Experiments on SNPs' depth lower than 10

Author: Fang Zhang
Date: 2016.7.10
E-mail: fza34@sfu.ca

Experiment SNPs' depth

After depth filter, 6925 SNPs in total including 4003 SNPs' frequency greater than 1. It is not relaible.
The number and propotion of SNPs that have depth lower than10.

sample	number_SNPs	unresi	propotion
ERR550643	92	1248	0.073717949
ERR550644	83	1263	0.065716548
ERR550658	103	1378	0.074746009
ERR550659	121	1446	0.083679115
ERR550670	51	1331	0.038317055
ERR550724	53	1491	0.035546613
ERR550738	66	1347	0.048997773
ERR550739	42	1415	0.029681979
ERR550777	172	1319	0.13040182
ERR550778	91	1347	0.067557535
ERR550779	727	1300	0.559230769
ERR550782	56	1404	0.03988604
ERR550783	90	1404	0.064102564
ERR550887	71	1383	0.051337672
ERR550910	24	1497	0.016032064
ERR550927	37	1345	0.027509294
ERR550940	63	1383	0.045553145
ERR550941	60	1331	0.045078888
ERR550946	42	1324	0.031722054
ERR550947	51	1309	0.038961039
ERR550957	54	1457	0.037062457
ERR550984	45	1397	0.032211883
ERR551007	24	1433	0.016748081
ERR551071	29	1397	0.020758769
ERR551079	57	1392	0.040948276
ERR551086	33	1360	0.024264706
ERR551090	55	1395	0.039426523
ERR551155	58	1355	0.042804428
ERR551156	69	1324	0.052114804
ERR551159	49	1433	0.034193999
ERR551167	62	1341	0.046234154
ERR551168	50	1368	0.036549708
ERR551184	56	1320	0.042424242
ERR551185	363	1244	0.291800643
ERR551201	34	1377	0.024691358
ERR551212	50	1399	0.035739814
ERR551214	79	1229	0.064279902
ERR551225	27	1384	0.019508671
ERR551293	36	1443	0.024948025
ERR551305	98	1398	0.070100143
ERR551311	48	1411	0.034018427
ERR551360	85	1399	0.060757684
ERR551361	141	1355	0.104059041
ERR551362	229	1339	0.171023152
ERR551369	65	1350	0.048148148
ERR551370	98	1336	0.073353293
ERR551412	73	1287	0.056721057
ERR551494	65	1422	0.045710267
ERR551520	23	1477	0.015572106
ERR551549	114	1498	0.076101469
ERR551554	43	1389	0.030957523
ERR551556	63	1376	0.045784884
ERR551557	500	1294	0.386398764
ERR551558	396	1308	0.302752294
ERR551572	45	1347	0.033407572
ERR551575	126	1197	0.105263158
ERR551636	51	1353	0.037694013
ERR551638	77	1379	0.055837563
ERR551680	47	1369	0.034331629
ERR551681	59	1337	0.044128646
ERR551688	71	1353	0.052475979
ERR551693	69	1344	0.051339286
ERR551694	67	1327	0.050489827
ERR551772	40	1473	0.027155465
ERR551804	93	1377	0.067538126
ERR551805	275	1328	0.207078313
ERR551806	347	1333	0.260315079
ERR551821	82	1405	0.058362989
ERR551822	88	1417	0.062103035
ERR551854	86	1298	0.066255778
ERR551855	70	1346	0.052005944
ERR551879	42	1398	0.030042918
ERR551927	91	1317	0.069096431
ERR551928	76	1341	0.056674124
ERR551930	55	1415	0.038869258
ERR551934	23	1481	0.015530047
ERR551943	829	1218	0.680623974
ERR551944	66	1354	0.048744461
ERR551945	48	1381	0.034757422
ERR551956	48	1367	0.035113387
ERR551957	47	1334	0.035232384
ERR551977	114	1314	0.086757991
ERR551978	58	1340	0.043283582
ERR551979	971	1103	0.880326383
ERR551980	585	1254	0.466507177
ERR551981	984	1187	0.828980623
ERR551982	183	1294	0.141421947
ERR551983	905	1026	0.882066277
ERR551990	30	1466	0.020463847
ERR552090	38	1469	0.025867937
ERR552130	35	1411	0.024805103
ERR552136	43	1405	0.030604982
ERR552141	48	1376	0.034883721
ERR552177	32	1383	0.023138106
ERR552190	26	1444	0.01800554
ERR552194	79	1429	0.055283415
ERR552219	60	1343	0.044676098
ERR552331	55	1388	0.03962536
ERR552358	37	1416	0.026129944
ERR552429	50	1406	0.035561878
ERR552444	54	1344	0.040178571
ERR552445	156	1286	0.121306376
ERR552479	60	1611	0.037243948
ERR552482	36	1436	0.025069638
ERR552493	69	1420	0.048591549
ERR552494	113	1415	0.079858657
ERR552549	55	1335	0.041198502
ERR552550	54	1318	0.040971168
ERR552555	41	1398	0.029327611
ERR552580	42	1401	0.029978587
ERR552668	116	1268	0.09148265
ERR552669	969	1227	0.789731051
ERR552670	432	1370	0.315328467
ERR552671	220	1372	0.160349854
ERR552689	67	1355	0.049446494
ERR552690	971	1158	0.83851468
ERR552743	43	1356	0.031710914
ERR552755	41	1337	0.030665669
ERR552760	48	1350	0.035555556
ERR552787	53	1391	0.038102085
ERR552830	64	1360	0.047058824
ERR552838	32	1376	0.023255814
ERR552894	62	1345	0.046096654
ERR552895	123	1288	0.095496894
ERR552907	66	1401	0.047109208
ERR552910	43	1384	0.031069364
ERR552911	68	1362	0.049926579
ERR552912	24	1419	0.016913319
ERR552939	98	1434	0.068340307
ERR552940	253	1487	0.170141224
ERR552949	82	1349	0.060785767
ERR552954	48	1383	0.034707158
ERR553068	48	1366	0.035139092
ERR553081	86	1338	0.064275037
ERR553082	53	1368	0.03874269
ERR553086	22	1463	0.015037594
ERR553098	55	1402	0.039229672
ERR553107	38	1372	0.027696793
ERR553116	53	1366	0.038799414
ERR553139	42	1406	0.029871977
ERR553156	50	1357	0.036845984
ERR553157	505	1306	0.386676876
ERR553171	36	1420	0.025352113
ERR553237	49	1392	0.035201149
ERR553251	38	1471	0.025832767
ERR553274	57	1312	0.043445122
ERR553275	113	1271	0.088906373
ERR553277	44	1382	0.031837916
ERR553291	46	1379	0.033357505
ERR553303	836	1272	0.657232704
ERR553304	95	1320	0.071969697
ERR553313	64	1390	0.046043165
ERR553324	36	1396	0.025787966
ERR619080	59	1398	0.042203147

Many samples have a lot of SNPs that have depth lower than 10. We should check the fastq files first. mrFAST cannot work on fastq files that contain reads of different lengths. If reads are cut at 100, a lot information would be lost. Calculate top 2 long reads and the coverage. Almost at leat 1 sequence of one sample have low coverage. ERR551979-ERR551983 all have very low coverage. Thus we should delete these sequences. For those samples that have several high coverage sequences, we choose the higher one.

