BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008823.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 = 1,842,022 number of mapped reads = 1,518,401 (82.43%) number of supplementary alignments = 12,031 (0.65%) number of secondary alignments = 0 number of mapped bases = 96,743,628 bp number of sequenced bases = 96,683,815 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 149,177 duplication rate = 7.73% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.1126 >>>>>>> ACTG content number of A's = 26,543,169 bp (27.45%) number of C's = 17,933,334 bp (18.55%) number of T's = 30,523,175 bp (31.57%) number of G's = 21,542,002 bp (22.28%) number of N's = 142,135 bp (0.15%) GC percentage = 40.83% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 851,020 number of insertions = 6,000 mapped reads with insertion percentage = 0.39% number of deletions = 34,448 mapped reads with deletion percentage = 2.24% homopolymer indels = 45% >>>>>>> Coverage mean coverageData = 0.0313X std coverageData = 0.4139X There is a 2.02% of reference with a coverageData >= 1X There is a 0.64% of reference with a coverageData >= 2X There is a 0.23% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% 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% 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 10385635 0.04166743881452556 0.561779691205335 chr2 243199373 9439540 0.03881399809365463 0.3651705357624032 chr3 198022430 9756358 0.04926895402707663 0.3783609912140802 chr4 191154276 5206786 0.02723865826574552 0.3114732506130689 chr5 180915260 1810863 0.010009454149970544 0.14172371504892034 chr6 171115067 5836301 0.0341074640726991 0.2842131543841101 chr7 159138663 6297938 0.03957515968322544 0.5008729813284039 chr8 146364022 13493858 0.09219381795889703 0.484333012302561 chr9 141213431 1593034 0.011281037424832486 0.18446082221700685 chr10 135534747 5314582 0.039211952046511 1.1381995113754029 chr11 135006516 1267524 0.009388613509587937 0.15748829706917486 chr12 133851895 5466151 0.04083730753307602 0.28840979269607026 chr13 115169878 1168060 0.010142061624828672 0.14610181120217663 chr14 107349540 1584667 0.01476174932840886 0.1823293326755305 chr15 102531392 1631630 0.015913467750442712 0.30364230464718855 chr16 90354753 3074934 0.034031790225800294 0.391199033117764 chr17 81195210 2310667 0.028458168899372267 0.23551839441259903 chr18 78077248 405340 0.005191525193101068 0.30453542137752343 chr19 59128983 1256582 0.021251540889854304 0.3824703097361432 chr20 63025520 1931875 0.03065226593925762 0.24548448742274706 chr21 48129895 443608 0.009216891081935666 0.13664728673510687 chr22 51304566 355396 0.0069271807113620255 0.1086687191578947 chrMT 16571 398781 24.06499306016535 15.268819211250822 chrX 155270560 6068093 0.03908076972221907 0.2906004276374379 chrY 59373566 245425 0.004133573516537646 0.2247762642703663