BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716799.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 = 1,061,637 number of mapped reads = 899,857 (84.76%) number of supplementary alignments = 1,030 (0.1%) number of secondary alignments = 0 number of mapped bases = 48,246,474 bp number of sequenced bases = 48,233,671 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 73,825 duplication rate = 7.06% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.3655 >>>>>>> ACTG content number of A's = 10,613,849 bp (22.01%) number of C's = 8,757,831 bp (18.16%) number of T's = 14,901,675 bp (30.89%) number of G's = 13,959,559 bp (28.94%) number of N's = 757 bp (0%) GC percentage = 47.1% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 299,275 number of insertions = 2,606 mapped reads with insertion percentage = 0.29% number of deletions = 7,392 mapped reads with deletion percentage = 0.82% homopolymer indels = 40.88% >>>>>>> Coverage mean coverageData = 0.0156X std coverageData = 0.1621X There is a 1.32% of reference with a coverageData >= 1X There is a 0.17% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% 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 4789744 0.019216578000020308 0.1921407848826196 chr2 243199373 4200766 0.017272931044933246 0.21199421254851233 chr3 198022430 3239388 0.0163586922956152 0.14995086942431754 chr4 191154276 3045131 0.015930226954483612 0.15536147183663226 chr5 180915260 2906512 0.016065598888673073 0.1460375029380189 chr6 171115067 2028169 0.011852661694601096 0.13894650803766045 chr7 159138663 2726247 0.017131267465782342 0.17516806421452857 chr8 146364022 3022500 0.0206505667082584 0.174397686055941 chr9 141213431 2131064 0.015091085776394739 0.15294505342869272 chr10 135534747 2514387 0.018551604335086118 0.18982148259364276 chr11 135006516 2078923 0.015398686386366715 0.15730912733215296 chr12 133851895 2267686 0.016941754915012597 0.15206179994699073 chr13 115169878 826203 0.0071737768099398354 0.09939644871876714 chr14 107349540 1502597 0.01399723743576358 0.1393419354163718 chr15 102531392 951006 0.009275266642239675 0.11397031054432646 chr16 90354753 1299136 0.01437817001170929 0.15085685203715735 chr17 81195210 1956158 0.024092036956367253 0.18962485270508764 chr18 78077248 1296449 0.0166046964155294 0.17554160042816383 chr19 59128983 1323459 0.022382576747514836 0.2156875178328351 chr20 63025520 1295290 0.02055183360645021 0.1747734768405921 chr21 48129895 662861 0.013772334221797076 0.1478172540470793 chr22 51304566 555229 0.010822214147567295 0.12331718040135467 chrMT 16571 4057 0.24482529720596222 0.6172613975676159 chrX 155270560 1473135 0.00948753582134308 0.11611625709729079 chrY 59373566 150377 0.002532726432500281 0.08283140618776935