sample	total_top2_1	total_1	second_top_length_1	propotion_1	average_depth_1	deleted	total_top2_2	total_2	second_top_length_2	propotion_2	average_depth_2
ERR550643	352629	503810	250	0.69	20.04	1	365368	503810	250	0.72	20.76
ERR550659	457109	888025	150	0.51	15.58	1	459162	888025	150	0.51	15.65
ERR550777	366537	366537	151	1	12.58	1	366537	366537	151	1	12.58
ERR550779	175080	213152	150	0.82	5.97	1	175478	213152	150	0.82	5.98
ERR550783	301101	709644	250	0.42	17.11	1	329686	709644	250	0.46	18.73
ERR550940	816797	986163	150	0.82	27.85	1	816667	986163	150	0.82	27.84
ERR550946	847041	1062557	150	0.79	28.88	1	850563	1062557	150	0.8	29.00
ERR551155	657758	773602	250	0.85	37.37	1	681991	773602	250	0.88	38.75
ERR551168	730841	884768	150	0.82	24.92	1	732908	884768	150	0.82	24.99
ERR551185	201119	310721	250	0.64	11.43	1	205086	310721	250	0.66	11.65
ERR551361	301576	388916	250	0.77	17.14	1	311362	388916	250	0.8	17.69
ERR551362	272194	343012	150	0.79	9.28	1	272760	343012	150	0.79	9.30
ERR551370	560956	668918	250	0.83	31.87	1	525685	668918	250	0.78	29.87
ERR551557	193635	245514	250	0.78	11.00	1	199966	245514	250	0.81	11.36
ERR551558	228464	283281	150	0.8	7.79	1	228863	283281	150	0.8	7.80
ERR551681	450011	561151	250	0.8	25.57	1	466319	561151	250	0.83	26.50
ERR551694	555662	634595	250	0.87	31.57	1	523829	634595	250	0.82	29.76
ERR551805	242169	313777	250	0.77	13.76	1	250503	313777	250	0.79	14.23
ERR551806	238910	295816	150	0.8	8.14	1	238726	295816	150	0.8	8.14
ERR551822	498401	827650	150	0.6	16.99	1	500159	827650	150	0.6	17.05
ERR551854	367993	536581	250	0.68	20.91	1	376291	536581	250	0.7	21.38
ERR551927	371298	519638	250	0.71	21.10	1	377836	519638	250	0.72	21.47
ERR551943	166621	200229	150	0.83	5.68	1	166831	200229	150	0.83	5.69
ERR551945	764186	764186	151	1	26.23	1	764186	764186	151	1	26.23
ERR551957	520790	679521	250	0.76	29.59	1	544932	679521	250	0.8	30.96
ERR551977	345033	505726	250	0.68	19.60	1	354319	505726	250	0.7	20.13
ERR551979	73517	105647	250	0.69	4.18	1	73419	105647	250	0.69	4.17
ERR551980	190883	251974	150	0.75	6.51	1	190285	251974	150	0.75	6.49
ERR551981	78999	125109	300	0.63	5.39	1	78150	125109	300	0.62	5.33
ERR551982	389417	517259	150	0.75	13.28	1	385982	517259	150	0.74	13.16
ERR551983	64960	91448	250	0.71	3.69	1	65482	91448	250	0.71	3.72
ERR552445	293200	446898	250	0.65	16.66	1	301814	446898	250	0.67	17.15
ERR552494	263183	622615	250	0.42	14.95	1	283860	622615	250	0.45	16.13
ERR552549	623022	762902	250	0.81	35.40	1	647569	762902	250	0.84	36.79
ERR552669	55934	155915	250	0.35	3.18	1	69726	155915	250	0.44	3.96
ERR552670	184521	345974	150	0.53	6.29	1	183221	345974	150	0.52	6.25
ERR552671	489347	489347	151	1	16.79	1	489347	489347	151	1	16.79
ERR552690	89514	125815	250	0.71	5.09	1	91766	125815	250	0.72	5.21
ERR552895	471918	517150	250	0.91	26.81	1	484124	517150	250	0.93	27.51
ERR552911	478195	617093	250	0.77	27.17	1	502770	617093	250	0.81	28.57
ERR552940	261884	567079	150	0.46	8.93	1	263299	567079	150	0.46	8.98
ERR553081	466048	660126	250	0.7	26.48	1	501668	660126	250	0.75	28.50
ERR553157	185233	273412	250	0.67	10.52	1	190554	273412	250	0.69	10.83
ERR553275	397740	523197	250	0.76	22.60	1	418654	523197	250	0.8	23.79
ERR553303	159293	186850	250	0.85	9.05	1	170553	186850	250	0.91	9.69
ERR550644	368387	500989	250	0.73	20.93		390100	500989	250	0.77	22.16
ERR550658	694536	694536	151	1	23.84		694536	694536	151	1	23.84
ERR550670	942945	1067515	250	0.88	53.58		975660	1067515	250	0.91	55.44
ERR550724	4406794	4406794	51	1	51.08		4406794	4406794	51	1	51.08
ERR550738	664927	802441	250	0.82	37.78		618779	802441	250	0.77	35.16
ERR550739	1202191	1603567	150	0.74	40.98		1209489	1603567	150	0.75	41.23
ERR550778	403711	492341	250	0.81	22.94		417005	492341	250	0.84	23.69
ERR550782	1142598	1142598	151	1	39.21		1142598	1142598	151	1	39.21
ERR550887	681613	681613	150	1	23.24		681613	681613	150	1	23.24
ERR550910	6148758	6148758	101	1	141.14		6148758	6148758	101	1	141.14
ERR550927	895354	1126439	150	0.79	30.52		897513	1126439	150	0.79	30.60
ERR550941	528566	694478	250	0.76	30.03		553340	694478	250	0.79	31.44
ERR550947	560003	817328	250	0.68	31.82		593168	817328	250	0.72	33.70
ERR550957	2847379	2847379	101	1	65.36		2847379	2847379	101	1	65.36
ERR550984	1232580	1232580	151	1	42.30		1232580	1232580	151	1	42.30
ERR551007	3221955	3221955	101	1	73.96		3221955	3221955	101	1	73.96
ERR551071	1538003	2275846	150	0.67	52.43		1527328	2275846	150	0.67	52.07
ERR551079	831236	1153100	150	0.72	28.34		830923	1153100	150	0.72	28.33
ERR551086	1381621	1709345	150	0.8	47.10		1385599	1709345	150	0.81	47.24
ERR551090	912137	1125813	150	0.81	31.10		912726	1125813	150	0.81	31.12
ERR551156	667053	734670	250	0.9	37.90		686748	734670	250	0.93	39.02
ERR551159	1178805	1178805	151	1	40.45		1178805	1178805	151	1	40.45
ERR551167	746944	746944	151	1	25.63		746944	746944	151	1	25.63
ERR551184	639791	840348	150	0.76	21.81		639780	840348	150	0.76	21.81
ERR551201	1836130	1836130	151	1	63.01		1836130	1836130	151	1	63.01
ERR551212	1112021	1392359	150	0.79	37.91		1110539	1392359	150	0.79	37.86
ERR551214	2950693	2950693	72	1	48.28		2950693	2950693	72	1	48.28
ERR551225	2359668	2359668	101	1	54.17		2359668	2359668	101	1	54.17
ERR551293	3593886	3593886	100	1	81.68		3593886	3593886	100	1	81.68
ERR551305	649772	649772	150	1	22.15		649772	649772	150	1	22.15
ERR551311	920836	1595233	250	0.57	52.32		934011	1595233	250	0.58	53.07
