONIC', '1', 317, '3', -3368)
('INTRONIC', '1', 317, '3', -3368)
('INTRONIC', '1', 317, '2j', -1019)
('INTRONIC', '1', 317, '3', -3368)
('INTRONIC', '1', 317, '3', -3368)
('INTRONIC', '1', 317, '3', -3368)
('INTRONIC', '1', 317, '2j', -1019)
('INTRONIC', '1', 317, '3', -3368)


2L
2358667
2
T
A
473
0
True
0
11
10
0
0
False
False
False
0.56299
0
30.047
0.18506
A
intron_variant
n.147+363T>A
None
AGAP004707-RA
-1
0.833333333333
0.840579710145
0.0108695652174
1.0
0.993827160494
0.06
0.0
0.0
0.0
True
None
None
None
('INTRONIC', 'AGAP004707-PA', 363, 'AGAP004707-PA', -3340)
('INTRONIC', 'AGAP004707-PB', 363, 'AGAP004707-PB', -3340)
('INTRONIC', 'AGAP004707-PC', 363, 'AGAP004707-PC', -3340)
('INTRONIC', '1', 363, '3', -3322)
('INTRONIC', '1', 363, '3', -3322)
('INTRONIC', '1', 363, '3', -3322)
('INTRONIC', '1', 363, '3', -3322)
('INTRONIC', '1', 363, '2j', -973)
('INTRONIC', '1', 363, '3', -3322)
('INTRONIC', '1', 363, '3', -3322)
('INTRONIC', '1', 363, '3', -3322)
('INTRONIC', '1', 363, '2j', -973)
('INTRONIC', '1', 363, '3', -3322)


2L
2358668
2
G
A
7
0
False
0
12
10
0
0
False
False
False
28.266
0
1.8604
-0.94482
A
intron_variant
n.147+364G>A
None
AGAP004707-RA
-1
0.00833333333333
0.00724637681159
0.0326086956522
0.0161290322581
0.00617283950617
0.0
0.0
0.0
0.0
True
None
None
None
('INTRONIC', 'AGAP004707-PA', 364, 'AGAP004707-PA', -3339)
('INTRONIC', 'AGAP004707-PB', 364, 'AGAP004707-PB', -3339)
('INTRONIC', 'AGAP004707-PC', 364, 'AGAP004707-PC', -3339)
('INTRONIC', '1', 364, '3', -3321)
('INTRONIC', '1', 364, '3', -3321)
('INTRONIC', '1', 364, '3', -3321)
('INTRONIC', '1', 364, '3', -3321)
('INTRONIC', '1', 364, '2j', -972)
('INTRONIC', '1', 364, '3', -3321)
('INTRONIC', '1', 364, '3', -3321)
('INTRONIC', '1', 364, '3', -3321)
('INTRONIC', '1', 364, '2j', -972)
('INTRONIC', '1', 364, '3', -3321)


2L
2358707
2
T
C
39
0
True
0
12
15
0
1
False
False
False
41.875
0
16.781
4.9414
C
intron_variant
n.147+403T>C
None
AGAP004707-RA
-1
0.0
0.0
0.423913043478
0.0
0.0
0.0
0.0
0.0
0.0
True
None
None
None
('INTRONIC', 'AGAP004707-PA', 403, 'AGAP004707-PA', -3300)
('INTRONIC', 'AGAP004707-PB', 403, 'AGAP004707-PB', -3300)
('INTRONIC', 'AGAP004707-PC', 403, 'AGAP004707-PC', -3300)
('INTRONIC', '1', 403, '3', -3282)
('INTRONIC', '1', 403, '3', -3282)
('INTRONIC', '1', 403, '3', -3282)
('INTRONIC', '1', 403, '3', -3282)
('INTRONIC', '1', 403, '2j', -933)
('INTRONIC', '1', 403, '3', -3282)
('INTRONIC', '1', 403, '3', -3282)
('INTRONIC', '1', 403, '3', -3282)
('INTRONIC', '1', 403, '2j', -933)
('INTRONIC', '1', 403, '3', -3282)


2L
2358709
2
A
C
2
0
False
0
12
16
0
1
False
False
False
4.3906
0
12.797
-1.2656
C
intron_variant
n.147+405A>C
None
AGAP004707-RA
-1
0.0
0.0
0.0108695652174
0.0
0.0
0.00181818181818
0.0
0.0
0.0
True
None
None
None
('INTRONIC', 'AGAP004707-PA', 405, 'AGAP004707-PA', -3298)
('INTRONIC', 'AGAP004707-PB', 405, 'AGAP004707-PB', -3298)
('INTRONIC', 'AGAP004707-PC', 405, 'AGAP004707-PC', -3298)
('INTRONIC', '1', 405, '3', -3280)
('INTRONIC', '1', 405, '3', -3280)
('INTRONIC', '1', 405, '3', -3280)
('INTRONIC', '1', 405, '3', -3280)
('INTRONIC', '1', 405, '2j', -931)
('INTRONIC', '1', 405, '3', -3280)
('INTRONIC', '1', 405, '3', -3280)
('INTRONIC', '1', 405, '3', -3280)
('INTRONIC', '1', 405, '2j', -931)
('INTRONIC', '1', 405, '3', -3280)


2L
2358716
2
T
C
1
0
False
0
9
15
0
0
False
False
False
25.453
0
1.0596
-2.9727
C
intron_variant
n.147+412T>C
None
AGAP004707-RA
-1
0.0
0.0
0.0
0.0
0.00617283950617
0.0
0.0
0.0
0.0
True
None
None
None
('INTRONIC', 'AGAP004707-PA', 412, 'AGAP004707-PA', -3291)
('INTRONIC', 'AGAP004707-PB', 412, 'AGAP004707-PB', -3291)
('INTRONIC', 'AGAP004707-PC', 412, 'AGAP004707-PC', -3291)
('INTRONIC', '1', 412, '3', -3273)
('INTRONIC', '1', 412, '3', -3273)
('INTRONIC', '1', 412, '3', -3273)
('INTRONIC', '1', 412, '3', -3273)
('INTRONIC', '1', 412, '2j', -924)
('INTRONIC', '1', 412, '3', -3273)
('INTRONIC', '1', 412, '3', -3273)
('INTRONIC', '1', 412, '3', -3273)
('INTRONIC', '1', 412, '2j', -924)
('INTRONIC', '1', 412, '3', -3273)


