BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716110.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 = 988,652 number of mapped reads = 886,952 (89.71%) number of supplementary alignments = 3,136 (0.32%) number of secondary alignments = 0 number of mapped bases = 50,932,517 bp number of sequenced bases = 50,916,962 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 15,705 duplication rate = 1.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.9475 >>>>>>> ACTG content number of A's = 12,662,149 bp (24.87%) number of C's = 9,974,465 bp (19.59%) number of T's = 15,973,374 bp (31.37%) number of G's = 12,306,631 bp (24.17%) number of N's = 343 bp (0%) GC percentage = 43.76% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 266,036 number of insertions = 3,672 mapped reads with insertion percentage = 0.41% number of deletions = 9,699 mapped reads with deletion percentage = 1.08% homopolymer indels = 39.34% >>>>>>> Coverage mean coverageData = 0.0165X std coverageData = 0.16X There is a 1.54% of reference with a coverageData >= 1X There is a 0.08% 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 4322591 0.017342347965504167 0.1908244920418387 chr2 243199373 4007642 0.016478833602913936 0.19921420173716106 chr3 198022430 3009891 0.01519974782654672 0.13128810473307928 chr4 191154276 3183701 0.016655138805265333 0.14167751375336407 chr5 180915260 2947855 0.016294120241708742 0.13316527525529007 chr6 171115067 2755247 0.016101720604182683 0.14459087971773363 chr7 159138663 2924251 0.018375490561963564 0.22009586489632388 chr8 146364022 2466820 0.01685400528280099 0.1704250481223454 chr9 141213431 1705369 0.012076535411139469 0.12625868511618138 chr10 135534747 2269955 0.016748140607810335 0.18789451700587356 chr11 135006516 1764522 0.013069902492706353 0.13784017979821306 chr12 133851895 2594097 0.019380353188126323 0.14687162010029156 chr13 115169878 1589817 0.013804104229406235 0.12289030001296707 chr14 107349540 1752694 0.01632698193210702 0.1374596421151427 chr15 102531392 1887787 0.018411795287047308 0.14394333233241974 chr16 90354753 1789406 0.019804226569021775 0.15222996830774824 chr17 81195210 1940289 0.02389659439269878 0.16639331635316165 chr18 78077248 952251 0.012196267470902663 0.18264294905489858 chr19 59128983 1332016 0.022527294271237508 0.19762994894377048 chr20 63025520 1649688 0.026174920889189015 0.17489735539992599 chr21 48129895 654225 0.013592903121853891 0.1276456641858509 chr22 51304566 465043 0.009064358911056766 0.10017826371924836 chrMT 16571 3505 0.21151409088166073 0.4967147619647362 chrX 155270560 2814067 0.018123635285401174 0.14565874451255778 chrY 59373566 149788 0.0025228061929108317 0.07578269620488068