ERR551360	531862	531862	151	1	18.25		531862	531862	151	1	18.25
ERR551369	634497	789026	250	0.8	36.05		664714	789026	250	0.84	37.77
ERR551412	501209	580388	250	0.86	28.48		510344	580388	250	0.87	29.00
ERR551494	997921	1252809	150	0.79	34.02		999254	1252809	150	0.79	34.07
ERR551520	7542333	7542333	101	1	173.13		7542333	7542333	101	1	173.13
ERR551549	3069058	3069058	101	1	70.45		3069058	3069058	101	1	70.45
ERR551554	1146272	1146272	151	1	39.34		1146272	1146272	151	1	39.34
ERR551556	557238	557238	151	1	19.12		557238	557238	151	1	19.12
ERR551572	966186	1156589	150	0.83	32.94		964154	1156589	150	0.83	32.87
ERR551575	2437684	2437684	72	1	39.89		2437684	2437684	72	1	39.89
ERR551636	905255	1116387	150	0.81	30.86		904961	1116387	150	0.81	30.85
ERR551638	696445	696445	150	1	23.74		696445	696445	150	1	23.74
ERR551680	856628	856628	151	1	29.40		856628	856628	151	1	29.40
ERR551688	714189	807272	250	0.88	40.58		741391	807272	250	0.91	42.12
ERR551693	617307	702723	250	0.87	35.07		636967	702723	250	0.9	36.19
ERR551772	4858274	4858274	51	1	56.31		4858274	4858274	51	1	56.31
ERR551804	528297	528297	151	1	18.13		528297	528297	151	1	18.13
ERR551821	751179	751179	151	1	25.78		751179	751179	151	1	25.78
ERR551855	549848	709020	250	0.77	31.24		574161	709020	250	0.8	32.62
ERR551879	1448715	1763371	150	0.82	49.39		1436155	1763371	150	0.81	48.96
ERR551928	485859	626266	250	0.77	27.61		507987	626266	250	0.81	28.86
ERR551930	1039805	1284539	150	0.8	35.45		1042954	1284539	150	0.81	35.56
ERR551934	4930930	4930930	101	1	113.19		4930930	4930930	101	1	113.19
ERR551944	626733	749579	250	0.83	35.61		646916	749579	250	0.86	36.76
ERR551956	1036490	1036490	151	1	35.57		1036490	1036490	151	1	35.57
ERR551978	579051	746633	250	0.77	32.90		610553	746633	250	0.81	34.69
ERR551990	2501148	2501148	101	1	57.41		2501148	2501148	101	1	57.41
ERR552090	3325371	3325371	100	1	75.58		3325371	3325371	100	1	75.58
ERR552130	1416680	1416680	151	1	48.62		1416680	1416680	151	1	48.62
ERR552136	1331643	1702445	150	0.78	45.40		1332191	1702445	150	0.78	45.42
ERR552141	775490	1344531	250	0.57	44.06		778789	1344531	250	0.57	44.25
ERR552177	2126018	2126018	101	1	48.80		2126018	2126018	101	1	48.80
ERR552190	2907157	2907157	101	1	66.73		2907157	2907157	101	1	66.73
ERR552194	833791	1147014	150	0.72	28.42		836118	1147014	150	0.72	28.50
ERR552219	772464	930462	250	0.83	43.89		723511	930462	250	0.77	41.11
ERR552331	1107102	1358539	150	0.81	37.74		1107211	1358539	150	0.81	37.75
ERR552358	1209857	1525080	150	0.79	41.25		1209470	1525080	150	0.79	41.23
ERR552429	1141376	1141376	151	1	39.17		1141376	1141376	151	1	39.17
ERR552444	688009	947208	150	0.72	23.45		686250	947208	150	0.72	23.39
ERR552479	19714536	19714536	51	1	228.51		19714536	19714536	51	1	228.51
ERR552482	1616551	2143831	150	0.75	55.11		1620080	2143831	150	0.75	55.23
ERR552493	1006307	1006307	151	1	34.53		1006307	1006307	151	1	34.53
ERR552550	635108	713215	250	0.89	36.09		657053	713215	250	0.92	37.33
ERR552555	1137494	1412348	150	0.8	38.78		1139900	1412348	150	0.8	38.86
ERR552580	1213962	1213962	151	1	41.66		1213962	1213962	151	1	41.66
ERR552668	480196	694259	250	0.69	27.28		555166	694259	250	0.79	31.54
ERR552689	771015	1014227	150	0.76	26.28		763536	1014227	150	0.75	26.03
ERR552743	874653	1227467	150	0.71	29.82		869799	1227467	150	0.7	29.65
ERR552755	932272	1145975	150	0.81	31.78		933642	1145975	150	0.81	31.83
ERR552760	916048	1122827	150	0.81	31.23		916825	1122827	150	0.81	31.26
ERR552787	1087121	1386109	150	0.78	37.06		1089473	1386109	150	0.78	37.14
ERR552830	703060	824463	250	0.85	39.95		661031	824463	250	0.8	37.56
ERR552838	1355502	1872386	150	0.72	46.21		1351777	1872386	150	0.72	46.08
ERR552894	573476	667626	250	0.85	32.58		592430	667626	250	0.88	33.66
ERR552907	849602	849602	150	1	28.96		849602	849602	150	1	28.96
ERR552910	909326	909326	151	1	31.21		909326	909326	151	1	31.21
ERR552912	3735481	3735481	101	1	85.75		3735481	3735481	101	1	85.75
ERR552939	942214	942214	151	1	32.34		942214	942214	151	1	32.34
ERR552949	565475	672440	250	0.84	32.13		531302	672440	250	0.79	30.19
ERR552954	1263899	1545167	150	0.81	43.09		1265777	1545167	150	0.81	43.15
ERR553068	952882	1037422	150	0.91	32.48		953885	1037422	150	0.91	32.52
ERR553082	843849	1039372	150	0.81	28.77		846859	1039372	150	0.81	28.87
ERR553086	4316346	4316346	101	1	99.08		4316346	4316346	101	1	99.08
ERR553098	1371902	1371902	150	1	46.77		1371902	1371902	150	1	46.77
ERR553107	1157028	1157028	151	1	39.71		1157028	1157028	151	1	39.71
ERR553116	639742	703989	150	0.9	21.81		639742	703989	150	0.9	21.81
ERR553139	1121756	1396599	150	0.8	38.24		1124357	1396599	150	0.8	38.33
ERR553156	604012	818966	150	0.73	20.59		600320	818966	150	0.73	20.47
ERR553171	1746795	1746795	101	1	40.10		1746795	1746795	101	1	40.10
ERR553237	921485	1137866	150	0.8	31.41		921637	1137866	150	0.8	31.42
ERR553251	4809482	4809482	51	1	55.75		4809482	4809482	51	1	55.75
ERR553274	726240	892990	150	0.81	24.76		727986	892990	150	0.81	24.82
ERR553277	907668	1203167	150	0.75	30.94		905914	1203167	150	0.75	30.88
ERR553291	892724	1083213	150	0.82	30.43		894784	1083213	150	0.82	30.50
ERR553304	513906	561524	250	0.91	29.20		527555	561524	250	0.93	29.97
ERR553313	1048464	1048464	151	1	35.98		1048464	1048464	151	1	35.98
ERR553324	1235342	1235342	151	1	42.39		1235342	1235342	151	1	42.39
ERR619080	669268	983056	300	0.68	45.63		718129	983056	300	0.73	48.96

