BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10251070.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP224945/SRP224945.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 = 4,040,658 number of mapped reads = 3,748,946 (92.78%) number of supplementary alignments = 27,667 (0.68%) number of secondary alignments = 0 number of mapped bases = 290,917,568 bp number of sequenced bases = 290,735,934 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 792,429 duplication rate = 18.55% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.2466 >>>>>>> ACTG content number of A's = 84,181,900 bp (28.95%) number of C's = 58,133,194 bp (20%) number of T's = 85,757,768 bp (29.5%) number of G's = 62,660,366 bp (21.55%) number of N's = 2,706 bp (0%) GC percentage = 41.55% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 1,671,288 number of insertions = 35,549 mapped reads with insertion percentage = 0.93% number of deletions = 101,145 mapped reads with deletion percentage = 2.65% homopolymer indels = 44.59% >>>>>>> Coverage mean coverageData = 0.094X std coverageData = 1.005X There is a 6.24% of reference with a coverageData >= 1X There is a 1.9% of reference with a coverageData >= 2X There is a 0.64% of reference with a coverageData >= 3X There is a 0.23% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 24318057 0.09756467968840085 2.0264934608472864 chr2 243199373 25440148 0.10460614139823461 1.4332577815495164 chr3 198022430 19627629 0.09911821100266267 0.4411345965125985 chr4 191154276 18112439 0.09475298894176974 0.5180127730002653 chr5 180915260 17411678 0.09624217437489795 0.46560667247191745 chr6 171115067 16291725 0.09520917874520074 0.5427214404438585 chr7 159138663 16381589 0.10293908903834388 1.4907747832983191 chr8 146364022 14175638 0.09685192990938715 0.6391618141521028 chr9 141213431 12436591 0.08806946274111845 0.995365124430448 chr10 135534747 17302625 0.12766191240981178 1.0461836369119237 chr11 135006516 13368732 0.09902286494082997 0.6322071599970018 chr12 133851895 13116292 0.09799108185954335 0.4588578540983534 chr13 115169878 8446865 0.07334265822526963 0.3751817848666341 chr14 107349540 8629215 0.08038427551715638 0.687211886618553 chr15 102531392 8814089 0.08596478432673575 0.41027071956832634 chr16 90354753 8273844 0.09157065594545978 0.8571089613635752 chr17 81195210 8107722 0.0998546835459875 0.5698571423402321 chr18 78077248 7027887 0.09001197122111682 1.1366859436990595 chr19 59128983 6135947 0.1037722397491599 1.9662970135900952 chr20 63025520 6098151 0.09675685341429947 0.49657245185006815 chr21 48129895 3397823 0.07059693356904269 0.41249206777065245 chr22 51304566 3687408 0.07187290113710347 0.4162775004628339 chrMT 16571 146285 8.827771407881238 5.834552134785481 chrX 155270560 13370845 0.08611320136927438 0.5044847549400655 chrY 59373566 798344 0.013446118429201305 1.0004812673759123