BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068191.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 = 2,147,955 number of mapped reads = 1,984,851 (92.41%) number of supplementary alignments = 16,858 (0.78%) number of secondary alignments = 0 number of mapped bases = 134,911,848 bp number of sequenced bases = 134,850,343 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 148,203 duplication rate = 5.55% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.6812 >>>>>>> ACTG content number of A's = 39,035,387 bp (28.95%) number of C's = 25,338,829 bp (18.79%) number of T's = 42,224,777 bp (31.31%) number of G's = 28,082,081 bp (20.82%) number of N's = 169,269 bp (0.13%) GC percentage = 39.61% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,149,521 number of insertions = 8,684 mapped reads with insertion percentage = 0.43% number of deletions = 35,722 mapped reads with deletion percentage = 1.78% homopolymer indels = 46.73% >>>>>>> Coverage mean coverageData = 0.0436X std coverageData = 0.6681X There is a 2.81% of reference with a coverageData >= 1X There is a 0.92% of reference with a coverageData >= 2X There is a 0.32% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.05% 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 21888072 0.08781551641550374 1.326671416788107 chr2 243199373 7557620 0.031075820248928028 0.26213865255538643 chr3 198022430 2899167 0.014640599047289744 0.32772430677511366 chr4 191154276 8173440 0.04275834248144154 0.30201043075421524 chr5 180915260 6335833 0.03502099822867347 0.26432034825817075 chr6 171115067 3418682 0.019978848501984926 0.20320868338293532 chr7 159138663 7468261 0.04692926821937671 0.40740656119067176 chr8 146364022 2417193 0.016514939716537717 0.22180547576606 chr9 141213431 2299081 0.016280894697615556 0.18457449031184156 chr10 135534747 3858467 0.02846847089329794 1.4854242156434971 chr11 135006516 18782556 0.13912332942507752 1.5843545720587535 chr12 133851895 18253613 0.13637171890618358 0.5278460528993584 chr13 115169878 3109857 0.027002346915744758 0.23782697722130827 chr14 107349540 6110646 0.056922889469298146 0.3378557079016855 chr15 102531392 4269755 0.04164339249388129 0.29213752229019346 chr16 90354753 1089689 0.012060118187695118 0.19802360124196575 chr17 81195210 2227190 0.027430066379531503 0.5772689365561837 chr18 78077248 780040 0.009990618521800358 0.17886327205743774 chr19 59128983 935065 0.015813987532983614 0.8891191394261138 chr20 63025520 3506054 0.05562911658642404 0.34006949692808264 chr21 48129895 531248 0.011037796778904254 0.2662879362061838 chr22 51304566 301714 0.005880841093168978 0.10170341110589752 chrMT 16571 102778 6.2022810934765555 5.636785914680134 chrX 155270560 8263318 0.05321883298417936 0.43958204712492877 chrY 59373566 332509 0.005600286834716985 0.0998193317530811