Samples should be deleted (45):

sample	total_top2_1	total_1	second_top_length_1	propotion_1	average_depth_1	deleted	total_top2_2	total_2	second_top_length_2	propotion_2	average_depth_2
ERR550643	352629	503810	250	0.69	20.04	1	365368	503810	250	0.72	20.76
ERR550659	457109	888025	150	0.51	15.58	1	459162	888025	150	0.51	15.65
ERR550777	366537	366537	151	1	12.58	1	366537	366537	151	1	12.58
ERR550779	175080	213152	150	0.82	5.97	1	175478	213152	150	0.82	5.98
ERR550783	301101	709644	250	0.42	17.11	1	329686	709644	250	0.46	18.73
ERR550940	816797	986163	150	0.82	27.85	1	816667	986163	150	0.82	27.84
ERR550946	847041	1062557	150	0.79	28.88	1	850563	1062557	150	0.8	29.00
ERR551155	657758	773602	250	0.85	37.37	1	681991	773602	250	0.88	38.75
ERR551168	730841	884768	150	0.82	24.92	1	732908	884768	150	0.82	24.99
ERR551185	201119	310721	250	0.64	11.43	1	205086	310721	250	0.66	11.65
ERR551361	301576	388916	250	0.77	17.14	1	311362	388916	250	0.8	17.69
ERR551362	272194	343012	150	0.79	9.28	1	272760	343012	150	0.79	9.30
ERR551370	560956	668918	250	0.83	31.87	1	525685	668918	250	0.78	29.87
ERR551557	193635	245514	250	0.78	11.00	1	199966	245514	250	0.81	11.36
ERR551558	228464	283281	150	0.8	7.79	1	228863	283281	150	0.8	7.80
ERR551681	450011	561151	250	0.8	25.57	1	466319	561151	250	0.83	26.50
ERR551694	555662	634595	250	0.87	31.57	1	523829	634595	250	0.82	29.76
ERR551805	242169	313777	250	0.77	13.76	1	250503	313777	250	0.79	14.23
ERR551806	238910	295816	150	0.8	8.14	1	238726	295816	150	0.8	8.14
ERR551822	498401	827650	150	0.6	16.99	1	500159	827650	150	0.6	17.05
ERR551854	367993	536581	250	0.68	20.91	1	376291	536581	250	0.7	21.38
ERR551927	371298	519638	250	0.71	21.10	1	377836	519638	250	0.72	21.47
ERR551943	166621	200229	150	0.83	5.68	1	166831	200229	150	0.83	5.69
ERR551945	764186	764186	151	1	26.23	1	764186	764186	151	1	26.23
ERR551957	520790	679521	250	0.76	29.59	1	544932	679521	250	0.8	30.96
ERR551977	345033	505726	250	0.68	19.60	1	354319	505726	250	0.7	20.13
ERR551979	73517	105647	250	0.69	4.18	1	73419	105647	250	0.69	4.17
ERR551980	190883	251974	150	0.75	6.51	1	190285	251974	150	0.75	6.49
ERR551981	78999	125109	300	0.63	5.39	1	78150	125109	300	0.62	5.33
ERR551982	389417	517259	150	0.75	13.28	1	385982	517259	150	0.74	13.16
ERR551983	64960	91448	250	0.71	3.69	1	65482	91448	250	0.71	3.72
ERR552445	293200	446898	250	0.65	16.66	1	301814	446898	250	0.67	17.15
ERR552494	263183	622615	250	0.42	14.95	1	283860	622615	250	0.45	16.13
ERR552549	623022	762902	250	0.81	35.40	1	647569	762902	250	0.84	36.79
ERR552669	55934	155915	250	0.35	3.18	1	69726	155915	250	0.44	3.96
ERR552670	184521	345974	150	0.53	6.29	1	183221	345974	150	0.52	6.25
ERR552671	489347	489347	151	1	16.79	1	489347	489347	151	1	16.79
ERR552690	89514	125815	250	0.71	5.09	1	91766	125815	250	0.72	5.21
ERR552895	471918	517150	250	0.91	26.81	1	484124	517150	250	0.93	27.51
ERR552911	478195	617093	250	0.77	27.17	1	502770	617093	250	0.81	28.57
ERR552940	261884	567079	150	0.46	8.93	1	263299	567079	150	0.46	8.98
ERR553081	466048	660126	250	0.7	26.48	1	501668	660126	250	0.75	28.50
ERR553157	185233	273412	250	0.67	10.52	1	190554	273412	250	0.69	10.83
ERR553275	397740	523197	250	0.76	22.60	1	418654	523197	250	0.8	23.79
ERR553303	159293	186850	250	0.85	9.05	1	170553	186850	250	0.91	9.69