2L
2358734
2
C
T
2
0
True
0
9
14
0
0
False
False
False
6.4297
1
16.016
-0.42896
T
intron_variant
n.147+430C>T
None
AGAP004707-RA
-1
0.0
0.0
0.0
0.0
0.0
0.00363636363636
0.0
0.0
0.0
True
None
None
None
('INTRONIC', 'AGAP004707-PA', 430, 'AGAP004707-PA', -3273)
('INTRONIC', 'AGAP004707-PB', 430, 'AGAP004707-PB', -3273)
('INTRONIC', 'AGAP004707-PC', 430, 'AGAP004707-PC', -3273)
('INTRONIC', '1', 430, '3', -3255)
('INTRONIC', '1', 430, '3', -3255)
('INTRONIC', '1', 430, '3', -3255)
('INTRONIC', '1', 430, '3', -3255)
('INTRONIC', '1', 430, '2j', -906)
('INTRONIC', '1', 430, '3', -3255)
('INTRONIC', '1', 430, '3', -3255)
('INTRONIC', '1', 430, '3', -3255)
('INTRONIC', '1', 430, '2j', -906)
('INTRONIC', '1', 430, '3', -3255)



...

In [24]:

    

def simplify_missense_effect(v):
    if v and v[0] == 'NON_SYNONYMOUS_CODING':
        return v[1]
    else:
        return ''

    
td_styles = {
    'FILTER_PASS': lambda v: 'background-color: red' if not v else '',
    'NoCoverage': lambda v: 'background-color: red' if v > 1 else '',
    'LowCoverage': lambda v: 'background-color: red' if v > 76 else '',
    'HighCoverage': lambda v: 'background-color: red' if v > 15 else '',
    'LowMQ': lambda v: 'background-color: red' if v > 76 else '',
    'HighMQ0': lambda v: 'background-color: red' if v > 1 else '',
    'RepeatDUST': lambda v: 'background-color: red' if v else '',
    'FS': lambda v: 'background-color: red' if v > 60 else '',
    'QD': lambda v: 'background-color: red' if v < 5 else '',
    'ReadPosRankSum': lambda v: 'background-color: red' if v < -8 else '',
    'HRun': lambda v: 'background-color: red' if v > 4 else '',
    'num_alleles': lambda v: 'background-color: orange' if v > 2 else '',
}


def tr_style(row):
    """Colour row by alternate allele count."""
    return 'background-color:rgba(0, 255, 0, %.3f)' % (min(1, row['AC']/100))


tbl_variants_phase1_missense = (
    tbl_variants_phase1_eff
    .select(lambda row: any(row[t] and row[t][0] == 'NON_SYNONYMOUS_CODING' for t in transcript_ids))
    .convert(transcript_ids, simplify_missense_effect)
)
tbl_variants_phase1_missense.displayall(td_styles=td_styles, tr_style=tr_style)


    

    








0|CHROM
1|POS
2|num_alleles
3|REF
4|ALT
5|AC
6|ALTIX
7|FILTER_PASS
8|NoCoverage
9|LowCoverage
10|HighCoverage
11|LowMQ
12|HighMQ0
13|RepeatDUST
14|RepeatMasker
15|RepeatTRF
16|FS
17|HRun
18|QD
19|ReadPosRankSum
20|SNPEFF_Allele
21|SNPEFF_Annotation
22|SNPEFF_HGVS_c
23|SNPEFF_HGVS_p
24|SNPEFF_Feature_ID
25|SNPEFF_CDS_pos
26|AF_AOM
27|AF_BFM
28|AF_GWA
29|AF_GNS
30|AF_BFS
31|AF_CMS
32|AF_GAS
33|AF_UGS
34|AF_KES
35|check_allele
36|exon_start
37|exon_end
38|exon
39|AGAP004707-RA
40|AGAP004707-RB
41|AGAP004707-RC
42|Davies-C1N2
43|Davies-C3N2
44|Davies-C5N2
45|Davies-C7N2
46|Davies-C8N2
47|Davies-C10N2
48|Davies-C11N2
49|Davies-C1N9
50|Davies-C8N9
51|Davies-C1N9ck




2L
2358254
2
G
A
1
0
True
0
0
10
0
0
False
False
False
9.8672
1
17.547
-0.049988
A
missense_variant
n.97G>A
p.Asp33Asn
AGAP004707-RA
97
0.0
0.0
0.0
0.0
0.0
0.00181818181818
0.0
0.0
0.0
True
2358158
2358304
1
D33N
D33N
D33N
D33N
D33N
D33N
D33N
D33N
D33N
D33N
D33N
D33N
D33N


2L
2359670
2
G
A
7
0
False
1
171
1
1
0
False
False
False
8.6641
6
14.406
-0.029007
A
intron_variant
n.147+1366G>
None
AGAP004707-RA
-1
0.0
0.0
0.0
0.0
0.0
0.0109090909091
0.0
0.0
0.0113636363636
True
2359640
2359672
2j







E60K



E60K



2L
2362002
2
A
T
2
0
True
0
1
3
0
0
False
False
False
0.5459
0
12.531
-0.55322
T
splice_region_variant&intron_varia
n.148-5A>T
None
AGAP004707-RA
-1
0.0
0.0144927536232
0.0
0.0
0.0
0.0
0.0
0.0
0.0
True
2361989
2362144
3



D54V
D54V
D54V
D54V
D65V
D54V
D54V
D54V
D65V
D54V


2L
2362019
2
G
T
2
0
True
0
0
6
0
0
False
False
False
3.9824
0
13.641
0.7749
T
missense_variant
n.160G>T
p.Gly54Cys
AGAP004707-RA
160
0.0
0.0144927536232
0.0
0.0
0.0
0.0
0.0
0.0
0.0
True
2361989
2362144
3
G54C
G54C
G54C
G60C
G60C
G60C
G60C
G71C
G60C
G60C
G60C
G71C
G60C


