Qualimap report: BAM QC

Summary

Globals

Reference size	2,966,890,203
Number of reads	33,947,806
Mapped reads	33,947,806 / 100%
Unmapped reads	0 / 0%
Mapped paired reads	33,947,806 / 100%
Mapped reads, first in pair	16,973,903 / 50%
Mapped reads, second in pair	16,973,903 / 50%
Mapped reads, both in pair	33,947,806 / 100%
Mapped reads, singletons	0 / 0%
Read min/max/mean length	20 / 145 / 110.67
Duplicated reads (estimated)	10,268,533 / 30.25%
Duplication rate	26.05%
Clipped reads	0 / 0%

ACGT Content

Number/percentage of A's	1,359,446,329 / 36.44%
Number/percentage of C's	507,319,911 / 13.6%
Number/percentage of T's	1,358,199,218 / 36.41%
Number/percentage of G's	505,292,381 / 13.55%
Number/percentage of N's	24,499 / 0%
GC Percentage	27.15%

Coverage

Mean	1.2606
Standard Deviation	5.7387

Mapping Quality

Mean Mapping Quality

4.37

Insert size

Mean	130.56
Standard Deviation	60.6
P25/Median/P75	90 / 120 / 151

Mismatches and indels

General error rate	20.71%
Mismatches	746,936,022
Insertions	8,558,978
Mapped reads with at least one insertion	17.82%
Deletions	5,888,011
Mapped reads with at least one deletion	14.89%
Homopolymer indels	45.95%

