BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716405.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 = 1,331,331 number of mapped reads = 994,119 (74.67%) number of supplementary alignments = 3,485 (0.26%) number of secondary alignments = 0 number of mapped bases = 55,955,749 bp number of sequenced bases = 55,938,999 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 23,728 duplication rate = 1.76% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.1969 >>>>>>> ACTG content number of A's = 14,040,422 bp (25.1%) number of C's = 11,320,811 bp (20.24%) number of T's = 17,083,141 bp (30.54%) number of G's = 13,493,907 bp (24.12%) number of N's = 718 bp (0%) GC percentage = 44.36% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 293,674 number of insertions = 3,538 mapped reads with insertion percentage = 0.35% number of deletions = 10,254 mapped reads with deletion percentage = 1.02% homopolymer indels = 40.73% >>>>>>> Coverage mean coverageData = 0.0181X std coverageData = 0.1743X There is a 1.67% of reference with a coverageData >= 1X There is a 0.1% 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 4562582 0.01830519812426064 0.20568831422879025 chr2 243199373 4694528 0.019303207660819093 0.26083083181199346 chr3 198022430 3684400 0.01860597307082839 0.1460094178522368 chr4 191154276 3536680 0.01850170487423467 0.15855979698968956 chr5 180915260 3318012 0.018340144441104638 0.14470824245760194 chr6 171115067 3161943 0.018478460461929982 0.1567627613405222 chr7 159138663 3088607 0.019408275410734095 0.21648916705009744 chr8 146364022 2806741 0.019176440778595167 0.16616576101640992 chr9 141213431 2325471 0.016467774938490092 0.1552544276179002 chr10 135534747 2697539 0.0199029330832779 0.1943695944740299 chr11 135006516 2524465 0.0186988382101498 0.16112274407087 chr12 133851895 2567938 0.019184920766344024 0.14922482783699273 chr13 115169878 1720215 0.014936327361569315 0.1304989675331758 chr14 107349540 1696236 0.015801055132606996 0.13806496699124712 chr15 102531392 1653816 0.016129850260884003 0.13746150850319694 chr16 90354753 1723145 0.019070883852673474 0.15742213767846658 chr17 81195210 1687414 0.020782186535387985 0.16121729927245015 chr18 78077248 1445383 0.018512217541273995 0.2080549251525535 chr19 59128983 1318526 0.0222991489638846 0.1982910648759799 chr20 63025520 1209542 0.01919130536328776 0.1504125826670249 chr21 48129895 718117 0.014920394071086172 0.14177626649466962 chr22 51304566 737770 0.014380201559447945 0.1296713232061404 chrMT 16571 14441 0.8714621929877496 1.0333703985749156 chrX 155270560 2881425 0.01855744579010986 0.1538842307331812 chrY 59373566 180813 0.0030453451288406696 0.08985656182493278