Qualimap report: BAM QC

Summary

Globals

Reference size	2,966,890,203
Number of reads	42,485,782
Mapped reads	42,485,782 / 100%
Unmapped reads	0 / 0%
Mapped paired reads	42,485,782 / 100%
Mapped reads, first in pair	21,242,891 / 50%
Mapped reads, second in pair	21,242,891 / 50%
Mapped reads, both in pair	42,485,782 / 100%
Mapped reads, singletons	0 / 0%
Read min/max/mean length	20 / 145 / 108.82
Duplicated reads (estimated)	10,949,878 / 25.77%
Duplication rate	21.24%
Clipped reads	0 / 0%

ACGT Content

Number/percentage of A's	1,673,723,878 / 36.47%
Number/percentage of C's	622,842,124 / 13.57%
Number/percentage of T's	1,672,907,613 / 36.45%
Number/percentage of G's	620,179,156 / 13.51%
Number/percentage of N's	30,839 / 0%
GC Percentage	27.08%

Coverage

Mean	1.551
Standard Deviation	7.5973

Mapping Quality

Mean Mapping Quality

4.66

Insert size

Mean	126.82
Standard Deviation	58.21
P25/Median/P75	87 / 116 / 149

Mismatches and indels

General error rate	21.04%
Mismatches	933,359,278
Insertions	11,044,602
Mapped reads with at least one insertion	18.23%
Deletions	7,423,015
Mapped reads with at least one deletion	14.96%
Homopolymer indels	45.24%

