BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525269.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 = 1,462,840 number of mapped reads = 1,336,582 (91.37%) number of supplementary alignments = 4,311 (0.29%) number of secondary alignments = 0 number of mapped bases = 77,279,733 bp number of sequenced bases = 77,256,907 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 44,296 duplication rate = 2.45% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9092 >>>>>>> ACTG content number of A's = 19,821,887 bp (25.66%) number of C's = 13,308,440 bp (17.23%) number of T's = 24,772,906 bp (32.07%) number of G's = 19,352,163 bp (25.05%) number of N's = 1,511 bp (0%) GC percentage = 42.28% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 380,867 number of insertions = 5,380 mapped reads with insertion percentage = 0.4% number of deletions = 14,656 mapped reads with deletion percentage = 1.09% homopolymer indels = 44.16% >>>>>>> Coverage mean coverageData = 0.025X std coverageData = 0.2481X There is a 2.28% of reference with a coverageData >= 1X There is a 0.16% 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 8660361 0.03474559447536943 0.418420494096103 chr2 243199373 6229746 0.025615797948623825 0.32947539313426827 chr3 198022430 7089318 0.03580058077259227 0.20395553807967806 chr4 191154276 4270535 0.022340776724241312 0.16768020874842302 chr5 180915260 3408898 0.018842512234733544 0.1479498856793239 chr6 171115067 4786748 0.027973854575880218 0.1961418609336382 chr7 159138663 5521644 0.03469706164365601 0.4259040477617714 chr8 146364022 4362440 0.02980541215244823 0.2586588057136027 chr9 141213431 2403915 0.01702327450708283 0.174998277612442 chr10 135534747 3993631 0.029465735454539933 0.26181424694635685 chr11 135006516 3410885 0.025264595377011284 0.20371268707170476 chr12 133851895 3138702 0.023449066597077316 0.16590273340504014 chr13 115169878 2385252 0.02071072785194754 0.15562882822725066 chr14 107349540 2803696 0.026117447731960473 0.17744840935066403 chr15 102531392 2029908 0.01979791711010809 0.15574635343569035 chr16 90354753 1972307 0.021828480899062388 0.17157689223988482 chr17 81195210 1710748 0.021069568020083942 0.16100545636330815 chr18 78077248 1597775 0.02046402813787699 0.31605527979602926 chr19 59128983 1260970 0.021325751535418765 0.2934189929449468 chr20 63025520 1338455 0.02123671490532724 0.15857851973550052 chr21 48129895 961872 0.019984917897701626 0.15998899709735726 chr22 51304566 626554 0.012212441286414936 0.11842894362257748 chrMT 16571 6194 0.3737855289360932 0.6981432841801901 chrX 155270560 3110649 0.020033733374826498 0.16408199525390302 chrY 59373566 198530 0.0033437439145898697 0.10265156752792118