samples' reads length at 150 (36):

sample	total_top2_1	total_1	second_top_length_1	propotion_1	average_depth_1	total_top2_2	total_2	second_top_length_2	propotion_2	average_depth_2
ERR553068	952882	1037422	150	0.91	32.48	953885	1037422	150	0.91	32.52
ERR553116	639742	703989	150	0.9	21.81	639742	703989	150	0.9	21.81
ERR551572	966186	1156589	150	0.83	32.94	964154	1156589	150	0.83	32.87
ERR551879	1448715	1763371	150	0.82	49.39	1436155	1763371	150	0.81	48.96
ERR553291	892724	1083213	150	0.82	30.43	894784	1083213	150	0.82	30.50
ERR551090	912137	1125813	150	0.81	31.10	912726	1125813	150	0.81	31.12
ERR551636	905255	1116387	150	0.81	30.86	904961	1116387	150	0.81	30.85
ERR552331	1107102	1358539	150	0.81	37.74	1107211	1358539	150	0.81	37.75
ERR552755	932272	1145975	150	0.81	31.78	933642	1145975	150	0.81	31.83
ERR552760	916048	1122827	150	0.81	31.23	916825	1122827	150	0.81	31.26
ERR552954	1263899	1545167	150	0.81	43.09	1265777	1545167	150	0.81	43.15
ERR553082	843849	1039372	150	0.81	28.77	846859	1039372	150	0.81	28.87
ERR553274	726240	892990	150	0.81	24.76	727986	892990	150	0.81	24.82
ERR551086	1381621	1709345	150	0.8	47.10	1385599	1709345	150	0.81	47.24
ERR551930	1039805	1284539	150	0.8	35.45	1042954	1284539	150	0.81	35.56
ERR552555	1137494	1412348	150	0.8	38.78	1139900	1412348	150	0.8	38.86
ERR553139	1121756	1396599	150	0.8	38.24	1124357	1396599	150	0.8	38.33
ERR553237	921485	1137866	150	0.8	31.41	921637	1137866	150	0.8	31.42
ERR550927	895354	1126439	150	0.79	30.52	897513	1126439	150	0.79	30.60
ERR551212	1112021	1392359	150	0.79	37.91	1110539	1392359	150	0.79	37.86
ERR551494	997921	1252809	150	0.79	34.02	999254	1252809	150	0.79	34.07
ERR552358	1209857	1525080	150	0.79	41.25	1209470	1525080	150	0.79	41.23
ERR552136	1331643	1702445	150	0.78	45.40	1332191	1702445	150	0.78	45.42
ERR552787	1087121	1386109	150	0.78	37.06	1089473	1386109	150	0.78	37.14
ERR551184	639791	840348	150	0.76	21.81	639780	840348	150	0.76	21.81
ERR552689	771015	1014227	150	0.76	26.28	763536	1014227	150	0.75	26.03
ERR552482	1616551	2143831	150	0.75	55.11	1620080	2143831	150	0.75	55.23
ERR553277	907668	1203167	150	0.75	30.94	905914	1203167	150	0.75	30.88
ERR550739	1202191	1603567	150	0.74	40.98	1209489	1603567	150	0.75	41.23
ERR553156	604012	818966	150	0.73	20.59	600320	818966	150	0.73	20.47
ERR551079	831236	1153100	150	0.72	28.34	830923	1153100	150	0.72	28.33
ERR552194	833791	1147014	150	0.72	28.42	836118	1147014	150	0.72	28.50
ERR552444	688009	947208	150	0.72	23.45	686250	947208	150	0.72	23.39
ERR552838	1355502	1872386	150	0.72	46.21	1351777	1872386	150	0.72	46.08
ERR552743	874653	1227467	150	0.71	29.82	869799	1227467	150	0.7	29.65
ERR551071	1538003	2275846	150	0.67	52.43	1527328	2275846	150	0.67	52.07

samples' reads length at 250 (24):

sample	total_top2_1	total_1	second_top_length_1	propotion_1	average_depth_1	total_top2_2	total_2	second_top_length_2	propotion_2	average_depth_2
ERR553304	513906	561524	250	0.91	29.20	527555	561524	250	0.93	29.97
ERR551156	667053	734670	250	0.9	37.90	686748	734670	250	0.93	39.02
ERR552550	635108	713215	250	0.89	36.09	657053	713215	250	0.92	37.33
ERR550670	942945	1067515	250	0.88	53.58	975660	1067515	250	0.91	55.44
ERR551688	714189	807272	250	0.88	40.58	741391	807272	250	0.91	42.12
ERR551693	617307	702723	250	0.87	35.07	636967	702723	250	0.9	36.19
ERR551412	501209	580388	250	0.86	28.48	510344	580388	250	0.87	29.00
ERR552830	703060	824463	250	0.85	39.95	661031	824463	250	0.8	37.56
ERR552894	573476	667626	250	0.85	32.58	592430	667626	250	0.88	33.66
ERR552949	565475	672440	250	0.84	32.13	531302	672440	250	0.79	30.19
ERR551944	626733	749579	250	0.83	35.61	646916	749579	250	0.86	36.76
ERR552219	772464	930462	250	0.83	43.89	723511	930462	250	0.77	41.11
ERR550738	664927	802441	250	0.82	37.78	618779	802441	250	0.77	35.16
ERR550778	403711	492341	250	0.81	22.94	417005	492341	250	0.84	23.69
ERR551369	634497	789026	250	0.8	36.05	664714	789026	250	0.84	37.77
ERR551855	549848	709020	250	0.77	31.24	574161	709020	250	0.8	32.62
ERR551928	485859	626266	250	0.77	27.61	507987	626266	250	0.81	28.86
ERR551978	579051	746633	250	0.77	32.90	610553	746633	250	0.81	34.69
ERR550941	528566	694478	250	0.76	30.03	553340	694478	250	0.79	31.44
ERR550644	368387	500989	250	0.73	20.93	390100	500989	250	0.77	22.16
ERR552668	480196	694259	250	0.69	27.28	555166	694259	250	0.79	31.54
ERR550947	560003	817328	250	0.68	31.82	593168	817328	250	0.72	33.70
ERR551311	920836	1595233	250	0.57	52.32	934011	1595233	250	0.58	53.07
ERR552141	775490	1344531	250	0.57	44.06	778789	1344531	250	0.57	44.25

sample's reads length at 300 (1):

sample	total_top2_1	total_1	second_top_length_1	propotion_1	average_depth_1	deleted	total_top2_2	total_2	second_top_length_2	propotion_2	average_depth_2
ERR619080	669268	983056	300	0.68	45.63		718129	983056	300	0.73	48.96

samples have uniform reads length (48):

