BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008664.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 = 1,928,342 number of mapped reads = 1,625,745 (84.31%) number of supplementary alignments = 11,464 (0.59%) number of secondary alignments = 0 number of mapped bases = 103,385,603 bp number of sequenced bases = 103,334,012 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 107,583 duplication rate = 5.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4402 >>>>>>> ACTG content number of A's = 26,938,785 bp (26.07%) number of C's = 19,115,435 bp (18.5%) number of T's = 32,495,542 bp (31.45%) number of G's = 24,701,997 bp (23.91%) number of N's = 82,253 bp (0.08%) GC percentage = 42.4% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 869,992 number of insertions = 6,993 mapped reads with insertion percentage = 0.43% number of deletions = 29,219 mapped reads with deletion percentage = 1.78% homopolymer indels = 44.57% >>>>>>> Coverage mean coverageData = 0.0334X std coverageData = 0.3209X There is a 2.6% of reference with a coverageData >= 1X There is a 0.52% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% 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 10838026 0.043482443319569505 0.6535636689390807 chr2 243199373 9312269 0.03829067848789232 0.3141974819688855 chr3 198022430 6975046 0.03522351483112292 0.2317558455103439 chr4 191154276 4697758 0.02457574111499342 0.20539303739729792 chr5 180915260 4575843 0.02529274202740001 0.19551081228165765 chr6 171115067 5177590 0.030257943328859522 0.23290167482565013 chr7 159138663 6287690 0.03951076301300835 0.40540680790971545 chr8 146364022 7173236 0.04900955782699112 0.320752340752143 chr9 141213431 3283845 0.02325448065913787 0.24869684091936503 chr10 135534747 6181722 0.04560986858963923 0.332803662044579 chr11 135006516 3846591 0.02849189145803896 0.29986333613414645 chr12 133851895 4749577 0.03548382337059927 0.23269166891518123 chr13 115169878 1873505 0.016267317744315054 0.15347876285663037 chr14 107349540 3772724 0.03514429591407658 0.23364726106729453 chr15 102531392 2522424 0.0246014801008456 0.20346966572806768 chr16 90354753 3415688 0.037803080486535114 0.267246344426305 chr17 81195210 3349044 0.04124681739230676 0.29335115959280367 chr18 78077248 1390241 0.01780596826363552 0.385404586187221 chr19 59128983 2948105 0.04985888223377696 0.43985784207100204 chr20 63025520 2525491 0.040070926824562494 0.2506929431124218 chr21 48129895 1498451 0.03113347743642491 0.22701873683693582 chr22 51304566 1541622 0.030048436624529676 0.21045418284097606 chrMT 16571 52274 3.154547100356044 2.5825542143231135 chrX 155270560 5087575 0.03276587010441644 0.24393350576243175 chrY 59373566 309266 0.005208816327454544 0.14206183850328472