BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10156406.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 8,427,592 number of mapped reads = 8,261,780 (98.03%) number of supplementary alignments = 1,062,885 (12.61%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,129,649 number of mapped paired reads (second in pair) = 4,132,131 number of mapped paired reads (both in pair) = 8,151,302 number of mapped paired reads (singletons) = 110,478 number of mapped bases = 943,918,600 bp number of sequenced bases = 943,243,466 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,712,087 duplication rate = 66.57% >>>>>>> Insert size mean insert size = 1,104,463.9952 std insert size = 9,764,125.988 median insert size = 158 >>>>>>> Mapping quality mean mapping quality = 52.7887 >>>>>>> ACTG content number of A's = 279,447,916 bp (29.63%) number of C's = 189,138,607 bp (20.05%) number of T's = 277,340,934 bp (29.4%) number of G's = 197,309,237 bp (20.92%) number of N's = 6,772 bp (0%) GC percentage = 40.97% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 7,757,295 number of insertions = 96,066 mapped reads with insertion percentage = 1.12% number of deletions = 287,956 mapped reads with deletion percentage = 3.4% homopolymer indels = 40.89% >>>>>>> Coverage mean coverageData = 0.3049X std coverageData = 5.3877X There is a 6.24% of reference with a coverageData >= 1X There is a 4.8% of reference with a coverageData >= 2X There is a 3.66% of reference with a coverageData >= 3X There is a 2.97% of reference with a coverageData >= 4X There is a 2.25% of reference with a coverageData >= 5X There is a 1.86% of reference with a coverageData >= 6X There is a 1.41% of reference with a coverageData >= 7X There is a 1.21% of reference with a coverageData >= 8X There is a 0.92% of reference with a coverageData >= 9X There is a 0.82% of reference with a coverageData >= 10X There is a 0.62% of reference with a coverageData >= 11X There is a 0.57% of reference with a coverageData >= 12X There is a 0.43% of reference with a coverageData >= 13X There is a 0.39% of reference with a coverageData >= 14X There is a 0.29% of reference with a coverageData >= 15X There is a 0.27% of reference with a coverageData >= 16X There is a 0.2% of reference with a coverageData >= 17X There is a 0.19% of reference with a coverageData >= 18X There is a 0.14% of reference with a coverageData >= 19X There is a 0.13% of reference with a coverageData >= 20X There is a 0.1% of reference with a coverageData >= 21X There is a 0.09% of reference with a coverageData >= 22X There is a 0.07% of reference with a coverageData >= 23X There is a 0.07% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% 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 80551413 0.3231743723519148 2.624210786995471 chr2 243199373 84438852 0.347200122098999 17.936953687587366 chr3 198022430 63487115 0.3206056758317732 1.7363277015876697 chr4 191154276 58782311 0.30751240427391746 1.9680879751997735 chr5 180915260 56678161 0.31328568413742436 1.703291340394691 chr6 171115067 56876048 0.3323848039635224 2.086837497603654 chr7 159138663 49167785 0.30896190826989667 2.089271679390806 chr8 146364022 46908406 0.32049137048174314 2.2537478385911016 chr9 141213431 39936476 0.2828093313588564 2.2710967975842187 chr10 135534747 46888787 0.34595399362792184 2.5136386931208565 chr11 135006516 44472671 0.32941129300751676 1.86560172378179 chr12 133851895 44060260 0.32917173118841536 1.8209816037360962 chr13 115169878 28854062 0.2505347969544606 1.5544599841266145 chr14 107349540 27989881 0.2607359193155369 1.5813179833812299 chr15 102531392 28692196 0.27983815922444516 1.6683756933494929 chr16 90354753 29454214 0.32598411286675755 1.9656413015802117 chr17 81195210 27700967 0.3411650391691825 1.8659948603095997 chr18 78077248 36982664 0.4736676169733851 3.0589496320162124 chr19 59128983 18691209 0.31610908985192593 2.170549857337381 chr20 63025520 21307906 0.3380837793960288 1.8035194161568449 chr21 48129895 11822307 0.2456333428527114 1.7638413050755029 chr22 51304566 12437265 0.24242023604682672 1.6035611278063555 chrMT 16571 894594 53.98551686681552 45.7625127304074 chrX 155270560 22129865 0.14252453910129517 1.1575367923737658 chrY 59373566 4713185 0.07938187509236012 1.241109904519347