sample	total_top2_1	total_1	second_top_length_1	propotion_1	average_depth_1	total_top2_2	total_2	second_top_length_2	propotion_2	average_depth_2
ERR550658	694536	694536	151	1	23.84	694536	694536	151	1	23.84
ERR550724	4406794	4406794	51	1	51.08	4406794	4406794	51	1	51.08
ERR550782	1142598	1142598	151	1	39.21	1142598	1142598	151	1	39.21
ERR550887	681613	681613	150	1	23.24	681613	681613	150	1	23.24
ERR550910	6148758	6148758	101	1	141.14	6148758	6148758	101	1	141.14
ERR550957	2847379	2847379	101	1	65.36	2847379	2847379	101	1	65.36
ERR550984	1232580	1232580	151	1	42.30	1232580	1232580	151	1	42.30
ERR551007	3221955	3221955	101	1	73.96	3221955	3221955	101	1	73.96
ERR551159	1178805	1178805	151	1	40.45	1178805	1178805	151	1	40.45
ERR551167	746944	746944	151	1	25.63	746944	746944	151	1	25.63
ERR551201	1836130	1836130	151	1	63.01	1836130	1836130	151	1	63.01
ERR551214	2950693	2950693	72	1	48.28	2950693	2950693	72	1	48.28
ERR551225	2359668	2359668	101	1	54.17	2359668	2359668	101	1	54.17
ERR551293	3593886	3593886	100	1	81.68	3593886	3593886	100	1	81.68
ERR551305	649772	649772	150	1	22.15	649772	649772	150	1	22.15
ERR551360	531862	531862	151	1	18.25	531862	531862	151	1	18.25
ERR551520	7542333	7542333	101	1	173.13	7542333	7542333	101	1	173.13
ERR551549	3069058	3069058	101	1	70.45	3069058	3069058	101	1	70.45
ERR551554	1146272	1146272	151	1	39.34	1146272	1146272	151	1	39.34
ERR551556	557238	557238	151	1	19.12	557238	557238	151	1	19.12
ERR551575	2437684	2437684	72	1	39.89	2437684	2437684	72	1	39.89
ERR551638	696445	696445	150	1	23.74	696445	696445	150	1	23.74
ERR551680	856628	856628	151	1	29.40	856628	856628	151	1	29.40
ERR551772	4858274	4858274	51	1	56.31	4858274	4858274	51	1	56.31
ERR551804	528297	528297	151	1	18.13	528297	528297	151	1	18.13
ERR551821	751179	751179	151	1	25.78	751179	751179	151	1	25.78
ERR551934	4930930	4930930	101	1	113.19	4930930	4930930	101	1	113.19
ERR551956	1036490	1036490	151	1	35.57	1036490	1036490	151	1	35.57
ERR551990	2501148	2501148	101	1	57.41	2501148	2501148	101	1	57.41
ERR552090	3325371	3325371	100	1	75.58	3325371	3325371	100	1	75.58
ERR552130	1416680	1416680	151	1	48.62	1416680	1416680	151	1	48.62
ERR552177	2126018	2126018	101	1	48.80	2126018	2126018	101	1	48.80
ERR552190	2907157	2907157	101	1	66.73	2907157	2907157	101	1	66.73
ERR552429	1141376	1141376	151	1	39.17	1141376	1141376	151	1	39.17
ERR552479	19714536	19714536	51	1	228.51	19714536	19714536	51	1	228.51
ERR552493	1006307	1006307	151	1	34.53	1006307	1006307	151	1	34.53
ERR552580	1213962	1213962	151	1	41.66	1213962	1213962	151	1	41.66
ERR552907	849602	849602	150	1	28.96	849602	849602	150	1	28.96
ERR552910	909326	909326	151	1	31.21	909326	909326	151	1	31.21
ERR552912	3735481	3735481	101	1	85.75	3735481	3735481	101	1	85.75
ERR552939	942214	942214	151	1	32.34	942214	942214	151	1	32.34
ERR553086	4316346	4316346	101	1	99.08	4316346	4316346	101	1	99.08
ERR553098	1371902	1371902	150	1	46.77	1371902	1371902	150	1	46.77
ERR553107	1157028	1157028	151	1	39.71	1157028	1157028	151	1	39.71
ERR553171	1746795	1746795	101	1	40.10	1746795	1746795	101	1	40.10
ERR553251	4809482	4809482	51	1	55.75	4809482	4809482	51	1	55.75
ERR553313	1048464	1048464	151	1	35.98	1048464	1048464	151	1	35.98
ERR553324	1235342	1235342	151	1	42.39	1235342	1235342	151	1	42.39

SNPs of 89 samples.

sample	reads length	mapping error rate (%)	GATK	mpileup	intersection	resi	unresi	unrepeted	repeted	depth_unfiltered	depth_filtered	propotion
ERR552668	250	8	1100	2717	796	17	779	709	70	31	678	0.956276
ERR552949	250	8	997	2682	929	18	911	837	74	242	595	0.710872
ERR550738	250	8	1012	2456	929	13	916	839	77	309	530	0.631704
ERR552830	250	8	1090	2169	903	11	892	810	82	342	468	0.577778
ERR552219	250	8	1071	2023	893	13	880	804	76	441	363	0.451493
ERR553304	250	8	1518	2149	1258	22	1236	1102	134	837	265	0.240472
ERR552550	250	8	1398	2045	1195	18	1177	1062	115	867	195	0.183616
ERR551156	250	8	1473	2081	1246	21	1225	1078	147	884	194	0.179963
ERR551688	250	8	1492	2135	1243	17	1226	1086	140	897	189	0.174033
ERR551305	150	8	2006	4474	1637	24	1613	1382	231	1184	198	0.143271
ERR551638	150	8	1885	3946	1585	24	1561	1364	197	1192	172	0.1261
ERR550887	150	8	1916	3726	1598	25	1573	1352	221	1195	157	0.116124
ERR551549	101	4	2067	3140	1604	25	1579	1371	208	1224	147	0.107221
ERR552194	150	8	2076	3473	1624	23	1601	1362	239	1222	140	0.10279
ERR553274	150	8	1904	2324	1493	18	1475	1250	225	1139	111	0.0888
ERR553171	101	4	1830	5314	1540	18	1522	1307	215	1196	111	0.084927
ERR551167	151	8	1468	1494	1396	23	1373	1196	177	1097	99	0.082776
ERR552907	150	8	1843	3358	1548	24	1524	1304	220	1204	100	0.076687
ERR553116	150	8	2137	2290	1577	20	1557	1318	239	1218	100	0.075873
ERR550670	250	8	1543	1787	1259	22	1237	1082	155	1002	80	0.073937
ERR550957	101	4	1779	2088	1527	20	1507	1298	209	1211	87	0.067026
ERR551928	250	8	1925	1618	1467	19	1448	1266	182	1183	83	0.065561
ERR551412	250	8	1954	1637	1494	22	1472	1238	234	1158	80	0.06462
ERR551369	250	8	2017	1671	1508	19	1489	1295	194	1213	82	0.06332
ERR553313	151	8	1786	2053	1506	24	1482	1294	188	1213	81	0.062597
ERR551184	150	8	1730	1668	1447	17	1430	1189	241	1116	73	0.061396
ERR550941	250	8	1997	1662	1490	21	1469	1265	204	1189	76	0.060079
ERR552760	150	8	1994	2192	1517	18	1499	1253	246	1178	75	0.059856
ERR551693	250	8	2006	1665	1515	21	1494	1291	203	1215	76	0.058869
ERR553156	150	8	1742	1691	1463	18	1445	1244	201	1171	73	0.058682
ERR550778	250	8	1902	1661	1492	26	1466	1264	202	1190	74	0.058544
ERR550644	250	8	1771	1608	1398	18	1380	1196	184	1126	70	0.058528
ERR553098	150	8	1774	2777	1516	24	1492	1284	208	1209	75	0.058411
ERR551494	150	8	1949	2105	1559	23	1536	1305	231	1229	76	0.058238
ERR550658	151	8	1518	1512	1405	23	1382	1216	166	1148	68	0.055921
ERR551855	250	8	1826	1632	1452	19	1433	1250	183	1181	69	0.0552
ERR550947	250	8	1854	1591	1435	19	1416	1228	188	1161	67	0.05456
ERR551930	150	8	2007	2226	1597	19	1578	1322	256	1250	72	0.054463
ERR551821	151	8	1558	1554	1448	24	1424	1233	191	1166	67	0.054339
ERR552787	150	8	1939	2025	1519	19	1500	1276	224	1207	69	0.054075
ERR551311	250	8	2078	1674	1543	23	1520	1317	203	1248	69	0.052392
ERR552444	150	8	1784	1719	1483	17	1466	1229	237	1165	64	0.052075
ERR552755	150	8	1955	2065	1508	17	1491	1230	261	1166	64	0.052033
ERR551636	150	8	1941	2132	1495	18	1477	1243	234	1182	61	0.049075
ERR553291	150	8	1926	1988	1530	19	1511	1285	226	1223	62	0.048249
ERR552689	150	8	1763	1654	1449	20	1429	1223	206	1164	59	0.048242
ERR553082	150	8	1890	1971	1514	19	1495	1266	229	1205	61	0.048183
ERR552331	150	8	1924	1785	1511	19	1492	1268	224	1207	61	0.048107
ERR551090	150	8	1913	1867	1535	23	1512	1276	236	1215	61	0.047806
ERR552954	150	8	1900	1730	1527	22	1505	1285	220	1224	61	0.047471
ERR553068	150	8	2044	2027	1527	24	1503	1292	211	1231	61	0.047214
ERR551804	151	8	1595	1566	1465	24	1441	1235	206	1177	58	0.046964
ERR551360	151	8	1573	1559	1466	24	1442	1236	206	1178	58	0.046926
ERR550927	150	8	1971	2411	1516	18	1498	1250	248	1192	58	0.0464
ERR552177	101	4	1637	1907	1473	19	1454	1215	239	1159	56	0.046091
ERR551956	151	8	1598	1541	1451	24	1427	1216	211	1160	56	0.046053
ERR552894	250	8	1943	1611	1480	20	1460	1273	187	1216	57	0.044776
ERR551079	150	8	1880	1718	1512	19	1493	1267	226	1211	56	0.044199
ERR552141	250	8	1938	1655	1508	26	1482	1291	191	1234	57	0.044152
ERR553139	150	8	1925	2115	1579	23	1556	1296	260	1239	57	0.043981
ERR552136	150	8	1948	1802	1561	24	1537	1299	238	1242	57	0.04388
ERR551978	250	8	1829	1584	1423	18	1405	1235	170	1181	54	0.043725
ERR552939	151	8	1547	1563	1433	23	1410	1211	199	1159	52	0.04294
ERR550782	151	8	1592	1564	1471	23	1448	1239	209	1186	53	0.042776
ERR551212	150	8	1920	1877	1540	24	1516	1297	219	1242	55	0.042406
ERR551201	151	8	1590	1534	1452	19	1433	1235	198	1183	52	0.042105
ERR552090	100	4	1673	1765	1536	22	1514	1288	226	1234	54	0.041925
ERR553277	150	8	1945	1741	1528	20	1508	1265	243	1212	53	0.041897
ERR619080	300	6.6	2020	1694	1551	19	1532	1301	231	1247	54	0.041507
ERR552910	151	8	1569	1521	1446	22	1424	1242	182	1192	50	0.040258
ERR551944	250	8	2028	1717	1543	23	1520	1295	225	1243	52	0.040154
ERR552429	151	8	1607	1585	1486	26	1460	1250	210	1200	50	0.04
ERR552555	150	8	1977	2054	1557	21	1536	1279	257	1228	51	0.039875
ERR553237	150	8	1962	1895	1542	22	1520	1285	235	1234	51	0.039689
ERR552743	150	8	1792	1687	1484	19	1465	1246	219	1197	49	0.039326
ERR551086	150	8	1908	1937	1541	18	1523	1248	275	1199	49	0.039263
ERR551990	101	4	1721	1865	1550	19	1531	1281	250	1232	49	0.038251
ERR551680	151	8	1589	1546	1467	20	1447	1240	207	1193	47	0.037903
ERR551556	151	8	1590	1519	1441	24	1417	1228	189	1182	46	0.037459
ERR550984	151	8	1578	1531	1455	22	1433	1241	192	1195	46	0.037067
ERR551225	101	4	1642	1750	1466	18	1448	1195	253	1151	44	0.03682
ERR552482	150	8	1962	2123	1592	25	1567	1305	262	1257	48	0.036782
ERR551554	151	8	1570	1555	1464	23	1441	1251	190	1205	46	0.036771
ERR552130	151	8	1604	1550	1456	20	1436	1225	211	1180	45	0.036735
ERR551879	150	8	1927	1772	1543	19	1524	1272	252	1226	46	0.036164
ERR551572	150	8	1856	1737	1498	18	1480	1228	252	1184	44	0.035831
ERR552493	151	8	1595	1570	1473	21	1452	1230	222	1187	43	0.034959
ERR552190	101	4	1660	1735	1506	19	1487	1269	218	1225	44	0.034673
ERR553107	151	8	1556	1518	1434	24	1410	1192	218	1151	41	0.034396
ERR552358	150	8	2025	1908	1559	24	1535	1285	250	1241	44	0.034241
ERR553324	151	8	1574	1535	1458	19	1439	1246	193	1204	42	0.033708
ERR551159	151	8	1615	1576	1475	22	1453	1252	201	1210	42	0.033546
ERR552580	151	8	1604	1561	1479	25	1454	1257	197	1215	42	0.033413
ERR550739	150	8	1859	1750	1544	19	1525	1273	252	1233	40	0.031422
ERR551293	100	4	1635	1737	1502	20	1482	1249	233	1210	39	0.031225
ERR552912	101	4	1634	1780	1491	18	1473	1212	261	1175	37	0.030528
ERR553086	101	4	1688	1764	1531	19	1512	1254	258	1216	38	0.030303
ERR552838	150	8	1821	1696	1517	19	1498	1224	274	1187	37	0.030229
ERR551071	150	8	1873	1701	1522	20	1502	1266	236	1228	38	0.030016
ERR551934	101	4	1695	1722	1545	19	1526	1263	263	1226	37	0.029295
ERR551007	101	4	1648	1720	1498	19	1479	1254	225	1218	36	0.028708
ERR550910	101	4	1720	1689	1562	19	1543	1284	259	1252	32	0.024922
ERR551520	101	4	1681	1665	1534	19	1515	1280	235	1251	29	0.022656

