BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230353.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 = 2,394,515 number of mapped reads = 1,954,919 (81.64%) number of supplementary alignments = 8,869 (0.37%) number of secondary alignments = 0 number of mapped bases = 127,628,060 bp number of sequenced bases = 127,573,237 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 86,124 duplication rate = 3.58% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.7488 >>>>>>> ACTG content number of A's = 34,948,555 bp (27.39%) number of C's = 21,595,975 bp (16.93%) number of T's = 43,853,104 bp (34.37%) number of G's = 26,930,748 bp (21.11%) number of N's = 244,855 bp (0.19%) GC percentage = 38.04% >>>>>>> Mismatches and indels general error rate = 0.0111 number of mismatches = 1,394,112 number of insertions = 11,247 mapped reads with insertion percentage = 0.57% number of deletions = 34,137 mapped reads with deletion percentage = 1.73% homopolymer indels = 48.45% >>>>>>> Coverage mean coverageData = 0.0412X std coverageData = 0.339X There is a 3.48% of reference with a coverageData >= 1X There is a 0.47% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 10008117 0.040152826740600174 0.5072209418710701 chr2 243199373 9722936 0.03997928070316201 0.32269053611206994 chr3 198022430 8954152 0.045217867491071595 0.24447223825814404 chr4 191154276 9660403 0.050537205874484334 0.2693872101518302 chr5 180915260 6748488 0.037301927985511005 0.22178981273515144 chr6 171115067 7857765 0.04592094160825709 0.3030838111090638 chr7 159138663 7514359 0.04721894012644809 0.5026422043241646 chr8 146364022 6685433 0.04567675108026206 0.5358562866234097 chr9 141213431 5423744 0.03840813130586707 0.3410811019929912 chr10 135534747 5948758 0.04389101785094268 0.33898065020473617 chr11 135006516 6100766 0.04518867815239377 0.33219384578639866 chr12 133851895 5873667 0.0438818367121362 0.244974353962408 chr13 115169878 4668688 0.0405374051017055 0.2304640462000065 chr14 107349540 4110417 0.03829002900245311 0.2376944208336295 chr15 102531392 3756195 0.03663458504493921 0.2183688386763751 chr16 90354753 3280622 0.03630823936843699 0.24526616313641467 chr17 81195210 2724560 0.03355567403545111 0.2243311753195988 chr18 78077248 2762056 0.035375939479834126 0.5465305069360102 chr19 59128983 1946969 0.032927490060162205 0.3503188131173126 chr20 63025520 2484250 0.03941657284223914 0.23552183894140422 chr21 48129895 1783704 0.03706020966802442 0.24092840036131843 chr22 51304566 1198889 0.02336807604999524 0.17271605615893107 chrMT 16571 30515 1.8414700380182245 2.0570876886130898 chrX 155270560 8059319 0.051905003756024325 0.2866232853305561 chrY 59373566 323288 0.005444982031229183 0.12069393321972165