2L
2362023
2
C
T
1
0
True
0
1
3
0
0
False
False
False
0.0
0
13.477
-1.1611
T
missense_variant
n.164C>T
p.Pro55Leu
AGAP004707-RA
164
0.0
0.0
0.0
0.0
0.00617283950617
0.0
0.0
0.0
0.0
True
2361989
2362144
3
P55L
P55L
P55L
P61L
P61L
P61L
P61L
P72L
P61L
P61L
P61L
P72L
P61L


2L
2390168
2
A
G
2
0
True
0
2
10
0
0
False
False
False
0.56982
1
15.219
-0.026001
G
missense_variant
n.752A>G
p.Lys251Arg
AGAP004707-RA
752
0.0
0.0
0.0
0.0
0.0
0.0
0.0178571428571
0.0
0.0
True
2390129
2390341
7
K251R
K251R
K251R
K257R
K214R
K257R
K257R
K268R
K257R
K257R
K257R
K268R
K257R


2L
2390177
2
G
A
198
0
True
0
3
8
0
0
False
False
False
0.12695
1
18.625
0.83496
A
missense_variant
n.761G>A
p.Arg254Lys
AGAP004707-RA
761
0.0
0.0
0.0
0.0
0.0
0.316363636364
0.214285714286
0.0
0.0
True
2390129
2390341
7
R254K
R254K
R254K
R260K
R217K
R260K
R260K
R271K
R260K
R260K
R260K
R271K
R260K


2L
2390311
2
G
A
1
0
True
0
0
10
0
0
False
False
False
0.0
3
14.07
-0.70996
A
missense_variant
n.895G>A
p.Glu299Lys
AGAP004707-RA
895
0.0
0.0
0.0
0.0
0.0
0.00181818181818
0.0
0.0
0.0
True
2390129
2390341
7
E299K
E299K
E299K
E305K
E262K
E305K
E305K
E316K
E305K
E305K
E305K
E316K
E305K


2L
2390448
2
G
A
6
0
True
0
0
15
0
0
False
False
False
0.71094
0
16.125
-0.65918
A
missense_variant
n.949G>A
p.Gly317Ser
AGAP004707-RA
949
0.0
0.0
0.0
0.0
0.0
0.0109090909091
0.0
0.0
0.0
True
2390425
2390485
8
G317S
G317S
G317S
G323S
G280S
G323S
G323S
G334S
G323S
G323S
G323S
G334S
G323S


2L
2391228
3
G
C
10
0
True
0
0
12
0
0
False
False
False
2.0352
0
14.867
-1.1777
C
missense_variant
n.1204G>C
p.Val402Leu
AGAP004707-RA
1204
0.0
0.0724637681159
0.0
0.0
0.0
0.0
0.0
0.0
0.0
True
2391156
2391320
10
V402L
V402L
V402L
V408L
V365L

V408L
V419L
V408L
V408L
V408L
V419L
V408L


2L
2391228
3
G
T
9
1
True
0
0
12
0
0
False
False
False
2.0352
0
14.867
-1.1777
None
None
None
None
None
None
0.0
0.0652173913043
0.0
0.0
0.0
0.0
0.0
0.0
0.0
True
2391156
2391320
10
V402L
V402L
V402L
V408L
V365L

V408L
V419L
V408L
V408L
V408L
V419L
V408L


2L
2399997
2
G
C
38
0
True
0
1
7
0
0
False
False
False
13.359
0
15.688
0.11798
C
missense_variant
n.1396G>C
p.Asp466His
AGAP004707-RA
1396
0.0
0.0
0.0
0.0
0.0
0.0690909090909
0.0
0.0
0.0
True
2399898
2400173
11i+
D466H
D466H
D466H
D472H
D429H
D417H
D472H
D483H
D472H
D472H
D472H
D483H
D472H


2L
2400071
3
G
A
16
0
True
0
0
8
0
0
False
False
False
5.6875
0
16.969
1.3232
A
missense_variant
n.1470G>A
p.Met490Ile
AGAP004707-RA
1470
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.181818181818
True
2399898
2400173
11i+
M490I
M490I
M490I
M496I
M453I
M441I
M496I
M507I
M496I
M496I
M496I
M507I
M496I


2L
2400071
3
G
T
2
1
True
0
0
8
0
0
False
False
False
5.6875
0
16.969
1.3232
None
None
None
None
None
None
0.0
0.0
0.0
0.0
0.0
0.00363636363636
0.0
0.0
0.0
True
2399898
2400173
11i+
M490I
M490I
M490I
M496I
M453I
M441I
M496I
M507I
M496I
M496I
M496I
M507I
M496I


2L
2400076
2
T
A
2
0
True
0
0
9
0
0
False
False
False
1.1055
1
10.469
-0.54199
A
missense_variant
n.1475T>A
p.Ile492Asn
AGAP004707-RA
1475
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.00970873786408
0.0
True
2399898
2400173
11i+
I492N
I492N
I492N
I498N
I455N
I443N
I498N
I509N
I498N
I498N
I498N
I509N
I498N


2L
2402484
2
G
T
1
0
True
0
4
13
0
0
False
False
False
1.8857
1
14.719
0.075989
T
missense_variant
n.1610G>T
p.Arg537Leu
AGAP004707-RA
1610
0.0
0.0
0.0
0.0
0.0
0.0
0.00892857142857
0.0
0.0
True
2402447
2402509
13a
R537L
R537L
R537L
R550L






R550L

R550L


2L
2402508
2
A
T
1
0
True
1
3
15
0
0
False
False
False
3.0098
0
11.156
-0.041992
T
missense_variant&splice_region_var
n.1634A>T
p.Gln545Leu
AGAP004707-RA
1634
0.0
0.0
0.0
0.0
0.00617283950617
0.0
0.0
0.0
0.0
True
2402447
2402509
13a
Q545L
Q545L
Q545L
Q558L






Q558L

Q558L


2L
2403206
2
G
A
1
0
False
0
1
16
0
0
False
False
False
4.8047
0
15.477
-0.20398
A
missense_variant
n.1756G>A
p.Ala586Thr
AGAP004707-RA
1756
0.0
0.0
0.0
0.0
0.0
0.00181818181818
0.0
0.0
0.0
True
2403086
2403269
14
A586T
A586T
A586T
A599T
A528T
A516T
A571T
A582T
A571T
A571T
A599T
A582T
A599T