Chromosome stats

Name	Length	Mapped bases	Mean coverage	Standard deviation
NC_027300.1	159038749	309571117	1.9465	4.8755
NC_027301.1	72943711	123312820	1.6905	4.0544
NC_027302.1	92503428	166869202	1.8039	4.2848
NC_027303.1	82398023	158131283	1.9191	4.5068
NC_027304.1	80503876	141173726	1.7536	4.3931
NC_027305.1	87043187	148621312	1.7074	4.6347
NC_027306.1	58785265	105097911	1.7878	4.4638
NC_027307.1	26434011	45584869	1.7245	7.7149
NC_027308.1	141712163	263788115	1.8614	5.8755
NC_027309.1	116138521	229323344	1.9746	4.6362
NC_027310.1	93888508	170002259	1.8107	4.4067
NC_027311.1	91880962	170106613	1.8514	5.919
NC_027312.1	107758822	212218635	1.9694	4.3279
NC_027313.1	93901823	177978102	1.8954	5.6348
NC_027314.1	103963436	193505868	1.8613	4.5162
NC_027315.1	87796322	163367115	1.8608	4.2902
NC_027316.1	57682537	95144428	1.6494	4.1686
NC_027317.1	70695409	131122031	1.8547	5.3294
NC_027318.1	82978132	154607290	1.8632	4.4198
NC_027319.1	86795997	166552434	1.9189	4.7872
NC_027320.1	58021487	107189215	1.8474	4.3461
NC_027321.1	63420196	124540706	1.9637	5.1927
NC_027322.1	49854004	96950033	1.9447	4.2723
NC_027323.1	48650976	89061885	1.8306	4.1945
NC_027324.1	51481326	97891098	1.9015	5.2019
NC_027325.1	47900953	79437509	1.6584	4.0205
NC_027326.1	43943985	81276160	1.8495	5.1971
NC_027327.1	39600944	75485924	1.9062	4.5025
NC_027328.1	42488238	74623529	1.7563	4.1915
NW_012341867.1	84119	128621	1.529	3.0711
NW_012341873.1	59724	53034	0.888	3.1054
NW_012397676.1	2137	0	0	0
NW_012520740.1	1225	0	0	0
NW_012533698.1	1213	0	0	0
NW_012527290.1	1219	0	0	0
NW_012539745.1	1207	0	0	0
NW_012553565.1	1141	262	0.2296	0.6307
NW_012447123.1	1419	0	0	0
NW_012433467.1	1507	586	0.3889	0.9942
NW_012355069.1	9880	3944	0.3992	1.2277
NW_012368724.1	4610	5070	1.0998	2.4615
NW_012410781.1	1777	393	0.2212	0.8792
NW_012461484.1	1351	0	0	0
NW_012376763.1	3776	1654	0.438	2.8399
NW_012426299.1	1570	0	0	0
NW_012407458.1	1845	990	0.5366	1.2413
NW_012396957.1	2167	0	0	0
NW_012373463.1	4061	0	0	0
NW_012372152.1	4188	0	0	0
NW_012529413.1	1217	2060	1.6927	1.7982
NW_012469258.1	1322	0	0	0
NW_012364231.1	5590	8768	1.5685	2.5422
NW_012416477.1	1684	287	0.1704	0.5471
NW_012355556.1	9562	2285	0.239	0.7959
NW_012504207.1	1242	270	0.2174	0.4754
NW_012470149.1	1319	8856	6.7142	5.4444
NW_012370782.1	4342	1513	0.3485	0.9481
NW_012560826.1	1064	828	0.7782	1.5891
NW_012384819.1	3173	837	0.2638	0.6636
NW_012498598.1	1250	0	0	0
NW_012531527.1	1215	287	0.2362	0.5471
NW_012418030.1	1663	283	0.1702	0.5403
NW_012429582.1	1539	0	0	0
NW_012549680.1	1184	224	0.1892	0.578
NW_012445221.1	1430	1192	0.8336	1.0588
NW_012570784.1	1010	382	0.3782	0.7688
NW_012352289.1	11960	33328	2.7866	5.9978
NW_012373575.1	4052	838	0.2068	0.7508
NW_012433088.1	1510	0	0	0
NW_012354549.1	10252	5426	0.5293	1.1157
NW_012482321.1	1284	1156	0.9003	1.5211
NW_012438876.1	1469	288	0.1961	0.5761
NW_012439628.1	1464	293	0.2001	0.4949
NW_012519567.1	1226	124	0.1011	0.4288
NW_012395687.1	2222	0	0	0
NW_012348838.1	17480	27376	1.5661	2.9088
NW_012564558.1	1038	328	0.316	0.7188
NW_012496755.1	1253	272	0.2171	0.6157
NW_012476999.1	1298	502	0.3867	0.6275
NW_012468184.1	1326	0	0	0
NW_012540724.1	1206	414	0.3433	1.0957
NW_012528379.1	1218	0	0	0
NW_012421097.1	1625	800	0.4923	0.8917
NW_012446751.1	1421	2114	1.4877	2.3445
NW_012482322.1	1284	277	0.2157	0.4317
NW_012528380.1	1218	0	0	0
NW_012396592.1	2181	0	0	0
NW_012438877.1	1469	1488	1.0129	1.6518
NW_012522946.1	1223	0	0	0
NW_012519568.1	1226	532	0.4339	0.8154
NW_012380504.1	3449	66	0.0191	0.1871
NW_012390387.1	2560	0	0	0
NW_012407014.1	1855	288	0.1553	0.4877
NW_012482323.1	1284	454	0.3536	1.0992
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	289	0.2355	0.623
NW_012407983.1	1834	0	0	0
NW_012394924.1	2262	0	0	0
NW_012381718.1	3352	289	0.0862	0.4029
NW_012361046.1	6638	0	0	0
