BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524347.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 = 4,138,188 number of mapped reads = 3,794,796 (91.7%) number of supplementary alignments = 17,743 (0.43%) number of secondary alignments = 0 number of mapped bases = 220,723,473 bp number of sequenced bases = 220,663,276 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 277,913 duplication rate = 5.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3432 >>>>>>> ACTG content number of A's = 55,396,562 bp (25.1%) number of C's = 41,638,645 bp (18.87%) number of T's = 70,767,110 bp (32.07%) number of G's = 52,828,714 bp (23.94%) number of N's = 32,245 bp (0.01%) GC percentage = 42.81% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 1,115,880 number of insertions = 15,761 mapped reads with insertion percentage = 0.41% number of deletions = 38,181 mapped reads with deletion percentage = 1% homopolymer indels = 41.94% >>>>>>> Coverage mean coverageData = 0.0713X std coverageData = 0.6019X There is a 5.71% of reference with a coverageData >= 1X There is a 0.96% of reference with a coverageData >= 2X There is a 0.22% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.03% 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 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 19114954 0.07668969458655832 1.1464137468656053 chr2 243199373 14243532 0.0585673055990979 0.9753750819473168 chr3 198022430 15353008 0.07753166143855522 0.3397049511022175 chr4 191154276 11456533 0.05993343826637705 0.3768292724480584 chr5 180915260 13147177 0.07267035959266233 0.32880329301254596 chr6 171115067 13913679 0.08131182860712084 0.39771241392945106 chr7 159138663 9375827 0.0589160850245424 0.7228021310963288 chr8 146364022 23022359 0.15729520605822106 0.7460712636217287 chr9 141213431 9390981 0.06650203832240292 0.4268126515851347 chr10 135534747 11123792 0.08207335938731637 0.5544708930304849 chr11 135006516 10590499 0.07844435449323053 0.4634328727515972 chr12 133851895 8604572 0.06428427479491418 0.3169617435620436 chr13 115169878 5702118 0.049510497875147524 0.27051737215617905 chr14 107349540 4679136 0.043587853287494295 0.2756817164373595 chr15 102531392 6886514 0.0671649322775214 0.31596366286527455 chr16 90354753 7097301 0.07854928229398181 0.37400189750919566 chr17 81195210 6354073 0.0782567469189377 0.4025380052348299 chr18 78077248 5082152 0.065091331087899 0.8368945027719399 chr19 59128983 4089977 0.06917042696303435 0.7643799261878643 chr20 63025520 5255623 0.0833888082161004 0.3652844975786211 chr21 48129895 3081864 0.06403221947606576 0.3620106113257855 chr22 51304566 1734748 0.033812740955649054 0.22716242720453633 chrMT 16571 171797 10.367328465391346 6.74954688909841 chrX 155270560 10591333 0.0682121131011571 0.378355522198872 chrY 59373566 659924 0.011114777913120462 0.31649103309504695