2L
2407811
2
G
A
1
0
True
0
2
14
0
0
False
False
False
0.0
1
10.789
-0.86914
A
missense_variant
n.2009G>A
p.Arg670Gln
AGAP004707-RA
2009
0.0
0.0
0.0108695652174
0.0
0.0
0.0
0.0
0.0
0.0
True
2407622
2407818
15
R670Q
R670Q
R670Q
R683Q
R612Q
R600Q
R655Q
R666Q
R655Q
R655Q
R683Q
R666Q
R683Q


2L
2407912
2
A
T
1
0
True
0
0
6
0
0
False
False
False
0.0
1
22.172
0.5332
T
missense_variant
n.2035A>T
p.Thr679Ser
AGAP004707-RA
2035
0.0
0.0
0.0
0.0
0.0
0.00181818181818
0.0
0.0
0.0
True
2407894
2407993
16
T679S
T679S
T679S
T692S
T621S
T609S
T664S
T675S
T664S
T664S
T692S
T675S
T692S


2L
2407987
2
A
G
1
0
True
0
2
7
0
0
False
False
False
0.0
0
14.102
1.0859
G
missense_variant
n.2110A>G
p.Met704Val
AGAP004707-RA
2110
0.0
0.00724637681159
0.0
0.0
0.0
0.0
0.0
0.0
0.0
True
2407894
2407993
16
M704V
M704V
M704V
M717V
M646V
M634V
M689V
M700V
M689V
M689V
M717V
M700V
M717V


2L
2408125
2
C
A
1
0
False
0
252
2
1
0
False
False
False
2.0879
2
7.0586
0.5918
A
missense_variant
n.2171C>A
p.Ala724Glu
AGAP004707-RA
2171
0.0
0.0
0.0
0.0
0.0
0.00181818181818
0.0
0.0
0.0
True
2408071
2408139
17
A724E
A724E
A724E
A737E
A666E
A654E
A709E
A720E
A709E
A709E
A737E
A720E
A737E


2L
2408136
2
G
A
1
0
False
0
318
2
1
0
False
False
False
2.0879
0
1.8799
-2.0742
A
missense_variant
n.2182G>A
p.Gly728Arg
AGAP004707-RA
2182
0.00833333333333
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
True
2408071
2408139
17
G728R
G728R
G728R
G741R
G670R
G658R
G713R
G724R
G713R
G713R
G741R
G724R
G741R


2L
2416980
2
C
T
32
0
True
0
2
11
0
0
False
False
False
2.0449
0
17.703
0.37305
T
missense_variant
n.2372C>T
p.Thr791Met
AGAP004707-RA
2372
0.0
0.0144927536232
0.0
0.129032258065
0.135802469136
0.0
0.0
0.0
0.0
True
2416794
2417071
18b+
T791M
T791M
T791M
T804M
T733M
T721M
T776M
T787M
T776M
T776M
T804M
T787M
T804M


2L
2417206
2
A
C
1
0
True
0
15
3
0
0
False
False
False
0.0
2
9.4297
0.31299
C
missense_variant
n.2485A>C
p.Ile829Leu
AGAP004707-RA
2485
0.0
0.0
0.0
0.0
0.0
0.00181818181818
0.0
0.0
0.0
True
2417185
2417358
19
I829L
I829L
I829L
I842L
I771L
I759L
I814L
I825L
I814L
I814L
I842L
I825L
I842L


2L
2417231
2
C
T
1
0
True
0
38
1
0
0
False
False
False
3.6992
0
13.688
-0.46802
T
missense_variant
n.2510C>T
p.Ala837Val
AGAP004707-RA
2510
0.0
0.0
0.0
0.0
0.0
0.00181818181818
0.0
0.0
0.0
True
2417185
2417358
19
A837V
A837V
A837V
A850V
A779V
A767V
A822V
A833V
A822V
A822V
A850V
A833V
A850V


2L
2417772
2
A
T
1
0
True
0
2
10
0
0
False
False
False
7.707
1
16.156
-0.035004
T
missense_variant
n.2773A>T
p.Met925Leu
AGAP004707-RA
2773
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.00485436893204
0.0
True
2417637
2417799
20c
M925L

M925L









M938L


2L
2421454
2
A
G
1
0
True
0
0
13
0
0
False
False
False
3.8008
1
14.094
0.88916
G
intron_variant
n.2801-1014A
None
AGAP004707-RA
-1
0.0
0.00724637681159
0.0
0.0
0.0
0.0
0.0
0.0
0.0
True
2421385
2421547
20d

M903V

M916V
M845V
M833V
M888V
M899V
M888V
M888V
M916V
M899V



2L
2422486
2
C
A
1
0
True
0
1
6
0
0
False
False
False
4.168
0
12.102
-0.45605
A
missense_variant
n.2819C>A
p.Pro940His
AGAP004707-RA
2819
0.0
0.0
0.0
0.0
0.00617283950617
0.0
0.0
0.0
0.0
True
2422468
2422655
21
P940H
P940H
P940H
P953H
P882H
P870H
P925H
P936H
P925H
P925H
P953H
P936H
P953H


2L
2422651
2
T
C
430
0
True
0
2
10
0
0
False
False
False
0.95117
0
27.203
-0.92822
C
missense_variant
n.2984T>C
p.Leu995Ser
AGAP004707-RA
2984
0.0
0.0
0.0
0.0
0.0
0.154545454545
0.642857142857
1.0
0.761363636364
True
2422468
2422655
21
L995S
L995S
L995S
L1008S
L937S
L925S
L980S
L991S
L980S
L980S
L1008S
L991S
L1008S


2L
2422652
2
A
T
775
0
True
0
2
9
0
0
False
False
False
0.73291
3
29.047
0.19104
T
missense_variant
n.2985A>T
p.Leu995Phe
AGAP004707-RA
2985
0.858333333333
0.847826086957
0.0
1.0
1.0
0.529090909091
0.357142857143
0.0
0.0
True
2422468
2422655
21
L995F
L995F
L995F
L1008F
L937F
L925F
L980F
L991F
L980F
L980F
L1008F
L991F
L1008F


