BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524387.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 = 831,104 number of mapped reads = 761,672 (91.65%) number of supplementary alignments = 2,784 (0.33%) number of secondary alignments = 0 number of mapped bases = 44,519,779 bp number of sequenced bases = 44,507,013 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 19,964 duplication rate = 1.92% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.028 >>>>>>> ACTG content number of A's = 11,480,898 bp (25.8%) number of C's = 7,479,944 bp (16.81%) number of T's = 14,331,348 bp (32.2%) number of G's = 11,209,203 bp (25.19%) number of N's = 5,620 bp (0.01%) GC percentage = 41.99% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 218,005 number of insertions = 3,376 mapped reads with insertion percentage = 0.44% number of deletions = 8,153 mapped reads with deletion percentage = 1.06% homopolymer indels = 42.73% >>>>>>> Coverage mean coverageData = 0.0144X std coverageData = 0.169X There is a 1.35% of reference with a coverageData >= 1X There is a 0.06% 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 3597803 0.014434479583503225 0.3057128811849068 chr2 243199373 3766317 0.015486540748606288 0.19109592184407823 chr3 198022430 2978825 0.015042866608595804 0.12774817485059176 chr4 191154276 2866729 0.01499693891231604 0.13546105807485653 chr5 180915260 2712584 0.014993671622836017 0.1283788016953217 chr6 171115067 2520956 0.014732519141637012 0.1344278201555613 chr7 159138663 2464552 0.015486821075026878 0.21678246993041117 chr8 146364022 2279283 0.015572699963109787 0.160976327982542 chr9 141213431 1870583 0.013246494945654283 0.1418020913049287 chr10 135534747 2100799 0.015500076891721353 0.15587495987201866 chr11 135006516 2014267 0.014919776168433234 0.1520660233763394 chr12 133851895 1992467 0.01488560920261906 0.12962663129359608 chr13 115169878 1401877 0.012172253929104622 0.11486386986571966 chr14 107349540 1331329 0.012401813738559104 0.12001428295106262 chr15 102531392 1303855 0.012716641943181655 0.11792523578612406 chr16 90354753 1296798 0.014352294228506163 0.1292941291954365 chr17 81195210 1188057 0.014632106992518401 0.1324359044133641 chr18 78077248 1213530 0.015542684086406324 0.24134187492896406 chr19 59128983 900189 0.015224158345493613 0.217348126207059 chr20 63025520 944064 0.014979075142894498 0.12824349873090582 chr21 48129895 589876 0.012255917034516697 0.12267392850078676 chr22 51304566 519633 0.010128396759072088 0.10530327861451748 chrMT 16571 2938 0.17729768873332932 0.4767513970906649 chrX 155270560 2520689 0.016234172144416817 0.14459985795583277 chrY 59373566 141779 0.002387914514011168 0.07425710262116049