NW_012442162.1	1448	446	0.308	1.0308
NW_012429583.1	1539	0	0	0
NW_012423211.1	1601	1121	0.7002	1.3849
NW_012378833.1	3595	282	0.0784	0.5378
NW_012457206.1	1369	562	0.4105	1.2442
NW_012492463.1	1261	1795	1.4235	2.7397
NW_012546132.1	1198	0	0	0
NW_012363797.1	5710	0	0	0
NW_012531528.1	1215	574	0.4724	0.7192
NW_012402924.1	1959	0	0	0
NW_012535801.1	1211	0	0	0
NW_012493984.1	1258	156	0.124	0.474
NW_012400629.1	2031	13625	6.7085	7.2957
NW_012511101.1	1234	0	0	0
NW_012539746.1	1207	0	0	0
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	275	0.1963	0.4991
NW_012446752.1	1421	458	0.3223	0.6858
NW_012444725.1	1433	549	0.3831	0.6396
NW_012571081.1	1009	208	0.2061	0.8616
NW_012363300.1	5854	174	0.0297	0.2384
NW_012567232.1	1024	141	0.1377	0.3394
NW_012409031.1	1812	0	0	0
NW_012387086.1	2907	921	0.3168	1.0399
NW_012573665.1	1001	1282	1.2807	3.7446
NW_012565825.1	1031	135	0.1309	0.4858
NW_012429811.1	1537	252	0.164	0.3691
NW_012349627.1	15483	8738	0.5644	1.215
NW_012420859.1	1628	1876	1.1523	2.7488
NW_012452095.1	1393	792	0.5686	0.9554
NW_012389619.1	2630	0	0	0
NW_012386820.1	2946	534	0.1813	0.5608
NW_012531529.1	1215	577	0.4749	0.6745
NW_012347580.1	25679	28017	1.091	3.3627
NW_012555226.1	1120	444	0.3964	1.1802
NW_012364800.1	5443	0	0	0
NW_012353190.1	11243	282	0.0251	0.2102
NW_012505793.1	1240	0	0	0
NW_012413356.1	1731	689	0.398	0.8594
NW_012345239.1	37994	1303	0.0343	0.4649
NW_012490052.1	1266	965	0.7622	1.2379
NW_012549844.1	1183	0	0	0
NW_012424506.1	1588	3630	2.2859	2.5585
NW_012441841.1	1450	281	0.1938	0.3953
NW_012491998.1	1262	0	0	0
NW_012513107.1	1232	286	0.2321	0.5373
NW_012451243.1	1397	0	0	0
NW_012569129.1	1016	2527	2.4872	6.6326
NW_012521802.1	1224	0	0	0
NW_012544600.1	1201	0	0	0
NW_012386013.1	3055	5128	1.6786	3.6222
NW_012409523.1	1802	829	0.46	1.3144
NW_012398119.1	2120	0	0	0
NW_012465939.1	1334	0	0	0
NW_012385979.1	3059	0	0	0
NW_012475328.1	1303	0	0	0
NW_012561850.1	1056	570	0.5398	1.1012
NW_012422041.1	1614	0	0	0
NW_012454789.1	1380	0	0	0
NW_012353499.1	10981	8274	0.7535	1.9829
NW_012487351.1	1272	0	0	0
NW_012510186.1	1235	287	0.2324	0.531
NW_012544601.1	1201	0	0	0
NW_012432836.1	1512	3548	2.3466	6.4322
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	1419	0.0368	0.2668
NW_012420276.1	1635	0	0	0
NW_012438878.1	1469	0	0	0
NW_012353439.1	11031	13642	1.2367	3.3432
NW_012456538.1	1372	1061	0.7733	0.9699
NW_012463053.1	1345	0	0	0
NW_012371260.1	4288	2180	0.5084	1.1785
NW_012433607.1	1506	1564	1.0385	4.1805
NW_012388595.1	2732	1346	0.4927	1.3352
NW_012550238.1	1180	443	0.3754	1.0902
NW_012462794.1	1346	286	0.2125	0.6127
NW_012347837.1	22988	23860	1.0379	2.9202
NW_012541630.1	1205	0	0	0
NW_012456321.1	1373	280	0.2039	0.4029
NW_012504208.1	1242	733	0.5902	1.2436
NW_012518474.1	1227	290	0.2363	0.4243
NW_012448184.1	1413	92	0.0651	0.2467
NW_012527291.1	1219	289	0.2371	0.6153
NW_012421337.1	1622	0	0	0
NW_012419568.1	1644	2389	1.4532	3.7518
NW_012467627.1	1328	675	0.5083	1.6437
NW_012422303.1	1611	0	0	0
NW_012548091.1	1192	580	0.4866	0.7994
NW_012362286.1	6188	2568	0.415	1.3437
NW_012533700.1	1213	1926	1.5878	1.578
NW_012477000.1	1298	0	0	0
NW_012354729.1	10127	11027	1.0889	3.2331
NW_012353083.1	11320	22191	1.9603	3.528
NW_012391306.1	2486	0	0	0
NW_012546552.1	1197	205	0.1713	0.5529
NW_012388639.1	2728	1207	0.4424	0.8147
NW_012449692.1	1405	949	0.6754	1.0524
NW_012535803.1	1211	0	0	0
NW_012520741.1	1225	546	0.4457	1.2521
NW_012517376.1	1228	0	0	0
NW_012351084.1	13261	28261	2.1311	5.7682
NW_012346956.1	37001	250	0.0068	0.1149
NW_012554833.1	1125	653	0.5804	0.8934
NW_012529414.1	1217	0	0	0
NW_012396358.1	2191	13709	6.257	5.1542
NW_012472625.1	1311	287	0.2189	0.6038
NW_012425468.1	1578	156	0.0989	0.4262
NW_012499224.1	1249	822	0.6581	1.2093
NW_012542491.1	1204	817	0.6786	0.9552
NW_012460997.1	1353	190	0.1404	0.5012
NW_012521803.1	1224	0	0	0
NW_012501957.1	1245	0	0	0
