BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173967.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 5,706,514 number of mapped reads = 5,563,247 (97.49%) number of supplementary alignments = 695,857 (12.19%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,785,312 number of mapped paired reads (second in pair) = 2,777,935 number of mapped paired reads (both in pair) = 5,473,448 number of mapped paired reads (singletons) = 89,799 number of mapped bases = 626,095,480 bp number of sequenced bases = 625,625,515 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,259,408 duplication rate = 63.13% >>>>>>> Insert size mean insert size = 999,879.1866 std insert size = 9,323,527.3651 median insert size = 156 >>>>>>> Mapping quality mean mapping quality = 52.4579 >>>>>>> ACTG content number of A's = 186,745,283 bp (29.85%) number of C's = 124,407,660 bp (19.89%) number of T's = 184,937,924 bp (29.56%) number of G's = 129,530,134 bp (20.7%) number of N's = 4,514 bp (0%) GC percentage = 40.59% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 5,832,858 number of insertions = 92,826 mapped reads with insertion percentage = 1.58% number of deletions = 181,739 mapped reads with deletion percentage = 3.17% homopolymer indels = 40.05% >>>>>>> Coverage mean coverageData = 0.2022X std coverageData = 3.8592X There is a 4.75% of reference with a coverageData >= 1X There is a 3.49% of reference with a coverageData >= 2X There is a 2.5% of reference with a coverageData >= 3X There is a 1.96% of reference with a coverageData >= 4X There is a 1.41% of reference with a coverageData >= 5X There is a 1.15% of reference with a coverageData >= 6X There is a 0.83% of reference with a coverageData >= 7X There is a 0.71% of reference with a coverageData >= 8X There is a 0.51% of reference with a coverageData >= 9X There is a 0.46% of reference with a coverageData >= 10X There is a 0.33% of reference with a coverageData >= 11X There is a 0.3% of reference with a coverageData >= 12X There is a 0.21% of reference with a coverageData >= 13X There is a 0.2% of reference with a coverageData >= 14X There is a 0.14% of reference with a coverageData >= 15X There is a 0.13% of reference with a coverageData >= 16X There is a 0.09% of reference with a coverageData >= 17X There is a 0.09% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.06% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% 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 52809962 0.21187494654225958 1.8960724566287102 chr2 243199373 54889646 0.22569813944380523 11.72752404862724 chr3 198022430 41284757 0.20848525593792583 1.2884269159145305 chr4 191154276 45493932 0.23799588977020844 4.563748374059398 chr5 180915260 38958376 0.21534046381714841 1.3115647933400232 chr6 171115067 36345047 0.21240120836349263 1.5057848521891755 chr7 159138663 33203257 0.2086435588565929 1.7804842858753975 chr8 146364022 31303327 0.21387309922379696 2.2938701111510813 chr9 141213431 26937853 0.19075985059806386 1.7063022194705504 chr10 135534747 31031120 0.22895324399727549 3.076453186440218 chr11 135006516 29840114 0.22102721323465602 1.392006320587751 chr12 133851895 27710209 0.20702141721639428 1.3152529737407028 chr13 115169878 19683410 0.1709076222169828 1.1563486633051905 chr14 107349540 18906001 0.17611627399614382 1.195699623550746 chr15 102531392 18025035 0.1758001588430595 1.2037802106284576 chr16 90354753 19790771 0.21903408888738815 1.7212912664740152 chr17 81195210 16957622 0.20885002945370792 1.4649291448014297 chr18 78077248 16870706 0.2160771086603872 2.321010381388985 chr19 59128983 11514153 0.19472942736052132 1.5801310459634132 chr20 63025520 13474350 0.21379196871362585 2.11960029376979 chr21 48129895 8977688 0.18653038823375784 3.005529877230973 chr22 51304566 7638723 0.14888973039943462 1.312793656299953 chrMT 16571 477143 28.79385673767425 22.976011361865336 chrX 155270560 17200410 0.11077702044740484 0.9585975697337064 chrY 59373566 6771868 0.11405526829902721 3.7806324798670166