SNP frequency. (6336 in total, 2705 occur more than once.)
SNPs of 103 samples using error rate 4%.

sample	reads length	GATK	mpileup	intersection	resi	unresi	unrepeted	repeted	depth_unfiltered	depth_filtered	propotion	deleted
ERR550738	250							0		0	#DIV/0!	1
ERR552219	250	1	1	1		1	1	0		1	1	1
ERR552668	250	98	117	84	1	83	78	5		78	1	1
ERR552830	250	3	3	3		3	2	1		2	1	1
ERR552949	250	1	2	1		1	1	0		1	1	1
ERR553304	250	1103	1437	988	18	970	895	75	48	847	0.946368715	1
ERR551156	250	1131	1563	1033	19	1014	936	78	96	840	0.897435897	1
ERR551688	250	1145	1565	1051	16	1035	953	82	101	852	0.894018888	1
ERR552550	250	1111	1560	987	13	974	908	66	103	805	0.886563877	1
ERR550670	250	1214	1667	1120	20	1100	1014	86	265	749	0.738658777	1
ERR551305	150	2006	4474	1637	24	1613	1382	231	1184	198	0.143270622	1
ERR551638	150	1885	3946	1585	24	1561	1364	197	1192	172	0.126099707	1
ERR552194	150	1748	3551	1563	23	1540	1340	200	1181	159	0.118656716	1
ERR550887	150	1916	3726	1598	25	1573	1352	221	1195	157	0.11612426	1
ERR551549	101	2067	3140	1604	25	1579	1371	208	1224	147	0.107221007	1
ERR553171	101	1830	5314	1540	18	1522	1307	215	1196	111	0.084927314
ERR550941	250	1667	1565	1429	21	1408	1234	174	1130	104	0.084278768
ERR551167	151	1468	1494	1396	23	1373	1196	177	1097	99	0.08277592
ERR553274	150	1591	2266	1401	18	1383	1205	178	1106	99	0.082157676
ERR550644	250	1516	1513	1347	18	1329	1175	154	1080	95	0.080851064
ERR551978	250	1557	1491	1382	19	1363	1215	148	1117	98	0.080658436
ERR553116	150	1720	2098	1496	20	1476	1284	192	1181	103	0.080218069
ERR553156	150	1506	1634	1404	19	1385	1227	158	1130	97	0.079054605
ERR551855	250	1580	1503	1405	19	1386	1233	153	1136	97	0.078669911
ERR552907	150	1843	3358	1548	24	1524	1304	220	1204	100	0.076687117
ERR551184	150	1490	1604	1374	18	1356	1165	191	1081	84	0.072103004
ERR550947	250	1562	1478	1378	20	1358	1200	158	1118	82	0.068333333
ERR550957	101	1779	2088	1527	20	1507	1298	209	1211	87	0.067026194
ERR552141	250	1647	1537	1450	26	1424	1256	168	1173	83	0.066082803
ERR550778	250	1617	1592	1433	26	1407	1236	171	1156	80	0.064724919
ERR552689	150	1494	1562	1376	20	1356	1196	160	1121	75	0.06270903
ERR553313	151	1786	2053	1506	24	1482	1294	188	1213	81	0.0625966
ERR550927	150	1642	2397	1444	17	1427	1227	200	1154	73	0.059494703
ERR551928	250	1641	1533	1416	20	1396	1227	169	1154	73	0.059494703
ERR551930	150	1648	2204	1490	19	1471	1274	197	1199	75	0.058869702
ERR553082	150	1577	1903	1442	19	1423	1246	177	1173	73	0.05858748
ERR553098	150	1774	2777	1516	24	1492	1284	208	1209	75	0.058411215
ERR551412	250	1574	1520	1388	23	1365	1194	171	1125	69	0.057788945
ERR552760	150	1640	2177	1439	18	1421	1214	207	1144	70	0.057660626
ERR552755	150	1618	2019	1429	17	1412	1201	211	1133	68	0.056619484
ERR553237	150	1636	1819	1471	22	1449	1259	190	1188	71	0.056393963
ERR550658	151	1518	1512	1405	23	1382	1216	166	1148	68	0.055921053
ERR552444	150	1490	1652	1391	17	1374	1182	192	1116	66	0.055837563
ERR551636	150	1633	2103	1418	18	1400	1210	190	1143	67	0.055371901
ERR551369	250	1685	1531	1433	19	1414	1250	164	1181	69	0.0552
ERR552743	150	1558	1592	1410	19	1391	1224	167	1157	67	0.054738562
ERR551944	250	1675	1565	1457	23	1434	1249	185	1181	68	0.054443555
ERR551821	151	1558	1554	1448	24	1424	1233	191	1166	67	0.054339011
ERR551693	250	1661	1515	1442	22	1420	1243	177	1176	67	0.05390185
ERR553068	150	1692	1833	1472	24	1448	1261	187	1194	67	0.053132435
ERR552894	250	1632	1505	1418	20	1398	1236	162	1171	65	0.052588997
ERR552954	150	1594	1612	1435	22	1413	1244	169	1179	65	0.052250804
ERR551079	150	1572	1598	1427	19	1408	1237	171	1175	62	0.050121261
ERR553291	150	1603	1913	1449	19	1430	1247	183	1185	62	0.049719326
ERR551494	150	1636	2035	1475	23	1452	1260	192	1200	60	0.047619048
ERR553277	150	1613	1620	1443	20	1423	1232	191	1174	58	0.047077922
ERR551804	151	1595	1566	1465	24	1441	1235	206	1177	58	0.046963563
ERR551360	151	1573	1559	1466	24	1442	1236	206	1178	58	0.046925566
ERR551212	150	1599	1743	1454	24	1430	1258	172	1199	59	0.046899841
ERR551311	250	1707	1544	1453	23	1430	1257	173	1199	58	0.046141607
ERR551086	150	1619	1868	1445	18	1427	1214	213	1158	56	0.046128501
ERR552177	101	1637	1907	1473	19	1454	1215	239	1159	56	0.046090535
ERR551956	151	1598	1541	1451	24	1427	1216	211	1160	56	0.046052632
ERR552787	150	1626	1933	1445	19	1426	1233	193	1177	56	0.04541768
ERR550739	150	1563	1612	1465	19	1446	1245	201	1189	56	0.04497992
ERR551090	150	1576	1769	1439	23	1416	1237	179	1183	54	0.043654002
ERR552555	150	1653	1981	1469	21	1448	1242	206	1188	54	0.043478261
ERR551572	150	1600	1600	1424	18	1406	1200	206	1148	52	0.043333333
ERR552939	151	1547	1563	1433	23	1410	1211	199	1159	52	0.042939719
ERR550782	151	1592	1564	1471	23	1448	1239	209	1186	53	0.042776433
ERR551201	151	1590	1534	1452	19	1433	1235	198	1183	52	0.042105263
ERR552136	150	1615	1667	1466	24	1442	1261	181	1208	53	0.042030135
ERR552090	100	1673	1765	1536	22	1514	1288	226	1234	54	0.041925466
ERR551879	150	1633	1601	1459	19	1440	1245	195	1194	51	0.040963855
ERR552331	150	1646	1687	1438	19	1419	1229	190	1179	50	0.040683483
ERR553139	150	1663	2085	1490	23	1467	1257	210	1206	51	0.040572792
ERR552910	151	1569	1521	1446	22	1424	1242	182	1192	50	0.040257649
ERR552429	151	1607	1585	1486	26	1460	1250	210	1200	50	0.04
ERR552358	150	1607	1793	1468	24	1444	1254	190	1204	50	0.039872408
ERR619080	300	1757	1612	1501	19	1482	1265	217	1215	50	0.039525692
ERR551990	101	1721	1865	1550	19	1531	1281	250	1232	49	0.038251366
ERR552482	150	1669	2075	1500	25	1475	1259	216	1211	48	0.038125496
ERR551680	151	1589	1546	1467	20	1447	1240	207	1193	47	0.037903226
ERR551556	151	1590	1519	1441	24	1417	1228	189	1182	46	0.037459283
ERR550984	151	1578	1531	1455	22	1433	1241	192	1195	46	0.037066882
ERR551225	101	1642	1750	1466	18	1448	1195	253	1151	44	0.036820084
ERR551554	151	1570	1555	1464	23	1441	1251	190	1205	46	0.036770584
ERR552130	151	1604	1550	1456	20	1436	1225	211	1180	45	0.036734694
ERR552838	150	1549	1558	1417	19	1398	1191	207	1149	42	0.035264484
ERR552493	151	1595	1570	1473	21	1452	1230	222	1187	43	0.03495935
ERR552190	101	1660	1735	1506	19	1487	1269	218	1225	44	0.034672971
ERR553107	151	1556	1518	1434	24	1410	1192	218	1151	41	0.034395973
ERR553324	151	1574	1535	1458	19	1439	1246	193	1204	42	0.033707865
ERR551159	151	1615	1576	1475	22	1453	1252	201	1210	42	0.033546326
ERR552580	151	1604	1561	1479	25	1454	1257	197	1215	42	0.033412888
ERR551071	150	1563	1549	1436	20	1416	1228	188	1189	39	0.031758958
ERR551293	100	1635	1737	1502	20	1482	1249	233	1210	39	0.03122498
ERR552912	101	1634	1780	1491	18	1473	1212	261	1175	37	0.030528053
ERR553086	101	1688	1764	1531	19	1512	1254	258	1216	38	0.03030303
ERR551934	101	1695	1722	1545	19	1526	1263	263	1226	37	0.029295329
ERR551007	101	1648	1720	1498	19	1479	1254	225	1218	36	0.028708134
ERR550910	101	1720	1689	1562	19	1543	1284	259	1252	32	0.024922118
ERR551520	101	1681	1665	1534	19	1515	1280	235	1251	29	0.02265625