2L
2422875
2
G
A
1
0
False
0
3
17
0
0
False
False
False
0.71289
0
14.867
-1.6621
A
missense_variant
n.3151G>A
p.Val1051Ile
AGAP004707-RA
3151
0.0
0.0
0.0
0.0
0.0
0.00181818181818
0.0
0.0
0.0
True
2422713
2422920
22
V1051I
V1051I
V1051I
V1064I
V993I
V981I
V1036I
V1047I
V1036I
V1036I
V1064I
V1047I
V1064I


2L
2424383
2
G
T
1
0
True
0
1
14
0
0
False
False
False
2.8906
0
18.156
-0.31494
T
missense_variant
n.3373G>T
p.Ala1125Ser
AGAP004707-RA
3373
0.0
0.0
0.0108695652174
0.0
0.0
0.0
0.0
0.0
0.0
True
2424207
2424418
23f+
A1125S
A1125S
A1125S
A1138S
A1067S
A1045S
A1100S
A1121S
A1110S
A1110S
A1138S
A1121S
A1138S


2L
2424384
2
C
T
11
0
True
0
1
14
0
0
False
False
False
5.4141
0
14.172
-2.3242
T
missense_variant
n.3374C>T
p.Ala1125Val
AGAP004707-RA
3374
0.0916666666667
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
True
2424207
2424418
23f+
A1125V
A1125V
A1125V
A1138V
A1067V
A1045V
A1100V
A1121V
A1110V
A1110V
A1138V
A1121V
A1138V


2L
2424401
2
A
G
2
0
False
0
0
16
0
0
False
False
False
4.1133
0
14.742
-1.7324
G
missense_variant
n.3391A>G
p.Ile1131Val
AGAP004707-RA
3391
0.0
0.0
0.0
0.0
0.0
0.00181818181818
0.00892857142857
0.0
0.0
True
2424207
2424418
23f+
I1131V
I1131V
I1131V
I1144V
I1073V
I1051V
I1106V
I1127V
I1116V
I1116V
I1144V
I1127V
I1144V


2L
2424720
2
T
G
11
0
False
0
2
8
0
0
False
False
False
1953.0
1
0.090027
1.6211
G
missense_variant
n.3478T>G
p.Ser1160Ala
AGAP004707-RA
3478
0.00833333333333
0.0144927536232
0.0108695652174
0.0
0.0
0.0109090909091
0.00892857142857
0.0
0.0
True
2424651
2424870
24h+
S1160A









S1173A
S1156A
S1173A


2L
2425077
2
G
A
5
0
True
0
0
14
0
0
False
False
False
0.66992
0
14.891
-0.61816
A
missense_variant
n.3760G>A
p.Val1254Ile
AGAP004707-RA
3760
0.0
0.0
0.054347826087
0.0
0.0
0.0
0.0
0.0
0.0
True
2424946
2425211
25
V1254I
V1228I
V1228I
V1241I
V1170I
V1148I
V1203I
V1224I
V1213I
V1213I
V1267I
V1250I
V1267I


2L
2425291
2
T
C
1
0
True
0
0
10
0
0
False
False
False
4.4258
0
15.32
-0.38403
C
missense_variant
n.3908T>C
p.Val1303Ala
AGAP004707-RA
3908
0.0
0.0
0.0
0.0
0.00617283950617
0.0
0.0
0.0
0.0
True
2425278
2425451
26
V1303A
V1277A
V1277A
V1290A
V1219A
V1197A
V1252A
V1273A
V1262A
V1262A
V1316A
V1299A
V1316A


2L
2425417
2
A
T
3
0
True
0
0
13
0
0
False
False
False
0.39111
1
14.141
0.104
T
missense_variant
n.4034A>T
p.Asn1345Ile
AGAP004707-RA
4034
0.0
0.0217391304348
0.0
0.0
0.0
0.0
0.0
0.0
0.0
True
2425278
2425451
26
N1345I
N1319I
N1319I
N1332I
N1261I
N1239I
N1294I
N1315I
N1304I
N1304I
N1358I
N1341I
N1358I


2L
2428015
2
C
T
1
0
True
0
3
12
0
0
False
False
False
0.66895
3
13.711
-0.55322
T
missense_variant
n.4096C>T
p.Leu1366Phe
AGAP004707-RA
4096
0.0
0.0
0.0
0.0
0.00617283950617
0.0
0.0
0.0
0.0
True
2427988
2428110
27l
L1366F
L1340F
L1340F
L1353F
L1282F
L1260F
L1315F
L1336F
L1325F
L1325F
L1379F
L1362F



2L
2429617
2
T
C
19
0
True
0
2
12
0
0
False
False
False
1.4502
0
15.531
-0.98291
C
missense_variant
n.4580T>C
p.Ile1527Thr
AGAP004707-RA
4580
0.0
0.13768115942
0.0
0.0
0.0
0.0
0.0
0.0
0.0
True
2429556
2429801
30
I1527T
I1501T
I1501T
I1511T
I1440T
I1418T
I1473T
I1494T
I1483T
I1483T
I1537T
I1520T
I1537T


2L
2429622
2
T
C
1
0
True
0
1
15
0
0
False
False
False
10.922
1
14.977
-0.098022
C
missense_variant
n.4585T>C
p.Phe1529Leu
AGAP004707-RA
4585
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.00485436893204
0.0
True
2429556
2429801
30
F1529L
F1503L
F1503L
F1513L
F1442L
F1420L
F1475L
F1496L
F1485L
F1485L
F1539L
F1522L
F1539L


2L
2429745
2
A
T
110
0
False
0
0
17
0
0
False
False
False
0.4541
1
16.484
1.9131
T
missense_variant
n.4708A>T
p.Asn1570Tyr
AGAP004707-RA
4708
0.0
0.260869565217
0.0
0.0967741935484
0.216049382716
0.06
0.0
0.0
0.0
True
2429556
2429801
30
N1570Y
N1544Y
N1544Y
N1554Y
N1483Y
N1461Y
N1516Y
N1537Y
N1526Y
N1526Y
N1580Y
N1563Y
N1580Y