NW_012446951.1	1420	0	0	0
NW_012388528.1	2739	0	0	0
NW_012398908.1	2091	893	0.4271	0.8151
NW_012405451.1	1892	3821	2.0196	2.7144
NW_012566822.1	1026	575	0.5604	1.2831
NW_012416393.1	1685	495	0.2938	0.7233
NW_012408154.1	1830	134	0.0732	0.3697
NW_012562700.1	1050	0	0	0
NW_012345662.1	37506	223	0.0059	0.0769
NW_012432352.1	1516	289	0.1906	0.5149
NW_012395553.1	2229	277	0.1243	0.4448
NW_012557761.1	1092	202	0.185	0.5715
NW_012408641.1	1820	0	0	0
NW_012437086.1	1481	270	0.1823	0.5527
NW_012530485.1	1216	466	0.3832	0.7573
NW_012444064.1	1437	1159	0.8065	1.3934
NW_012434172.1	1502	290	0.1931	0.3942
NW_012369546.1	4494	216	0.0481	0.3026
NW_012346704.1	37008	0	0	0
NW_012495075.1	1256	222	0.1768	0.3815
NW_012467926.1	1327	0	0	0
NW_012400506.1	2035	0	0	0
NW_012360473.1	6877	7340	1.0673	2.1743
NW_012565826.1	1031	0	0	0
NW_012543258.1	1203	1201	0.9983	1.3483
NW_012450296.1	1402	996	0.7104	1.01
NW_012531530.1	1215	422	0.3473	0.7769
NW_012518475.1	1227	1237	1.0081	1.4159
NW_012426190.1	1571	172	0.1095	0.4479
NW_012341991.1	11024	2535	0.23	1.087
NW_012473619.1	1308	0	0	0
NW_012461992.1	1349	0	0	0
NW_012402006.1	1987	232	0.1168	0.4635
NW_012491999.1	1262	0	0	0
NW_012470150.1	1319	0	0	0
NW_012501265.1	1246	859	0.6894	0.9131
NW_012356584.1	8898	1344	0.151	0.5822
NW_012496756.1	1253	0	0	0
NW_012549681.1	1184	0	0	0
NW_012374279.1	3988	922	0.2312	1.0399
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	974	0.712	0.9522
NW_012344859.1	39060	849	0.0217	0.2004
NW_012357142.1	8560	7948	0.9285	1.602
NW_012501958.1	1245	969	0.7783	1.0902
NW_012506648.1	1239	841	0.6788	0.6215
NW_012414232.1	1717	3068	1.7868	4.841
NW_012358275.1	7907	5475	0.6924	2.2563
NW_012364885.1	5420	0	0	0
NW_012411667.1	1761	6658	3.7808	4.5795
NW_012477751.1	1296	0	0	0
NW_012455227.1	1378	5692	4.1306	3.3203
NW_012493491.1	1259	180	0.143	0.5059
NW_012536824.1	1210	0	0	0
NW_012358785.1	7644	332	0.0434	0.3591
NW_012477001.1	1298	3961	3.0516	3.5256
NW_012425096.1	1582	866	0.5474	1.5384
NW_012346447.1	37041	832	0.0225	0.2413
NW_012349331.1	16160	22820	1.4121	3.0051
NW_012562812.1	1049	0	0	0
NW_012553183.1	1146	0	0	0
NW_012349648.1	15450	13481	0.8726	1.7176
NW_012348791.1	17612	23800	1.3514	4.2508
NW_012444561.1	1434	292	0.2036	0.4017
NW_012353362.1	11093	8723	0.7864	1.9959
NW_012381646.1	3358	1282	0.3818	0.9603
NW_012473296.1	1287	0	0	0
NW_012505794.1	1240	1555	1.254	1.797
NW_012504209.1	1242	0	0	0
NW_012570472.1	1011	2216	2.1919	3.3938
NW_012531531.1	1215	0	0	0
NW_012463528.1	1343	0	0	0
NW_012404895.1	1906	687	0.3604	1.2773
NW_012404931.1	1905	404	0.2121	0.6072
NW_012504966.1	1241	0	0	0
NW_012571408.1	1008	578	0.5734	1.0421
NW_012499862.1	1248	537	0.4303	1.0614
NW_012539747.1	1207	232	0.1922	0.5824
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	435	0.194	0.4929
NW_012466206.1	1333	568	0.4261	1.2218
NW_012442503.1	1446	1226	0.8479	1.7085
NW_012429049.1	1544	0	0	0
NW_012385696.1	3101	920	0.2967	0.8968
NW_012385722.1	3097	1266	0.4088	1.1844
NW_012455456.1	1377	558	0.4052	0.7875
NW_012543259.1	1203	1406	1.1687	1.7444
NW_012471357.1	1315	334	0.254	0.4344
NW_012444902.1	1432	929	0.6487	1.248
NW_012549987.1	1182	145	0.1227	0.4694
NW_012342741.1	31419	696	0.0222	0.2178
NW_012547586.1	1194	986	0.8258	1.0911
NW_012514188.1	1231	0	0	0
NW_012511102.1	1234	0	0	0
NW_012436303.1	1486	0	0	0
NW_012466488.1	1332	581	0.4362	1.1581
NW_012504967.1	1241	0	0	0
NW_012383033.1	3254	7422	2.2809	4.0077
NW_012532640.1	1214	0	0	0
NW_012545179.1	1200	0	0	0
NW_012372498.1	4153	3622	0.8721	1.8115
NW_012383564.1	3217	10321	3.2083	6.4424
NW_012368648.1	4621	1155	0.2499	0.7981
NW_012370841.1	4335	1815	0.4187	1.0538
NW_012501959.1	1245	0	0	0
NW_012527292.1	1219	1081	0.8868	1.3903
NW_012350122.1	14581	9294	0.6374	1.9832
NW_012535804.1	1211	1479	1.2213	2.3247
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