SNP frequency. (6233 in total, 2539 occur more than once.)
SNPs of 104 samples (combine multi-sequenced samples) using error rate 4%. 6403 SNPs in total.

sample	reads length	GATK	mpileup	intersection	resi	unresi	unrepeted	repeted	depth_unfiltered	depth_filtered	propotion	deleted	total_reads	mapped_reads	propotion
ERR550670	250	1214	1667	1120	20	1100	1014	86	265	749	0.738658777	1			0
ERR550738	250							0		0	#DIV/0!	1			0
ERR550887	150	1916	3726	1598	25	1573	1352	221	1195	157	0.11612426	1			0
ERR551305	150	2006	4474	1637	24	1613	1382	231	1184	198	0.143270622	1			0
ERR551549	101	2067	3140	1604	25	1579	1371	208	1224	147	0.107221007	1			0
ERR551638	150	1885	3946	1585	24	1561	1364	197	1192	172	0.126099707	1			0
ERR551688	250	1145	1565	1051	16	1035	953	82	101	852	0.894018888	1			0
ERR551892	150	1584	1886	1396	19	1377	1207	170	1019	188	0.155758078	1			0
ERR552194	150	1748	3551	1563	23	1540	1340	200	1181	159	0.118656716	1			0
ERR552219	250	1	1	1		1	1	0		1	1	1			0
ERR552668	250	1400	1930	1289	19	1270	1156	114	59	1097	0.948961938	1			0
ERR552830	250	3	3	3		3	2	1		2	1	1			0
ERR552949	250	1	2	1		1	1	0		1	1	1			0
ERR553304	250	1459	1667	1330	24	1306	1160	146	618	542	0.467241379	1			0
ERR552550	250	1620	1502	1420	20	1400	1235	165	1174	61	0.049392713		2396642	1357790	0.566539
ERR551156	250	1636	1519	1445	23	1422	1248	174	1172	76	0.060897436		2533326	1465744	0.578585
ERR551293	100	1635	1737	1502	20	1482	1249	233	1210	39	0.03122498		4736584	2897215	0.611668
ERR551167	151	1532	1531	1442	24	1418	1227	191	1177	50	0.040749796		2609952	2213025	0.847918
ERR551978	250	1605	1487	1408	19	1389	1230	159	1158	72	0.058536585		1689220	1354323	0.801745
ERR551855	250	1629	1506	1426	19	1407	1246	161	1163	83	0.066613162		1672044	1359999	0.813375
ERR552141	250	1647	1537	1450	26	1424	1256	168	1173	83	0.066082803		1298916	1133219	0.872434
ERR551369	250	1685	1531	1433	19	1414	1250	164	1181	69	0.0552		1216086	1076319	0.885068
ERR550927	150	1642	2397	1444	17	1427	1227	200	1154	73	0.059494703		912228	813745	0.892041
ERR550941	250	1667	1565	1429	21	1408	1234	174	1130	104	0.084278768		991408	885211	0.892883
ERR550947	250	1562	1478	1378	20	1358	1200	158	1118	82	0.068333333		1040720	929919	0.893534
ERR552894	250	1632	1505	1418	20	1398	1236	162	1171	65	0.052588997		1100050	984405	0.894873
ERR551693	250	1661	1515	1442	22	1420	1243	177	1176	67	0.05390185		1186480	1071011	0.902679
ERR550644	250	1516	1513	1347	18	1329	1175	154	1080	95	0.080851064		698066	638463	0.914617
ERR551412	250	1574	1520	1388	23	1365	1194	171	1125	69	0.057788945		946542	882508	0.93235
ERR552689	150	1494	1562	1376	20	1356	1196	160	1121	75	0.06270903		1305814	1220508	0.934672
ERR551311	250	1707	1544	1453	23	1430	1257	173	1199	58	0.046141607		1571140	1495360	0.951768
ERR550957	101	1779	2088	1527	20	1507	1298	209	1211	87	0.067026194		5688770	5419416	0.952652
ERR551071	150	1563	1549	1436	20	1416	1228	188	1189	39	0.031758958		2609908	2491248	0.954535
ERR552910	151	1569	1521	1446	22	1424	1242	182	1192	50	0.040257649		1707738	1632389	0.955878
ERR552130	151	1604	1550	1456	20	1436	1225	211	1180	45	0.036734694		2587326	2473775	0.956113
ERR551184	150	1490	1604	1374	18	1356	1165	191	1081	84	0.072103004		1089680	1042094	0.95633
ERR551879	150	1633	1601	1459	19	1440	1245	195	1194	51	0.040963855		2455200	2349251	0.956847
ERR551554	151	1570	1555	1464	23	1441	1251	190	1205	46	0.036770584		2128132	2038519	0.957891
ERR550778	250	1617	1592	1433	26	1407	1236	171	1156	80	0.064724919		768996	737139	0.958573
ERR553171	101	1830	5314	1540	18	1522	1307	215	1196	111	0.084927314		3490754	3350274	0.959757
ERR553156	150	1506	1634	1404	19	1385	1227	158	1130	97	0.079054605		1026854	986525	0.960726
ERR553324	151	1574	1535	1458	19	1439	1246	193	1204	42	0.033707865		2279068	2202337	0.966332
ERR552444	150	1490	1652	1391	17	1374	1182	192	1116	66	0.055837563		1170018	1131219	0.966839
ERR552743	150	1558	1592	1410	19	1391	1224	167	1157	67	0.054738562		1488232	1441487	0.96859
ERR551944	250	1675	1565	1457	23	1434	1249	185	1181	68	0.054443555		1194088	1159478	0.971016
ERR552838	150	1549	1558	1417	19	1398	1191	207	1149	42	0.035264484		2304516	2241974	0.972861
ERR619080	300	1757	1612	1501	19	1482	1265	217	1215	50	0.039525692		1276754	1242556	0.973215
ERR552755	150	1618	2019	1429	17	1412	1201	211	1133	68	0.056619484		1586098	1563844	0.985969
ERR551636	150	1633	2103	1418	18	1400	1210	190	1143	67	0.055371901		1554552	1541447	0.99157
ERR551201	151	1590	1534	1452	19	1433	1235	198	1183	52	0.042105263		1882986	1867816	0.991944
ERR550739	150	1563	1612	1465	19	1446	1245	201	1189	56	0.04497992		2062790	2057266	0.997322
ERR553277	150	1613	1620	1443	20	1423	1232	191	1174	58	0.047077922		1558832	1555926	0.998136
ERR552760	150	1640	2177	1439	18	1421	1214	207	1144	70	0.057660626		1575228	1574607	0.999606
ERR551572	150	1600	1600	1424	18	1406	1200	206	1148	52	0.043333333		1655372	1658634	1.001971
ERR551956	151	1598	1541	1451	24	1427	1216	211	1160	56	0.046052632		1937780	1946675	1.00459
ERR553274	150	1591	2266	1401	18	1383	1205	178	1106	99	0.082157676		1240566	1255259	1.011844
ERR551079	150	1572	1598	1427	19	1408	1237	171	1175	62	0.050121261		1428506	1448239	1.013814
ERR551821	151	1558	1554	1448	24	1424	1233	191	1166	67	0.054339011		1046466	1061690	1.014548
ERR550984	151	1578	1531	1455	22	1433	1241	192	1195	46	0.037066882		1890834	1924620	1.017868
ERR550658	151	1518	1512	1405	23	1382	1216	166	1148	68	0.055921053		863140	879385	1.018821
ERR552177	101	1637	1907	1473	19	1454	1215	239	1159	56	0.046090535		4243410	4325673	1.019386
ERR551159	151	1615	1576	1475	22	1453	1252	201	1210	42	0.033546326		2184496	2228021	1.019925
ERR552787	150	1626	1933	1445	19	1426	1233	193	1177	56	0.04541768		1858836	1897547	1.020825
ERR552429	151	1607	1585	1486	26	1460	1250	210	1200	50	0.04		2138840	2187578	1.022787
ERR551928	250	1641	1533	1416	20	1396	1227	169	1154	73	0.059494703		1540416	1575697	1.022904
ERR552358	150	1607	1793	1468	24	1444	1254	190	1204	50	0.039872408		2074686	2124352	1.023939
ERR552907	150	1843	3358	1548	24	1524	1304	220	1204	100	0.076687117		1696604	1737404	1.024048
ERR552136	150	1615	1667	1466	24	1442	1261	181	1208	53	0.042030135		2283730	2339834	1.024567
ERR551086	150	1619	1868	1445	18	1427	1214	213	1158	56	0.046128501		2356740	2414651	1.024573
ERR550782	151	1592	1564	1471	23	1448	1239	209	1186	53	0.042776433		1663660	1704847	1.024757
ERR552939	151	1547	1563	1433	23	1410	1211	199	1159	52	0.042939719		1039346	1065337	1.025007
ERR551494	150	1636	2035	1475	23	1452	1260	192	1200	60	0.047619048		1695738	1738414	1.025167
ERR551680	151	1589	1546	1467	20	1447	1240	207	1193	47	0.037903226		1619014	1660271	1.025483
ERR553107	151	1556	1518	1434	24	1410	1192	218	1151	41	0.034395973		2154118	2210031	1.025956
ERR553237	150	1636	1819	1471	22	1449	1259	190	1188	71	0.056393963		1574448	1616065	1.026433
ERR552580	151	1604	1561	1479	25	1454	1257	197	1215	42	0.033412888		2216172	2275218	1.026643
ERR552954	150	1594	1612	1435	22	1413	1244	169	1179	65	0.052250804		2161554	2221847	1.027893
ERR551212	150	1599	1743	1454	24	1430	1258	172	1199	59	0.046899841		1903672	1959041	1.029085
ERR552493	151	1595	1570	1473	21	1452	1230	222	1187	43	0.03495935		1419088	1462726	1.030751
ERR553082	150	1577	1903	1442	19	1423	1246	177	1173	73	0.05858748		1437966	1484797	1.032568
ERR551360	151	1573	1559	1466	24	1442	1236	206	1178	58	0.046925566		978804	1012069	1.033985
ERR553098	150	1774	2777	1516	24	1492	1284	208	1209	75	0.058411215		2740220	2834681	1.034472
ERR551090	150	1576	1769	1439	23	1416	1237	179	1183	54	0.043654002		1559170	1614942	1.03577
ERR552912	101	1634	1780	1491	18	1473	1212	261	1175	37	0.030528053		7453348	7722772	1.036148
ERR552331	150	1646	1687	1438	19	1419	1229	190	1179	50	0.040683483		1891906	1960811	1.036421
ERR551804	151	1595	1566	1465	24	1441	1235	206	1177	58	0.046963563		985532	1021450	1.036445
ERR551556	151	1590	1519	1441	24	1417	1228	189	1182	46	0.037459283		1043540	1082667	1.037494
ERR553291	150	1603	1913	1449	19	1430	1247	183	1185	62	0.049719326		1518524	1577282	1.038694
ERR553139	150	1663	2085	1490	23	1467	1257	210	1206	51	0.040572792		1907698	1989008	1.042622
ERR552090	100	1673	1765	1536	22	1514	1288	226	1234	54	0.041925466		6578088	6873152	1.044856
ERR552482	150	1669	2075	1500	25	1475	1259	216	1211	48	0.038125496		2782946	2908465	1.045103
ERR551934	101	1695	1722	1545	19	1526	1263	263	1226	37	0.029295329		9843072	10403752	1.056962
ERR551225	101	1642	1750	1466	18	1448	1195	253	1151	44	0.036820084		4710218	4982704	1.05785
ERR553313	151	1786	2053	1506	24	1482	1294	188	1213	81	0.0625966		2096346	2219112	1.058562
ERR552555	150	1653	1981	1469	21	1448	1242	206	1188	54	0.043478261		1940278	2068603	1.066137
ERR551930	150	1648	2204	1490	19	1471	1274	197	1199	75	0.058869702		1774338	1894144	1.067522
ERR550910	101	1720	1689	1562	19	1543	1284	259	1252	32	0.024922118		12285252	13127870	1.068588
ERR553116	150	1720	2098	1496	20	1476	1284	192	1181	103	0.080218069		1192486	1274638	1.068891
ERR553068	150	1692	1833	1472	24	1448	1261	187	1194	67	0.053132435		1778566	1903448	1.070215
ERR553086	101	1688	1764	1531	19	1512	1254	258	1216	38	0.03030303		8614066	9230646	1.071578
ERR551520	101	1681	1665	1534	19	1515	1280	235	1251	29	0.02265625		15067184	16187939	1.074384
ERR551007	101	1648	1720	1498	19	1479	1254	225	1218	36	0.028708134		6431514	6962325	1.082533
ERR551990	101	1721	1865	1550	19	1531	1281	250	1232	49	0.038251366		4992594	5490661	1.099761
ERR552190	101	1660	1735	1506	19	1487	1269	218	1225	44	0.034672971		5801280	6418256	1.106352