BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9867860.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 = 2,133,981 number of mapped reads = 1,967,522 (92.2%) number of supplementary alignments = 8,588 (0.4%) number of secondary alignments = 0 number of mapped bases = 116,225,922 bp number of sequenced bases = 116,191,402 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 97,555 duplication rate = 3.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9136 >>>>>>> ACTG content number of A's = 29,228,244 bp (25.16%) number of C's = 21,704,944 bp (18.68%) number of T's = 37,257,430 bp (32.07%) number of G's = 27,985,634 bp (24.09%) number of N's = 15,150 bp (0.01%) GC percentage = 42.77% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 576,844 number of insertions = 9,665 mapped reads with insertion percentage = 0.49% number of deletions = 21,677 mapped reads with deletion percentage = 1.09% homopolymer indels = 41.62% >>>>>>> Coverage mean coverageData = 0.0375X std coverageData = 0.3522X There is a 3.31% of reference with a coverageData >= 1X There is a 0.32% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 9289693 0.03727049089277896 0.6536826738843613 chr2 243199373 9844163 0.04047774827116844 0.5034512068010407 chr3 198022430 7791331 0.039345699373550765 0.21946557342722084 chr4 191154276 7453090 0.03898992037196176 0.25720568191348636 chr5 180915260 7113492 0.03931946923659176 0.22145124286797557 chr6 171115067 6647652 0.038849016141869024 0.2548037641872799 chr7 159138663 6401958 0.040228803480647564 0.41094474870205094 chr8 146364022 5954852 0.04068521702690023 0.37975779908287566 chr9 141213431 4884841 0.03459190082280488 0.2840641356589977 chr10 135534747 5693631 0.042008644469598636 0.36537285948505904 chr11 135006516 5289968 0.03918305691260117 0.3043261965806763 chr12 133851895 5284975 0.0394837517989566 0.22305009755937494 chr13 115169878 3634247 0.031555533991275045 0.19837194092520494 chr14 107349540 3386690 0.03154824883273836 0.20492089063983374 chr15 102531392 3329805 0.032475956241772276 0.20132319745414495 chr16 90354753 3405147 0.037686418112393046 0.235457326680314 chr17 81195210 3141360 0.03868898177614172 0.2387685416688547 chr18 78077248 3039832 0.03893364684165097 0.49915949651027786 chr19 59128983 2398509 0.04056401578900824 0.4742858106680034 chr20 63025520 2466417 0.03913362396692641 0.22498528490938824 chr21 48129895 1557110 0.03235224178236832 0.23869504534867272 chr22 51304566 1373830 0.026777928498605757 0.18138933221090386 chrMT 16571 16239 0.9799649990948042 1.1354553466994726 chrX 155270560 6430212 0.041412950400900206 0.2506137308921601 chrY 59373566 396878 0.0066844224919891115 0.2569563540741029