BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716731.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 = 1,668,712 number of mapped reads = 1,500,209 (89.9%) number of supplementary alignments = 8,760 (0.52%) number of secondary alignments = 0 number of mapped bases = 87,163,680 bp number of sequenced bases = 87,137,460 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 58,248 duplication rate = 2.81% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2956 >>>>>>> ACTG content number of A's = 21,425,773 bp (24.59%) number of C's = 18,102,472 bp (20.77%) number of T's = 27,526,911 bp (31.59%) number of G's = 20,081,144 bp (23.05%) number of N's = 1,160 bp (0%) GC percentage = 43.82% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 439,473 number of insertions = 5,762 mapped reads with insertion percentage = 0.38% number of deletions = 16,433 mapped reads with deletion percentage = 1.09% homopolymer indels = 41.51% >>>>>>> Coverage mean coverageData = 0.0282X std coverageData = 0.2826X There is a 2.51% of reference with a coverageData >= 1X There is a 0.21% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% 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 6878480 0.02759664137406502 0.403623441050668 chr2 243199373 8536135 0.03509932979967017 0.3619508480474116 chr3 198022430 6490431 0.032776241560110136 0.2112332294246929 chr4 191154276 4840980 0.025324989329561218 0.19783632855308883 chr5 180915260 4682202 0.025880636050270165 0.17549948351216385 chr6 171115067 4358675 0.02547218708683321 0.18988427254653775 chr7 159138663 5077072 0.03190344762416409 0.591278369554942 chr8 146364022 6522212 0.0445615794843353 0.29572668069618874 chr9 141213431 3753726 0.026581933272338664 0.20292140295893416 chr10 135534747 4577796 0.033775811010293914 0.38416653881858065 chr11 135006516 2399070 0.017770031188716846 0.1745662956218656 chr12 133851895 4337806 0.032407505325195436 0.213339651253867 chr13 115169878 2351947 0.020421546335231855 0.1543566742835519 chr14 107349540 2338496 0.02178394057394191 0.16296606327441718 chr15 102531392 2238682 0.021834113009994053 0.1634050746709728 chr16 90354753 2464036 0.027270684919032426 0.19179736844719444 chr17 81195210 3915798 0.0482269582158849 0.24777902368333707 chr18 78077248 1667297 0.02135445398895207 0.2961008488078878 chr19 59128983 1878267 0.03176558947411627 0.34950569296555783 chr20 63025520 2173435 0.03448499909243113 0.214498669618898 chr21 48129895 973326 0.02022289888644054 0.1659583755701674 chr22 51304566 1346644 0.02624803414183447 0.17716531951029352 chrMT 16571 23336 1.4082433166374992 1.4691871418216238 chrX 155270560 3120111 0.020094672164510774 0.17558783498365207 chrY 59373566 217720 0.0036669517205687122 0.11120440961490222