Chromosome stats

Name	Length	Mapped bases	Mean coverage	Standard deviation
NC_027300.1	159038749	249795942	1.5707	4.0446
NC_027301.1	72943711	100761808	1.3814	3.5517
NC_027302.1	92503428	135691632	1.4669	3.714
NC_027303.1	82398023	128276483	1.5568	3.8841
NC_027304.1	80503876	114675110	1.4245	3.7322
NC_027305.1	87043187	121394162	1.3946	3.7409
NC_027306.1	58785265	85526811	1.4549	3.7143
NC_027307.1	26434011	36970990	1.3986	4.7027
NC_027308.1	141712163	214525758	1.5138	4.3862
NC_027309.1	116138521	184145431	1.5856	3.9111
NC_027310.1	93888508	137467072	1.4642	3.7622
NC_027311.1	91880962	138380751	1.5061	4.8933
NC_027312.1	107758822	172531316	1.6011	3.7607
NC_027313.1	93901823	144675983	1.5407	4.3532
NC_027314.1	103963436	156618067	1.5065	3.8871
NC_027315.1	87796322	131940310	1.5028	3.7931
NC_027316.1	57682537	78451826	1.3601	3.6439
NC_027317.1	70695409	106281766	1.5034	4.0519
NC_027318.1	82978132	124779741	1.5038	3.8534
NC_027319.1	86795997	134903873	1.5543	3.9908
NC_027320.1	58021487	86162852	1.485	3.9515
NC_027321.1	63420196	100351310	1.5823	4.0243
NC_027322.1	49854004	77505211	1.5546	3.6643
NC_027323.1	48650976	72242501	1.4849	3.6551
NC_027324.1	51481326	78834938	1.5313	4.0326
NC_027325.1	47900953	64725112	1.3512	3.6242
NC_027326.1	43943985	66569209	1.5149	4.4018
NC_027327.1	39600944	60693873	1.5326	3.7914
NC_027328.1	42488238	60160115	1.4159	3.6008
NW_012341867.1	84119	115061	1.3678	2.847
NW_012341873.1	59724	44238	0.7407	2.2551
NW_012397676.1	2137	0	0	0
NW_012520740.1	1225	0	0	0
NW_012533698.1	1213	276	0.2275	0.9055
NW_012527290.1	1219	292	0.2395	0.4258
NW_012539745.1	1207	0	0	0
NW_012553565.1	1141	234	0.2051	0.5986
NW_012447123.1	1419	0	0	0
NW_012433467.1	1507	2163	1.4353	1.7391
NW_012355069.1	9880	2591	0.2622	0.714
NW_012368724.1	4610	5410	1.1735	2.2412
NW_012410781.1	1777	196	0.1103	0.4503
NW_012461484.1	1351	0	0	0
NW_012376763.1	3776	1565	0.4145	2.4404
NW_012426299.1	1570	0	0	0
NW_012407458.1	1845	800	0.4336	0.7792
NW_012396957.1	2167	0	0	0
NW_012373463.1	4061	270	0.0665	0.3538
NW_012372152.1	4188	0	0	0
NW_012529413.1	1217	1139	0.9359	1.1592
NW_012469258.1	1322	0	0	0
NW_012364231.1	5590	6895	1.2335	2.2708
NW_012416477.1	1684	0	0	0
NW_012355556.1	9562	581	0.0608	0.3214
NW_012504207.1	1242	0	0	0
NW_012470149.1	1319	8659	6.5648	6.4002
NW_012370782.1	4342	697	0.1605	0.5086
NW_012560826.1	1064	0	0	0
NW_012384819.1	3173	0	0	0
NW_012498598.1	1250	0	0	0
NW_012531527.1	1215	0	0	0
NW_012418030.1	1663	444	0.267	0.6604
NW_012429582.1	1539	0	0	0
NW_012549680.1	1184	835	0.7052	2.1211
NW_012445221.1	1430	244	0.1706	0.4117
NW_012570784.1	1010	214	0.2119	0.6023
NW_012352289.1	11960	29863	2.4969	5.2732
NW_012373575.1	4052	739	0.1824	0.6966
NW_012433088.1	1510	0	0	0
NW_012354549.1	10252	3995	0.3897	1.1447
NW_012482321.1	1284	180	0.1402	0.5029
NW_012438876.1	1469	470	0.3199	0.7172
NW_012439628.1	1464	0	0	0
