BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716617.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 = 3,671,747 number of mapped reads = 3,235,364 (88.12%) number of supplementary alignments = 11,801 (0.32%) number of secondary alignments = 0 number of mapped bases = 182,653,146 bp number of sequenced bases = 182,600,917 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 127,432 duplication rate = 2.83% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.8252 >>>>>>> ACTG content number of A's = 43,290,802 bp (23.71%) number of C's = 36,235,531 bp (19.84%) number of T's = 56,827,786 bp (31.12%) number of G's = 46,245,415 bp (25.33%) number of N's = 1,383 bp (0%) GC percentage = 45.17% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 954,292 number of insertions = 11,668 mapped reads with insertion percentage = 0.36% number of deletions = 33,270 mapped reads with deletion percentage = 1.02% homopolymer indels = 40.25% >>>>>>> Coverage mean coverageData = 0.059X std coverageData = 0.4181X There is a 4.94% of reference with a coverageData >= 1X There is a 0.68% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% 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 15575601 0.06248971792932865 0.5366528528472538 chr2 243199373 11703237 0.04812198672897072 0.6392635821341912 chr3 198022430 10654438 0.0538041978375884 0.2783232423322053 chr4 191154276 11202099 0.058602398201126296 0.30960283088321455 chr5 180915260 10511016 0.05809911225841314 0.2795251262433868 chr6 171115067 10779214 0.06299395014700838 0.3867198391322306 chr7 159138663 10529794 0.0661674152685322 0.6548826074791473 chr8 146364022 9569709 0.06538293269913012 0.38476486737945387 chr9 141213431 6154856 0.04358548585934436 0.3110212757189579 chr10 135534747 8091912 0.059703597631683335 0.5094986100139008 chr11 135006516 6486867 0.04804854752343954 0.35380434241755315 chr12 133851895 9286126 0.06937612650160836 0.3144302378148193 chr13 115169878 5550510 0.04819411200557146 0.25691134181079095 chr14 107349540 6233081 0.05806341601463779 0.30324974923908765 chr15 102531392 6823833 0.06655359755576126 0.31952886416200665 chr16 90354753 6479664 0.07171359319636456 0.34457624656336105 chr17 81195210 8397521 0.10342384729345487 0.4151552065293212 chr18 78077248 3420419 0.043808139856568715 0.5283172543528468 chr19 59128983 5263142 0.08901120453906673 0.5434704872906073 chr20 63025520 5351335 0.08490743114852524 0.37166986408147873 chr21 48129895 2307378 0.047940640635098 0.2846770896925318 chr22 51304566 1751282 0.03413501246653173 0.21819440995228265 chrMT 16571 9670 0.5835495745579627 1.4742455372798018 chrX 155270560 9988405 0.06432903314060309 0.33188909600145144 chrY 59373566 532037 0.008960839576319199 0.22309786786535032