BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524639.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 = 1,799,759 number of mapped reads = 1,640,482 (91.15%) number of supplementary alignments = 6,789 (0.38%) number of secondary alignments = 0 number of mapped bases = 95,599,742 bp number of sequenced bases = 95,567,798 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 97,666 duplication rate = 4.59% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8555 >>>>>>> ACTG content number of A's = 22,780,690 bp (23.84%) number of C's = 17,869,467 bp (18.7%) number of T's = 30,789,250 bp (32.22%) number of G's = 24,127,660 bp (25.25%) number of N's = 731 bp (0%) GC percentage = 43.94% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 484,033 number of insertions = 6,329 mapped reads with insertion percentage = 0.38% number of deletions = 19,065 mapped reads with deletion percentage = 1.15% homopolymer indels = 43.05% >>>>>>> Coverage mean coverageData = 0.0309X std coverageData = 0.3022X There is a 2.65% of reference with a coverageData >= 1X There is a 0.31% of reference with a coverageData >= 2X There is a 0.05% 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 9447495 0.037903596637378086 0.5871358349603027 chr2 243199373 8390895 0.034502124312631346 0.3516650387219097 chr3 198022430 5994500 0.030271823247497772 0.19776378639928116 chr4 191154276 4418362 0.023114115427896573 0.22507245580221036 chr5 180915260 5786394 0.03198400179177809 0.20227312508594156 chr6 171115067 6036563 0.03527779935357767 0.22649944353016077 chr7 159138663 6107280 0.03837709758815807 0.35719386780387197 chr8 146364022 8553088 0.058437093235931985 0.4014277937920467 chr9 141213431 3448212 0.02441844218061666 0.22482814121358866 chr10 135534747 4117637 0.030380674263552506 0.33429817349350216 chr11 135006516 4874577 0.036106235050166025 0.25356656585015513 chr12 133851895 3231737 0.02414412586388859 0.18523382579817788 chr13 115169878 2336520 0.02028759638001874 0.16172202756928775 chr14 107349540 1772636 0.016512748913502562 0.15363364926928036 chr15 102531392 2465974 0.02405091701086044 0.17696096835271571 chr16 90354753 2784514 0.030817570825521487 0.21251037764190633 chr17 81195210 2051484 0.025266071730093438 0.18690605673444038 chr18 78077248 2507318 0.032113298870370025 0.4060571876214533 chr19 59128983 1974638 0.03339543316684476 0.37951145486275156 chr20 63025520 1825476 0.02896407677397981 0.20329156346943741 chr21 48129895 902927 0.01876021129902735 0.1985000014283377 chr22 51304566 1774303 0.034583724965142476 0.21263408959171956 chrMT 16571 11881 0.7169754390199746 0.9099536998754757 chrX 155270560 4486076 0.028891993433913035 0.21185530645619244 chrY 59373566 299255 0.005040205939457974 0.20466552889171905