2L
2429788
2
T
C
2
0
False
0
0
24
0
0
False
False
False
6.2383
0
19.406
-0.46509
C
missense_variant
n.4751T>C
p.Ile1584Thr
AGAP004707-RA
4751
0.0
0.0
0.0
0.0
0.0123456790123
0.0
0.0
0.0
0.0
True
2429556
2429801
30
I1584T
I1558T
I1558T
I1568T
I1497T
I1475T
I1530T
I1551T
I1540T
I1540T
I1594T
I1577T
I1594T


2L
2429897
2
A
G
11
0
True
0
1
13
0
0
False
False
False
3.5234
1
16.906
-0.56006
G
missense_variant
n.4790A>G
p.Glu1597Gly
AGAP004707-RA
4790
0.0
0.0
0.0
0.0645161290323
0.0432098765432
0.0
0.0
0.0
0.0
True
2429872
2430142
31
E1597G
E1571G
E1571G
E1581G
E1510G
E1488G
E1543G
E1564G
E1553G
E1553G
E1607G
E1590G
E1607G


2L
2429915
2
A
C
7
0
True
0
1
13
0
0
False
False
False
5.2461
0
16.406
-1.6729
C
missense_variant
n.4808A>C
p.Lys1603Thr
AGAP004707-RA
4808
0.0
0.0507246376812
0.0
0.0
0.0
0.0
0.0
0.0
0.0
True
2429872
2430142
31
K1603T
K1577T
K1577T
K1587T
K1516T
K1494T
K1549T
K1570T
K1559T
K1559T
K1613T
K1596T
K1613T


2L
2429958
2
A
C
1
0
True
0
1
14
0
0
False
False
False
1.0488
0
12.539
-1.8672
C
missense_variant
n.4851A>C
p.Leu1617Phe
AGAP004707-RA
4851
0.0
0.0
0.0
0.0
0.0
0.00181818181818
0.0
0.0
0.0
True
2429872
2430142
31
L1617F
L1591F
L1591F
L1601F
L1530F
L1508F
L1563F
L1584F
L1573F
L1573F
L1627F
L1610F
L1627F


2L
2430106
2
T
A
3
0
False
0
0
18
0
0
False
False
False
1.6719
0
15.719
-1.3877
A
missense_variant
n.4999T>A
p.Leu1667Met
AGAP004707-RA
4999
0.0
0.0217391304348
0.0
0.0
0.0
0.0
0.0
0.0
0.0
True
2429872
2430142
31
L1667M
L1641M
L1641M
L1651M
L1580M
L1558M
L1613M
L1634M
L1623M
L1623M
L1677M
L1660M
L1677M


2L
2430229
2
G
A
4
0
False
0
1
18
0
0
False
False
False
20.531
0
14.383
0.22498
A
missense_variant
n.5041G>A
p.Val1681Ile
AGAP004707-RA
5041
0.0
0.0
0.0
0.0
0.0
0.00727272727273
0.0
0.0
0.0
True
2430224
2430528
32
V1681I
V1655I
V1655I
V1665I
V1594I
V1572I
V1627I
V1648I
V1637I
V1637I
V1691I
V1674I
V1691I


2L
2430236
2
G
T
7
0
False
0
1
17
0
0
False
False
False
1.0479
1
14.352
-0.62988
T
missense_variant
n.5048G>T
p.Ser1683Ile
AGAP004707-RA
5048
0.0
0.0
0.0
0.0
0.0
0.0127272727273
0.0
0.0
0.0
True
2430224
2430528
32
S1683I
S1657I
S1657I
S1667I
S1596I
S1574I
S1629I
S1650I
S1639I
S1639I
S1693I
S1676I
S1693I


2L
2430424
2
G
T
28
0
True
0
1
10
0
0
False
False
False
4.4297
3
17.094
-0.71924
T
missense_variant
n.5236G>T
p.Ala1746Ser
AGAP004707-RA
5236
0.0
0.0
0.0
0.112903225806
0.12962962963
0.0
0.0
0.0
0.0
True
2430224
2430528
32
A1746S
A1720S
A1720S
A1730S
A1659S
A1637S
A1692S
A1713S
A1702S
A1702S
A1756S
A1739S
A1756S


2L
2430451
2
C
T
1
0
True
0
2
10
0
0
False
False
False
0.56689
0
16.047
0.098022
T
missense_variant
n.5263C>T
p.His1755Tyr
AGAP004707-RA
5263
0.0
0.0
0.0
0.0
0.0
0.0
0.00892857142857
0.0
0.0
True
2430224
2430528
32
H1755Y
H1729Y
H1729Y
H1739Y
H1668Y
H1646Y
H1701Y
H1722Y
H1711Y
H1711Y
H1765Y
H1748Y
H1765Y


2L
2430817
2
G
A
13
0
True
0
0
9
0
0
False
False
False
1.3701
0
14.648
-0.66504
A
missense_variant
n.5557G>A
p.Val1853Ile
AGAP004707-RA
5557
0.0
0.0
0.0
0.0806451612903
0.0493827160494
0.0
0.0
0.0
0.0
True
2430601
2431617
33
V1853I
V1827I
V1827I
V1837I
V1766I
V1744I
V1799I
V1820I
V1809I
V1809I
V1863I
V1846I
V1863I


2L
2430863
2
T
C
52
0
True
0
1
8
0
0
False
False
False
1.4785
0
15.812
0.78809
C
missense_variant
n.5603T>C
p.Ile1868Thr
AGAP004707-RA
5603
0.0
0.0
0.0
0.177419354839
0.253086419753
0.0
0.0
0.0
0.0
True
2430601
2431617
33
I1868T
I1842T
I1842T
I1852T
I1781T
I1759T
I1814T
I1835T
I1824T
I1824T
I1878T
I1861T
I1878T


2L
2430880
2
C
T
29
0
True
0
1
10
0
0
False
False
False
19.312
1
16.547
-1.8408
T
missense_variant
n.5620C>T
p.Pro1874Ser
AGAP004707-RA
5620
0.0
0.210144927536
0.0
0.0
0.0
0.0
0.0
0.0
0.0
True
2430601
2431617
33
P1874S
P1848S
P1848S
P1858S
P1787S
P1765S
P1820S
P1841S
P1830S
P1830S
P1884S
P1867S
P1884S


