BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716240.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 = 2,240,650 number of mapped reads = 1,968,427 (87.85%) number of supplementary alignments = 29,332 (1.31%) number of secondary alignments = 0 number of mapped bases = 154,998,290 bp number of sequenced bases = 154,932,306 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 96,981 duplication rate = 3.15% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1211 >>>>>>> ACTG content number of A's = 39,410,600 bp (25.44%) number of C's = 27,542,240 bp (17.78%) number of T's = 48,976,399 bp (31.61%) number of G's = 38,994,105 bp (25.17%) number of N's = 8,962 bp (0.01%) GC percentage = 42.95% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,305,595 number of insertions = 14,671 mapped reads with insertion percentage = 0.73% number of deletions = 38,038 mapped reads with deletion percentage = 1.91% homopolymer indels = 44.12% >>>>>>> Coverage mean coverageData = 0.0501X std coverageData = 0.5445X There is a 4.21% of reference with a coverageData >= 1X There is a 0.53% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 12025543 0.048246792532565044 0.8648292312527871 chr2 243199373 13354730 0.05491268269018111 0.8152743973537241 chr3 198022430 10204688 0.05153299047991684 0.2637246451360796 chr4 191154276 9711154 0.050802703466596794 0.29170291966707085 chr5 180915260 9305648 0.051436501265841254 0.27165913846075174 chr6 171115067 8897798 0.05199891602765758 0.34081043976546477 chr7 159138663 8743466 0.05494243721275954 0.7437583849358896 chr8 146364022 7949945 0.054316251298423594 0.7303367057172675 chr9 141213431 6499354 0.046025041343269964 0.5777700285547808 chr10 135534747 7342595 0.054175000599661724 0.5229859327776242 chr11 135006516 6968287 0.05161444948331235 0.5197183783195853 chr12 133851895 7150337 0.05341976667569779 0.2753089716067999 chr13 115169878 5051620 0.04386233699058013 0.2399101391762532 chr14 107349540 4646106 0.04328016682698407 0.3295081609055674 chr15 102531392 4431637 0.04322224553432377 0.24745592797430752 chr16 90354753 4566047 0.05053466307411631 0.3167259434171802 chr17 81195210 4252666 0.052375823647725035 0.3087839512101119 chr18 78077248 4193726 0.05371252326926277 1.167569876741788 chr19 59128983 3357174 0.05677713076850992 0.6441178191772283 chr20 63025520 3135051 0.04974256459922901 0.28581134291405375 chr21 48129895 1976093 0.04105749659333352 0.2639393790489282 chr22 51304566 1755957 0.034226134960385395 0.2104615040361419 chrMT 16571 32337 1.951421157443727 2.0289650988198273 chrX 155270560 9014650 0.05805768975136046 0.3917136053604134 chrY 59373566 431681 0.007270592438392533 0.20176829674854851