BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716425.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 = 945,399 number of mapped reads = 863,908 (91.38%) number of supplementary alignments = 2,874 (0.3%) number of secondary alignments = 0 number of mapped bases = 49,961,285 bp number of sequenced bases = 49,945,126 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 24,029 duplication rate = 1.96% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4172 >>>>>>> ACTG content number of A's = 12,579,579 bp (25.19%) number of C's = 9,660,689 bp (19.34%) number of T's = 15,815,373 bp (31.67%) number of G's = 11,888,599 bp (23.8%) number of N's = 886 bp (0%) GC percentage = 43.15% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 257,099 number of insertions = 3,462 mapped reads with insertion percentage = 0.4% number of deletions = 9,975 mapped reads with deletion percentage = 1.15% homopolymer indels = 43.34% >>>>>>> Coverage mean coverageData = 0.0161X std coverageData = 0.1796X There is a 1.51% of reference with a coverageData >= 1X There is a 0.07% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 4176132 0.016754750633098725 0.2680927908797829 chr2 243199373 3944053 0.016217365001183617 0.26016251974863924 chr3 198022430 2848557 0.014385021939181335 0.12656456832137514 chr4 191154276 3071171 0.016066452000268096 0.14975406987604548 chr5 180915260 2834548 0.0156678214983081 0.13158035217307804 chr6 171115067 2653876 0.015509306378029235 0.14669635122321392 chr7 159138663 2846962 0.01788981977308682 0.21877347303508438 chr8 146364022 2630527 0.017972497366873397 0.22191955344989592 chr9 141213431 1669238 0.011820674479610938 0.1366561972476326 chr10 135534747 2201950 0.01624638735629912 0.18319554085183226 chr11 135006516 1759925 0.013035852284344557 0.1410439410489279 chr12 133851895 2476969 0.018505296469654015 0.1445437833473209 chr13 115169878 1517583 0.013176908983093653 0.12082951920150052 chr14 107349540 1666849 0.015527304541780059 0.13192850887612953 chr15 102531392 1869486 0.018233303611054068 0.14228191364166587 chr16 90354753 1721691 0.01905479172744792 0.14839480299315577 chr17 81195210 2184840 0.026908483887165265 0.17689606168393315 chr18 78077248 925862 0.01185828168533809 0.1882789188122247 chr19 59128983 1302864 0.022034270401708075 0.2163897380892116 chr20 63025520 1638162 0.025992042588462577 0.1747497521104094 chr21 48129895 637886 0.01325342596321891 0.13977344699399605 chr22 51304566 464649 0.009056679282697763 0.0994059498698398 chrMT 16571 30303 1.8286766037052682 1.7494119107645638 chrX 155270560 2699386 0.01738504710744909 0.14564216227469362 chrY 59373566 187816 0.003163293240631698 0.14217560577390242