NW_012519567.1	1226	286	0.2333	0.6343
NW_012395687.1	2222	0	0	0
NW_012348838.1	17480	15196	0.8693	2.2111
NW_012564558.1	1038	1216	1.1715	1.4873
NW_012496755.1	1253	458	0.3655	0.9626
NW_012476999.1	1298	0	0	0
NW_012468184.1	1326	0	0	0
NW_012540724.1	1206	0	0	0
NW_012528379.1	1218	0	0	0
NW_012421097.1	1625	0	0	0
NW_012446751.1	1421	1670	1.1752	3.5952
NW_012482322.1	1284	0	0	0
NW_012528380.1	1218	0	0	0
NW_012396592.1	2181	0	0	0
NW_012438877.1	1469	1298	0.8836	2.6933
NW_012522946.1	1223	293	0.2396	0.5494
NW_012519568.1	1226	270	0.2202	0.5192
NW_012380504.1	3449	1259	0.365	0.946
NW_012390387.1	2560	516	0.2016	0.866
NW_012407014.1	1855	0	0	0
NW_012482323.1	1284	256	0.1994	0.5926
NW_012363396.1	5825	0	0	0
NW_012533699.1	1213	0	0	0
NW_012507489.1	1238	0	0	0
NW_012481921.1	1285	0	0	0
NW_012518473.1	1227	290	0.2363	0.5677
NW_012407983.1	1834	565	0.3081	0.859
NW_012394924.1	2262	2093	0.9253	2.228
NW_012381718.1	3352	0	0	0
NW_012361046.1	6638	0	0	0
NW_012442162.1	1448	0	0	0
NW_012429583.1	1539	0	0	0
NW_012423211.1	1601	1445	0.9026	0.9526
NW_012378833.1	3595	496	0.138	0.7215
NW_012457206.1	1369	486	0.355	0.7546
NW_012492463.1	1261	1037	0.8224	1.7331
NW_012546132.1	1198	0	0	0
NW_012363797.1	5710	866	0.1517	0.9207
NW_012531528.1	1215	573	0.4716	0.6878
NW_012402924.1	1959	0	0	0
NW_012535801.1	1211	0	0	0
NW_012493984.1	1258	379	0.3013	0.7016
NW_012400629.1	2031	9243	4.551	7.6755
NW_012511101.1	1234	191	0.1548	0.506
NW_012539746.1	1207	291	0.2411	0.4301
NW_012535802.1	1211	0	0	0
NW_012548973.1	1188	0	0	0
NW_012419630.1	1643	0	0	0
NW_012508364.1	1237	0	0	0
NW_012450472.1	1401	287	0.2049	0.4899
NW_012446752.1	1421	0	0	0
NW_012444725.1	1433	0	0	0
NW_012571081.1	1009	0	0	0
NW_012363300.1	5854	488	0.0834	0.3658
NW_012567232.1	1024	0	0	0
NW_012409031.1	1812	561	0.3096	0.7899
NW_012387086.1	2907	2165	0.7448	2.2526
NW_012573665.1	1001	1272	1.2707	3.5599
NW_012565825.1	1031	291	0.2823	0.6891
NW_012429811.1	1537	0	0	0
NW_012349627.1	15483	9593	0.6196	1.4027
NW_012420859.1	1628	702	0.4312	1.0637
NW_012452095.1	1393	0	0	0
NW_012389619.1	2630	0	0	0
NW_012386820.1	2946	289	0.0981	0.297
NW_012531529.1	1215	0	0	0
NW_012347580.1	25679	16324	0.6357	2.8036
NW_012555226.1	1120	288	0.2571	0.6627
NW_012364800.1	5443	0	0	0
NW_012353190.1	11243	0	0	0
NW_012505793.1	1240	0	0	0
NW_012413356.1	1731	1402	0.8099	1.8739
NW_012345239.1	37994	285	0.0075	0.1217
NW_012490052.1	1266	0	0	0
NW_012549844.1	1183	510	0.4311	0.7971
NW_012424506.1	1588	2411	1.5183	2.5971
NW_012441841.1	1450	0	0	0
NW_012491998.1	1262	0	0	0
NW_012513107.1	1232	0	0	0
NW_012451243.1	1397	0	0	0
NW_012569129.1	1016	1293	1.2726	4.4823
NW_012521802.1	1224	865	0.7067	0.9381
NW_012544600.1	1201	0	0	0
NW_012386013.1	3055	4181	1.3686	3.5319
NW_012409523.1	1802	268	0.1487	0.5154
NW_012398119.1	2120	496	0.234	0.6302
NW_012465939.1	1334	0	0	0
NW_012385979.1	3059	0	0	0
