BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240266.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 = 1,633,231 number of mapped reads = 1,278,025 (78.25%) number of supplementary alignments = 7,157 (0.44%) number of secondary alignments = 0 number of mapped bases = 77,820,725 bp number of sequenced bases = 77,781,378 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 153,368 duplication rate = 10.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1022 >>>>>>> ACTG content number of A's = 20,932,874 bp (26.91%) number of C's = 13,450,331 bp (17.29%) number of T's = 25,565,549 bp (32.87%) number of G's = 17,813,843 bp (22.9%) number of N's = 18,781 bp (0.02%) GC percentage = 40.19% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 711,491 number of insertions = 5,430 mapped reads with insertion percentage = 0.42% number of deletions = 23,240 mapped reads with deletion percentage = 1.8% homopolymer indels = 49.22% >>>>>>> Coverage mean coverageData = 0.0251X std coverageData = 0.2662X There is a 1.74% of reference with a coverageData >= 1X There is a 0.51% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% 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 5692479 0.022838374392655975 0.31568669828548895 chr2 243199373 9180849 0.03775029880525226 0.3810334104319709 chr3 198022430 4900602 0.024747711660744694 0.21615333459171324 chr4 191154276 5820288 0.03044811825187735 0.2479453838015802 chr5 180915260 3789022 0.02094362852531069 0.19792588792315205 chr6 171115067 3683363 0.021525649754734925 0.22665132554062503 chr7 159138663 4059397 0.025508552877561878 0.35032553285631407 chr8 146364022 4700509 0.03211519426543225 0.3809893184876582 chr9 141213431 2686320 0.019023119691780593 0.22058086903044263 chr10 135534747 3652781 0.026950882197020666 0.249845856926339 chr11 135006516 4035621 0.02989204609946382 0.2817933135184511 chr12 133851895 4049663 0.030254805133688993 0.23955994758764523 chr13 115169878 2110077 0.018321431233955115 0.18363104346581036 chr14 107349540 2777933 0.02587745601890795 0.22276884958685997 chr15 102531392 2022658 0.019727207058692815 0.20472805513025932 chr16 90354753 2332355 0.025813307242398196 0.2182506413583363 chr17 81195210 1768949 0.0217863713881644 0.21097001867003662 chr18 78077248 1795457 0.022995905286005983 0.3188949282410668 chr19 59128983 1208436 0.02043728707459758 0.24367968423697584 chr20 63025520 1476232 0.0234227658891192 0.2092789276747399 chr21 48129895 1200175 0.024936164934496532 0.21867917928266403 chr22 51304566 651606 0.012700740904815372 0.14819317063196083 chrMT 16571 30984 1.869772494116227 2.9480481918488217 chrX 155270560 4023268 0.025911338247250476 0.22945095506450494 chrY 59373566 171701 0.002891876159164838 0.07012484598600499