BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237328.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,302,570 number of mapped reads = 2,037,251 (88.48%) number of supplementary alignments = 22,818 (0.99%) number of secondary alignments = 0 number of mapped bases = 121,860,724 bp number of sequenced bases = 121,781,570 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 498,153 duplication rate = 18.65% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.3364 >>>>>>> ACTG content number of A's = 31,028,382 bp (25.48%) number of C's = 20,837,825 bp (17.11%) number of T's = 41,129,656 bp (33.77%) number of G's = 28,773,268 bp (23.63%) number of N's = 12,439 bp (0.01%) GC percentage = 40.74% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 838,017 number of insertions = 9,492 mapped reads with insertion percentage = 0.46% number of deletions = 45,560 mapped reads with deletion percentage = 2.2% homopolymer indels = 40.43% >>>>>>> Coverage mean coverageData = 0.0394X std coverageData = 0.6217X There is a 2.1% of reference with a coverageData >= 1X There is a 0.89% of reference with a coverageData >= 2X There is a 0.42% of reference with a coverageData >= 3X There is a 0.21% of reference with a coverageData >= 4X There is a 0.1% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% 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 0.01% 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 15757229 0.06321841420808336 0.635659842247703 chr2 243199373 8272929 0.03401706549629961 1.2213818012558468 chr3 198022430 6797545 0.03432714667727287 0.31767980042241145 chr4 191154276 4406166 0.0230503135592949 0.47959764860484777 chr5 180915260 10909040 0.06029916989865863 0.42067882225067926 chr6 171115067 14524653 0.08488237333302742 0.7054658486460033 chr7 159138663 7745922 0.048674042209340414 0.8008659525896379 chr8 146364022 7167469 0.04897015606745215 0.4853401040718437 chr9 141213431 7397463 0.05238498170899905 0.4704304440322595 chr10 135534747 4844345 0.035742457983855606 0.7655763035912658 chr11 135006516 2410765 0.017856656637224827 0.25790634637472576 chr12 133851895 2244799 0.016770767421708896 0.22435303288865793 chr13 115169878 6345181 0.055094101949122495 0.47223613113652796 chr14 107349540 3252042 0.030293953751455292 0.3091794748260835 chr15 102531392 1842297 0.017968126288580966 0.2679500973377888 chr16 90354753 928817 0.010279669515559408 0.25143639841794513 chr17 81195210 3273717 0.04031909025175254 0.3700415436237457 chr18 78077248 3448705 0.044170422092745895 1.5057193760933127 chr19 59128983 1576371 0.0266598699997935 0.4017102599916576 chr20 63025520 1032021 0.016374652680374552 0.2512407263071641 chr21 48129895 1157200 0.024043268741807976 0.36650571347706334 chr22 51304566 860146 0.01676548633117762 0.21083309620870475 chrMT 16571 16331 0.9855168668155211 1.4588883370813877 chrX 155270560 5167298 0.033279315795602206 0.3227688117652447 chrY 59373566 482273 0.008122688807338943 0.4518093885550327