BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013185.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 = 2,853,658 number of mapped reads = 2,569,665 (90.05%) number of supplementary alignments = 21,220 (0.74%) number of secondary alignments = 0 number of mapped bases = 168,204,991 bp number of sequenced bases = 168,126,047 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 98,577 duplication rate = 2.34% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.0193 >>>>>>> ACTG content number of A's = 46,096,272 bp (27.42%) number of C's = 32,063,250 bp (19.07%) number of T's = 51,123,176 bp (30.41%) number of G's = 38,823,018 bp (23.09%) number of N's = 20,331 bp (0.01%) GC percentage = 42.16% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 1,309,851 number of insertions = 11,957 mapped reads with insertion percentage = 0.46% number of deletions = 46,069 mapped reads with deletion percentage = 1.77% homopolymer indels = 44.7% >>>>>>> Coverage mean coverageData = 0.0543X std coverageData = 0.6018X There is a 4.65% of reference with a coverageData >= 1X There is a 0.53% 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 0.01% 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 9378824 0.03762808679220903 0.7317118894021075 chr2 243199373 25337245 0.10418301941921536 0.8361844761317179 chr3 198022430 9898161 0.04998504967341326 0.24955085059040852 chr4 191154276 7747709 0.040531183304526236 0.2382651575721619 chr5 180915260 9666730 0.05343236385919021 0.26019876021815397 chr6 171115067 8486552 0.04959558587555589 0.3755238885342967 chr7 159138663 14522106 0.09125441753899868 1.6478032177964466 chr8 146364022 11100622 0.07584255917755527 0.5207291588252841 chr9 141213431 3412894 0.024168338491825186 0.46765355949108484 chr10 135534747 5559089 0.0410159691374198 0.5329033258667781 chr11 135006516 7541385 0.05585941496334888 0.42220323233353446 chr12 133851895 5187252 0.038753668747087966 0.2387270759846998 chr13 115169878 4172054 0.03622521854195244 0.20961534137724733 chr14 107349540 8082388 0.07529038317257811 0.3292239265554677 chr15 102531392 3460635 0.03375195569372549 0.21683704459632103 chr16 90354753 5098563 0.05642827666188186 0.3230806927359632 chr17 81195210 4158044 0.05121045933620961 0.26309673913829146 chr18 78077248 4571238 0.05854763221162713 1.0560614899792538 chr19 59128983 2504632 0.04235878706048436 0.7054020835376209 chr20 63025520 3670692 0.05824136000781906 0.2947260434288392 chr21 48129895 4454684 0.09255544812636719 0.35961666877398507 chr22 51304566 2243129 0.04372182000331121 0.23530914230616118 chrMT 16571 57804 3.4882626274817454 2.633414501218877 chrX 155270560 7541868 0.04857242738095361 0.3098641061700225 chrY 59373566 350691 0.005906517388563119 0.10959695413737854