2L
2430881
2
C
T
80
0
True
0
1
9
0
0
False
False
False
2.4453
1
18.562
-1.4189
T
missense_variant
n.5621C>T
p.Pro1874Leu
AGAP004707-RA
5621
0.0
0.0724637681159
0.0
0.451612903226
0.259259259259
0.0
0.0
0.0
0.0
True
2430601
2431617
33
P1874L
P1848L
P1848L
P1858L
P1787L
P1765L
P1820L
P1841L
P1830L
P1830L
P1884L
P1867L
P1884L


2L
2431019
2
T
C
12
0
True
0
0
5
0
0
False
False
False
0.85107
1
13.523
-1.6211
C
missense_variant
n.5759T>C
p.Phe1920Ser
AGAP004707-RA
5759
0.0
0.0
0.0
0.0
0.0
0.0145454545455
0.0357142857143
0.0
0.0
True
2430601
2431617
33
F1920S
F1894S
F1894S
F1904S
F1833S
F1811S
F1866S
F1887S
F1876S
F1876S
F1930S
F1913S
F1930S


2L
2431061
2
C
T
16
0
True
0
0
8
0
0
False
False
False
1.5
1
16.688
-0.46802
T
missense_variant
n.5801C>T
p.Ala1934Val
AGAP004707-RA
5801
0.0
0.115942028986
0.0
0.0
0.0
0.0
0.0
0.0
0.0
True
2430601
2431617
33
A1934V
A1908V
A1908V
A1918V
A1847V
A1825V
A1880V
A1901V
A1890V
A1890V
A1944V
A1927V
A1944V


2L
2431079
2
T
C
44
0
True
0
0
6
0
0
False
False
False
3.4004
0
15.953
2.1738
C
missense_variant
n.5819T>C
p.Ile1940Thr
AGAP004707-RA
5819
0.0
0.0434782608696
0.0
0.0
0.0
0.0690909090909
0.0
0.0
0.0
True
2430601
2431617
33
I1940T
I1914T
I1914T
I1924T
I1853T
I1831T
I1886T
I1907T
I1896T
I1896T
I1950T
I1933T
I1950T


2L
2431232
2
G
A
1
0
True
0
0
7
0
0
False
False
False
3.1719
2
12.328
-0.80713
A
missense_variant
n.5972G>A
p.Gly1991Glu
AGAP004707-RA
5972
0.0
0.0
0.0108695652174
0.0
0.0
0.0
0.0
0.0
0.0
True
2430601
2431617
33
G1991E
G1965E
G1965E
G1975E
G1904E
G1882E
G1937E
G1958E
G1947E
G1947E
G2001E
G1984E
G2001E


2L
2431331
2
C
A
1
0
True
0
1
5
0
0
False
False
False
4.1406
2
12.797
-0.031006
A
missense_variant
n.6071C>A
p.Thr2024Lys
AGAP004707-RA
6071
0.0
0.0
0.0
0.0
0.0
0.00181818181818
0.0
0.0
0.0
True
2430601
2431617
33
T2024K
T1998K
T1998K
T2008K
T1937K
T1915K
T1970K
T1991K
T1980K
T1980K
T2034K
T2017K
T2034K


2L
2431417
2
A
G
2
0
True
0
0
5
0
0
False
False
False
10.93
0
13.789
-1.9297
G
missense_variant
n.6157A>G
p.Ile2053Val
AGAP004707-RA
6157
0.0
0.0
0.0
0.0
0.0
0.00363636363636
0.0
0.0
0.0
True
2430601
2431617
33
I2053V
I2027V
I2027V
I2037V
I1966V
I1944V
I1999V
I2020V
I2009V
I2009V
I2063V
I2046V
I2063V


2L
2431487
2
G
C
5
0
True
0
1
6
0
0
False
False
False
0.69678
1
14.32
-0.78418
C
missense_variant
n.6227G>C
p.Ser2076Thr
AGAP004707-RA
6227
0.0
0.0
0.0
0.0
0.0
0.00909090909091
0.0
0.0
0.0
True
2430601
2431617
33
S2076T
S2050T
S2050T
S2060T
S1989T
S1967T
S2022T
S2043T
S2032T
S2032T
S2086T
S2069T
S2086T

In [25]:

    

def simplify_intron_effect(v):
    if v and v[0] in ['SPLICE_REGION', 'SPLICE_CORE']:
        if math.fabs(v[2]) < math.fabs(v[4]):
            return v[1], v[2]
        else:
            return v[3], v[4]
    else:
        return ''

    
td_styles = {
    'FILTER_PASS': lambda v: 'background-color: red' if not v else '',
    'NoCoverage': lambda v: 'background-color: red' if v > 1 else '',
    'LowCoverage': lambda v: 'background-color: red' if v > 76 else '',
    'HighCoverage': lambda v: 'background-color: red' if v > 15 else '',
    'LowMQ': lambda v: 'background-color: red' if v > 76 else '',
    'HighMQ0': lambda v: 'background-color: red' if v > 1 else '',
    'RepeatDUST': lambda v: 'background-color: red' if v else '',
    'FS': lambda v: 'background-color: red' if v > 60 else '',
    'QD': lambda v: 'background-color: red' if v < 5 else '',
    'ReadPosRankSum': lambda v: 'background-color: red' if v < -8 else '',
    'HRun': lambda v: 'background-color: red' if v > 4 else '',
    'num_alleles': lambda v: 'background-color: orange' if v > 2 else '',
}


def tr_style(row):
    """Colour row by alternate allele count."""
    return 'background-color:rgba(0, 255, 0, %.3f)' % (min(1, row['AC']/100))


tbl_variants_phase1_splice = (
    tbl_variants_phase1_eff
    .select(lambda row: any(row[t] and row[t][0] in ['SPLICE_REGION', 'SPLICE_CORE'] for t in transcript_ids))
    .convert(transcript_ids, simplify_intron_effect)
)
tbl_variants_phase1_splice.displayall(td_styles=td_styles, tr_style=tr_style)


    

    