NW_012475328.1	1303	288	0.221	0.4149
NW_012561850.1	1056	688	0.6515	0.9736
NW_012422041.1	1614	0	0	0
NW_012454789.1	1380	278	0.2014	0.571
NW_012353499.1	10981	7669	0.6984	1.4063
NW_012487351.1	1272	224	0.1761	0.5004
NW_012510186.1	1235	0	0	0
NW_012544601.1	1201	162	0.1349	0.4949
NW_012432836.1	1512	2040	1.3492	3.63
NW_012501956.1	1245	0	0	0
NW_012567426.1	1023	0	0	0
NW_012382015.1	3329	0	0	0
NW_012419712.1	1642	0	0	0
NW_012497984.1	1251	0	0	0
NW_012345002.1	38580	1535	0.0398	0.3268
NW_012420276.1	1635	184	0.1125	0.4555
NW_012438878.1	1469	0	0	0
NW_012353439.1	11031	11744	1.0646	4.2212
NW_012456538.1	1372	365	0.266	0.6667
NW_012463053.1	1345	570	0.4238	1.1634
NW_012371260.1	4288	1596	0.3722	0.9994
NW_012433607.1	1506	422	0.2802	1.2108
NW_012388595.1	2732	940	0.3441	0.9836
NW_012550238.1	1180	0	0	0
NW_012462794.1	1346	228	0.1694	0.5501
NW_012347837.1	22988	18056	0.7855	1.7991
NW_012541630.1	1205	0	0	0
NW_012456321.1	1373	0	0	0
NW_012504208.1	1242	0	0	0
NW_012518474.1	1227	0	0	0
NW_012448184.1	1413	0	0	0
NW_012527291.1	1219	578	0.4742	0.7131
NW_012421337.1	1622	0	0	0
NW_012419568.1	1644	2355	1.4325	4.1989
NW_012467627.1	1328	707	0.5324	0.9194
NW_012422303.1	1611	268	0.1664	0.5467
NW_012548091.1	1192	204	0.1711	0.5494
NW_012362286.1	6188	1705	0.2755	0.9512
NW_012533700.1	1213	1162	0.958	1.4991
NW_012477000.1	1298	0	0	0
NW_012354729.1	10127	5577	0.5507	2.1215
NW_012353083.1	11320	12091	1.0681	2.3434
NW_012391306.1	2486	0	0	0
NW_012546552.1	1197	0	0	0
NW_012388639.1	2728	438	0.1606	0.7726
NW_012449692.1	1405	535	0.3808	0.7728
NW_012535803.1	1211	0	0	0
NW_012520741.1	1225	289	0.2359	0.5692
NW_012517376.1	1228	0	0	0
NW_012351084.1	13261	13706	1.0336	2.8583
NW_012346956.1	37001	0	0	0
NW_012554833.1	1125	292	0.2596	0.5053
NW_012529414.1	1217	0	0	0
NW_012396358.1	2191	10548	4.8142	3.2348
NW_012472625.1	1311	289	0.2204	0.6257
NW_012425468.1	1578	193	0.1223	0.47
NW_012499224.1	1249	790	0.6325	1.383
NW_012542491.1	1204	771	0.6404	1.0019
NW_012460997.1	1353	0	0	0
NW_012521803.1	1224	0	0	0
NW_012501957.1	1245	0	0	0
NW_012446951.1	1420	113	0.0796	0.3846
NW_012388528.1	2739	291	0.1062	0.3077
NW_012398908.1	2091	578	0.2764	1.0136
NW_012405451.1	1892	3095	1.6358	2.5179
NW_012566822.1	1026	0	0	0
NW_012416393.1	1685	0	0	0
NW_012408154.1	1830	162	0.0885	0.4047
NW_012562700.1	1050	0	0	0
NW_012345662.1	37506	146	0.0039	0.0866
NW_012432352.1	1516	1430	0.9433	2.4315
NW_012395553.1	2229	0	0	0
NW_012557761.1	1092	992	0.9084	1.2294
NW_012408641.1	1820	0	0	0
NW_012437086.1	1481	553	0.3734	0.7711
NW_012530485.1	1216	2091	1.7196	2.7122
NW_012444064.1	1437	276	0.1921	0.5451
NW_012434172.1	1502	0	0	0
NW_012369546.1	4494	252	0.0561	0.3268
NW_012346704.1	37008	220	0.0059	0.1076
NW_012495075.1	1256	0	0	0
NW_012467926.1	1327	160	0.1206	0.4681
NW_012400506.1	2035	0	0	0
NW_012360473.1	6877	6645	0.9663	2.0885
NW_012565826.1	1031	0	0	0
