BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524643.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 1,318,186 number of mapped reads = 1,210,430 (91.83%) number of supplementary alignments = 5,211 (0.4%) number of secondary alignments = 0 number of mapped bases = 70,584,801 bp number of sequenced bases = 70,561,347 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 49,991 duplication rate = 3.2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9189 >>>>>>> ACTG content number of A's = 16,778,076 bp (23.78%) number of C's = 12,638,704 bp (17.91%) number of T's = 23,301,915 bp (33.02%) number of G's = 17,842,091 bp (25.29%) number of N's = 561 bp (0%) GC percentage = 43.2% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 350,340 number of insertions = 4,694 mapped reads with insertion percentage = 0.39% number of deletions = 13,753 mapped reads with deletion percentage = 1.13% homopolymer indels = 42.62% >>>>>>> Coverage mean coverageData = 0.0228X std coverageData = 0.2225X There is a 2.05% of reference with a coverageData >= 1X There is a 0.17% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 6925295 0.02778446437652005 0.39304751234802193 chr2 243199373 6334589 0.026046896921892968 0.26618667443014477 chr3 198022430 4453792 0.022491351106033796 0.16561073319541886 chr4 191154276 3219551 0.016842683655164482 0.1690366337051092 chr5 180915260 4271798 0.02361214858271215 0.16772342188127853 chr6 171115067 4536277 0.026510096857806215 0.18715530169090452 chr7 159138663 4438233 0.02788909317404533 0.26073171068975726 chr8 146364022 6237891 0.042619018764051185 0.2814475558556415 chr9 141213431 2562011 0.018142828071361004 0.17958007490747563 chr10 135534747 3155679 0.023283173281018484 0.25119583946286317 chr11 135006516 3571697 0.026455737884532923 0.20430708420828386 chr12 133851895 2314297 0.017289983081673965 0.1468274468488814 chr13 115169878 1715067 0.014891628173818158 0.13398175243050955 chr14 107349540 1304054 0.012147737195706661 0.12438772338375131 chr15 102531392 1841109 0.0179565395932594 0.14690296040847112 chr16 90354753 2118981 0.023451793399291345 0.1761315607880702 chr17 81195210 1589093 0.019571265349273684 0.15756180429865269 chr18 78077248 1866514 0.023905991153786568 0.2828614412250961 chr19 59128983 1454127 0.02459245747554968 0.2863130410196459 chr20 63025520 1316949 0.020895488049920096 0.16101334113841423 chr21 48129895 634478 0.013182617581027343 0.14662903500056262 chr22 51304566 1303915 0.025415184293733233 0.17470627529499938 chrMT 16571 6423 0.3876048518496168 0.7161766119519435 chrX 155270560 3209737 0.02067189684895836 0.1680515900476642 chrY 59373566 203244 0.00342313951632954 0.12355260638495173