0|CHROM
1|POS
2|num_alleles
3|REF
4|ALT
5|AC
6|ALTIX
7|FILTER_PASS
8|NoCoverage
9|LowCoverage
10|HighCoverage
11|LowMQ
12|HighMQ0
13|RepeatDUST
14|RepeatMasker
15|RepeatTRF
16|FS
17|HRun
18|QD
19|ReadPosRankSum
20|SNPEFF_Allele
21|SNPEFF_Annotation
22|SNPEFF_HGVS_c
23|SNPEFF_HGVS_p
24|SNPEFF_Feature_ID
25|SNPEFF_CDS_pos
26|AF_AOM
27|AF_BFM
28|AF_GWA
29|AF_GNS
30|AF_BFS
31|AF_CMS
32|AF_GAS
33|AF_UGS
34|AF_KES
35|check_allele
36|exon_start
37|exon_end
38|exon
39|AGAP004707-RA
40|AGAP004707-RB
41|AGAP004707-RC
42|Davies-C1N2
43|Davies-C3N2
44|Davies-C5N2
45|Davies-C7N2
46|Davies-C8N2
47|Davies-C10N2
48|Davies-C11N2
49|Davies-C1N9
50|Davies-C8N9
51|Davies-C1N9ck




2L
2362002
2
A
T
2
0
True
0
1
3
0
0
False
False
False
0.5459
0
12.531
-0.55322
T
splice_region_variant&intron_varia
n.148-5A>T
None
AGAP004707-RA
-1
0.0
0.0144927536232
0.0
0.0
0.0
0.0
0.0
0.0
0.0
True
2361989
2362144
3
('AGAP004707-PA', -5)
('AGAP004707-PB', -5)
('AGAP004707-PC', -5)












2L
2362003
2
C
T
2
0
True
0
1
3
0
0
False
False
False
0.50195
0
14.062
0.024994
T
splice_region_variant&intron_varia
n.148-4C>T
None
AGAP004707-RA
-1
0.0
0.0144927536232
0.0
0.0
0.0
0.0
0.0
0.0
0.0
True
2361989
2362144
3
('AGAP004707-PA', -4)
('AGAP004707-PB', -4)
('AGAP004707-PC', -4)












2L
2382263
2
A
G
166
0
True
0
45
1
0
0
False
False
False
5.957
0
25.375
-2.8809
G
splice_region_variant&intron_varia
n.492-7A>G
None
AGAP004707-RA
-1
0.00833333333333
0.0
0.0
0.0
0.0
0.0
0.0
0.47572815534
0.761363636364
True
None
None
None
('AGAP004707-PA', -7)
('AGAP004707-PB', -7)
('AGAP004707-PC', -7)
('5', -7)

('5', -7)
('5', -7)
('5', -7)
('5', -7)
('5', -7)
('5', -7)
('5', -7)
('5', -7)


2L
2390126
2
C
T
2
0
True
0
2
11
0
0
False
False
False
3.4746
0
14.32
-1.0264
T
splice_region_variant&intron_varia
n.713-3C>T
None
AGAP004707-RA
-1
0.0
0.0
0.0
0.0
0.0
0.00363636363636
0.0
0.0
0.0
True
None
None
None
('AGAP004707-PA', -3)
('AGAP004707-PB', -3)
('AGAP004707-PC', -3)
('7', -3)
('7', -3)
('7', -3)
('7', -3)
('7', -3)
('7', -3)
('7', -3)
('7', -3)
('7', -3)
('7', -3)


2L
2400176
2
A
G
1
0
True
0
0
7
0
0
False
False
False
0.0
0
22.203
0.74316
G
splice_region_variant&intron_varia
n.1572+3A>G
None
AGAP004707-RA
-1
0.0
0.0
0.0108695652174
0.0
0.0
0.0
0.0
0.0
0.0
True
None
None
None
('AGAP004707-PA', 3)
('AGAP004707-PB', 3)
('AGAP004707-PC', 3)
('11i+', 3)
('11i+', 3)
('11i+', 3)
('11i+', 3)
('11i+', 3)
('11i+', 3)
('11i+', 3)
('11i+', 3)
('11i+', 3)
('11i+', 3)


2L
2407888
2
T
C
4
0
True
0
2
9
0
0
False
False
False
5.7578
0
16.281
-0.76416
C
splice_region_variant&intron_varia
n.2017-6T>C
None
AGAP004707-RA
-1
0.0
0.0
0.0434782608696
0.0
0.0
0.0
0.0
0.0
0.0
True
None
None
None
('AGAP004707-PA', -6)
('AGAP004707-PB', -6)
('AGAP004707-PC', -6)
('16', -6)
('16', -6)
('16', -6)
('16', -6)
('16', -6)
('16', -6)
('16', -6)
('16', -6)
('16', -6)
('16', -6)


2L
2417362
2
A
G
496
0
False
5
712
0
0
0
False
False
False
63.062
1
28.844
1.251
G
splice_region_variant&intron_varia
n.2637+4A>G
None
AGAP004707-RA
-1
0.838983050847
0.840579710145
0.0666666666667
1.0
1.0
0.0967153284672
0.0
0.0
0.0
True
None
None
None
('AGAP004707-PA', 4)
('AGAP004707-PB', 4)
('AGAP004707-PC', 4)
('19', 4)
('19', 4)
('19', 4)
('19', 4)
('19', 4)
('19', 4)
('19', 4)
('19', 4)
('19', 4)
('19', 4)


2L
2425766
2
T
A
79
0
True
0
1
9
0
0
False
False
False
9.9062
0
21.391
1.6143
A
intron_variant
n.4068+315T>
None
AGAP004707-RA
-1
0.0
0.0
0.0
0.0
0.0
0.0145454545455
0.633928571429
0.0
0.0
True
None
None
None












('27k', -4)


2L
2429868
2
C
A
2
0
True
0
0
14
0
0
False
False
False
8.5469
0
14.961
-0.014
A
splice_region_variant&intron_varia
n.4765-4C>A
None
AGAP004707-RA
-1
0.0
0.0
0.0217391304348
0.0
0.0
0.0
0.0
0.0
0.0
True
None
None
None
('AGAP004707-PA', -4)
('AGAP004707-PB', -4)
('AGAP004707-PC', -4)
('31', -4)
('31', -4)
('31', -4)
('31', -4)
('31', -4)
('31', -4)
('31', -4)
('31', -4)
('31', -4)
('31', -4)