NW_012543258.1	1203	724	0.6018	0.7984
NW_012450296.1	1402	636	0.4536	1.7265
NW_012531530.1	1215	581	0.4782	0.6409
NW_012518475.1	1227	1129	0.9201	2.361
NW_012426190.1	1571	3001	1.9102	4.3189
NW_012341991.1	11024	2162	0.1961	1.1398
NW_012473619.1	1308	0	0	0
NW_012461992.1	1349	0	0	0
NW_012402006.1	1987	194	0.0976	0.4251
NW_012491999.1	1262	298	0.2361	0.4207
NW_012470150.1	1319	585	0.4435	0.7878
NW_012501265.1	1246	1590	1.2761	2.1143
NW_012356584.1	8898	871	0.0979	0.4105
NW_012496756.1	1253	176	0.1405	0.5032
NW_012549681.1	1184	0	0	0
NW_012374279.1	3988	1088	0.2728	0.8485
NW_012464297.1	1340	0	0	0
NW_012478487.1	1294	0	0	0
NW_012522947.1	1223	0	0	0
NW_012457445.1	1368	523	0.3823	0.6231
NW_012344859.1	39060	1693	0.0433	0.384
NW_012357142.1	8560	6172	0.721	1.6484
NW_012501958.1	1245	1259	1.0112	2.1676
NW_012506648.1	1239	0	0	0
NW_012414232.1	1717	581	0.3384	1.0912
NW_012358275.1	7907	1842	0.233	0.9696
NW_012364885.1	5420	708	0.1306	0.4885
NW_012411667.1	1761	4730	2.686	2.7643
NW_012477751.1	1296	0	0	0
NW_012455227.1	1378	5290	3.8389	3.6895
NW_012493491.1	1259	0	0	0
NW_012536824.1	1210	0	0	0
NW_012358785.1	7644	0	0	0
NW_012477001.1	1298	982	0.7565	1.4361
NW_012425096.1	1582	577	0.3647	0.7628
NW_012346447.1	37041	766	0.0207	0.2318
NW_012349331.1	16160	20389	1.2617	3.0113
NW_012562812.1	1049	0	0	0
NW_012553183.1	1146	0	0	0
NW_012349648.1	15450	13276	0.8593	1.7799
NW_012348791.1	17612	28419	1.6136	8.0268
NW_012444561.1	1434	2957	2.0621	3.8943
NW_012353362.1	11093	7987	0.72	1.954
NW_012381646.1	3358	1117	0.3326	0.8473
NW_012473296.1	1287	287	0.223	0.4152
NW_012505794.1	1240	606	0.4887	0.9271
NW_012504209.1	1242	0	0	0
NW_012570472.1	1011	538	0.5321	0.8486
NW_012531531.1	1215	0	0	0
NW_012463528.1	1343	0	0	0
NW_012404895.1	1906	198	0.1039	0.4379
NW_012404931.1	1905	570	0.2992	0.8866
NW_012504966.1	1241	134	0.108	0.4448
NW_012571408.1	1008	569	0.5645	1.2894
NW_012499862.1	1248	761	0.6098	0.9082
NW_012539747.1	1207	524	0.4341	0.752
NW_012531532.1	1215	0	0	0
NW_012559670.1	1074	0	0	0
NW_012520742.1	1225	0	0	0
NW_012563100.1	1047	0	0	0
NW_012395298.1	2242	0	0	0
NW_012466206.1	1333	801	0.6009	1.2258
NW_012442503.1	1446	2010	1.39	4.0007
NW_012429049.1	1544	0	0	0
NW_012385696.1	3101	2328	0.7507	2.3006
NW_012385722.1	3097	520	0.1679	0.4743
NW_012455456.1	1377	272	0.1975	0.5861
NW_012543259.1	1203	1299	1.0798	1.2158
NW_012471357.1	1315	289	0.2198	0.4136
NW_012444902.1	1432	0	0	0
NW_012549987.1	1182	1113	0.9416	0.9438
NW_012342741.1	31419	142	0.0045	0.0933
NW_012547586.1	1194	2035	1.7044	2.2603
NW_012514188.1	1231	0	0	0
NW_012511102.1	1234	0	0	0
NW_012436303.1	1486	290	0.1952	0.5889
NW_012466488.1	1332	0	0	0
NW_012504967.1	1241	0	0	0
NW_012383033.1	3254	5269	1.6192	3.135
NW_012532640.1	1214	1701	1.4012	2.232
NW_012545179.1	1200	0	0	0
NW_012372498.1	4153	5462	1.3152	2.3151
NW_012383564.1	3217	9214	2.8642	4.0237
