BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716391.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 = 3,272,191 number of mapped reads = 3,027,703 (92.53%) number of supplementary alignments = 46,354 (1.42%) number of secondary alignments = 0 number of mapped bases = 241,297,323 bp number of sequenced bases = 241,195,650 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 164,405 duplication rate = 3.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9144 >>>>>>> ACTG content number of A's = 59,265,776 bp (24.57%) number of C's = 46,941,250 bp (19.46%) number of T's = 75,041,565 bp (31.11%) number of G's = 59,932,503 bp (24.85%) number of N's = 14,556 bp (0.01%) GC percentage = 44.31% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,934,938 number of insertions = 22,732 mapped reads with insertion percentage = 0.74% number of deletions = 58,073 mapped reads with deletion percentage = 1.89% homopolymer indels = 43.94% >>>>>>> Coverage mean coverageData = 0.0779X std coverageData = 0.8126X There is a 6.19% of reference with a coverageData >= 1X There is a 1.04% of reference with a coverageData >= 2X There is a 0.24% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 23631393 0.09480976578991152 1.3699500622934475 chr2 243199373 21214722 0.08723181206556811 1.3388307190089552 chr3 198022430 16857810 0.08513081068644597 0.35977829559896 chr4 191154276 9979704 0.05220758964345637 0.36225995917137377 chr5 180915260 13065857 0.07222086738288412 0.32997799436692493 chr6 171115067 15645612 0.09143328097460875 0.4396820976045611 chr7 159138663 14318515 0.08997508669530546 1.406648431536905 chr8 146364022 15903031 0.10865396278875146 1.0960211233606192 chr9 141213431 11828664 0.08376444022523609 0.7549818727175712 chr10 135534747 13737075 0.10135463638708087 0.7966839485747754 chr11 135006516 8861313 0.06563618751557147 0.6216676081615785 chr12 133851895 11820632 0.08831127867110138 0.37097188276957804 chr13 115169878 7388961 0.06415706197066563 0.30217599045006655 chr14 107349540 6146135 0.057253482408960485 0.3723540640904731 chr15 102531392 4178006 0.04074855435494331 0.2583860900879263 chr16 90354753 6824495 0.07553000559915204 0.3871855891456844 chr17 81195210 7504568 0.09242624041492103 0.44231154473926626 chr18 78077248 5957320 0.07630033271664494 1.243403879584202 chr19 59128983 4774354 0.08074473393191965 1.0803805951739411 chr20 63025520 4385512 0.06958311490329631 0.36465887093434113 chr21 48129895 3414292 0.07093911175164624 0.36401880025895816 chr22 51304566 3307475 0.06446745890024681 0.3154094663703302 chrMT 16571 12367 0.7463037837185444 1.3354337872127644 chrX 155270560 9926094 0.06392772718794858 0.4437138547775816 chrY 59373566 613416 0.01033146636333078 0.32272585916523566