NW_012368648.1	4621	1096	0.2372	0.708
NW_012370841.1	4335	1508	0.3479	0.9851
NW_012501959.1	1245	0	0	0
NW_012527292.1	1219	2199	1.8039	2.515
NW_012350122.1	14581	9278	0.6363	1.7119
NW_012535804.1	1211	469	0.3873	0.7781
NW_012353418.1	11045	5069	0.4589	1.6982
NW_012382787.1	3271	5433	1.661	3.9703
NW_012487352.1	1272	1921	1.5102	2.7771
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NW_012420500.1	1633	471	0.2884	0.6923
NW_012455008.1	1380	288	0.2087	0.5229
NW_012480790.1	1289	577	0.4476	0.9563
NW_012443532.1	1441	577	0.4004	0.7413
NW_012358221.1	7932	1340	0.1689	0.5395
NW_012394730.1	2274	289	0.1271	0.469
NW_012531526.1	1216	290	0.2385	0.4236
NW_012461483.1	1352	290	0.2145	0.6101
NW_012497983.1	1252	0	0	0
NW_012376216.1	3826	1451	0.3792	0.8395
NW_012426697.1	1567	0	0	0
NW_012354482.1	10296	13202	1.2822	3.3791
NW_012485544.1	1277	936	0.733	1.0946
NW_012422661.1	1608	0	0	0
NW_012558151.1	1089	480	0.4408	0.7642
NW_012393489.1	2340	0	0	0
NW_012566435.1	1029	869	0.8445	1.3303
NW_012495074.1	1257	0	0	0
NW_012461244.1	1353	0	0	0
NW_012570471.1	1012	578	0.5711	1.097
NW_012489561.1	1268	290	0.2287	0.42
NW_012433885.1	1505	0	0	0
NW_012359286.1	7412	0	0	0
NW_012469004.1	1324	1399	1.0566	2.7049
NW_012505792.1	1241	0	0	0
NW_012548090.1	1193	1375	1.1526	1.836
NW_012411492.1	1765	0	0	0
NW_012450663.1	1401	232	0.1656	0.5341
NW_012547585.1	1195	1157	0.9682	2.3931
NW_012473618.1	1309	0	0	0
NW_012516303.1	1230	0	0	0
NW_012384329.1	3180	0	0	0
NW_012412409.1	1748	0	0	0
NW_012395721.1	2221	601	0.2706	0.5735
NW_012427622.1	1558	539	0.346	1.1781
NW_012348545.1	18665	41199	2.2073	6.8227
NW_012412206.1	1752	771	0.4401	1.2766
NW_012528378.1	1219	0	0	0
NW_012349740.1	15252	17193	1.1273	2.9341
NW_012392322.1	2413	0	0	0
NW_012566436.1	1029	0	0	0
NW_012341884.1	44131	13237	0.2999	1.0929
NW_012403267.1	1951	0	0	0
NW_012526228.1	1221	0	0	0
NW_012538775.1	1209	0	0	0
NW_012510185.1	1236	132	0.1068	0.434
NW_012355637.1	9521	3813	0.4005	1.1663
NW_012367147.1	4896	5141	1.05	2.1242
NW_012414766.1	1710	288	0.1684	0.4547
NW_012543257.1	1204	0	0	0
NW_012554585.1	1129	13667	12.1054	12.9525
NW_012550955.1	1174	130	0.1107	0.3823
NW_012473295.1	1310	140	0.1069	0.3089
NW_012506647.1	1240	280	0.2258	0.6245
NW_012416322.1	1687	293	0.1737	0.3752
NW_012361141.1	6602	846	0.1281	0.4858
NW_012498597.1	1251	858	0.6859	1.138
NW_012561447.1	1060	0	0	0
NC_001960.1	16665	10296969	617.8799	946.8744

Summary

Globals

ACGT Content

Coverage

Mapping Quality

Insert size

Mismatches and indels

Chromosome stats

Coverage across reference

Coverage Histogram

Coverage Histogram (0-50X)

Genome Fraction Coverage

Duplication Rate Histogram

Mapped Reads Nucleotide Content

Mapped Reads GC-content Distribution

Homopolymer Indels

Mapping Quality Across Reference

Mapping Quality Histogram

Insert Size Across Reference

Insert Size Histogram

Contents