BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240250.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 = 1,602,451 number of mapped reads = 1,265,509 (78.97%) number of supplementary alignments = 9,709 (0.61%) number of secondary alignments = 0 number of mapped bases = 81,855,939 bp number of sequenced bases = 81,817,484 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 179,758 duplication rate = 10.93% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.308 >>>>>>> ACTG content number of A's = 22,607,683 bp (27.63%) number of C's = 14,944,476 bp (18.27%) number of T's = 26,229,985 bp (32.06%) number of G's = 18,027,992 bp (22.03%) number of N's = 7,348 bp (0.01%) GC percentage = 40.3% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 680,978 number of insertions = 5,621 mapped reads with insertion percentage = 0.44% number of deletions = 21,939 mapped reads with deletion percentage = 1.72% homopolymer indels = 48.79% >>>>>>> Coverage mean coverageData = 0.0264X std coverageData = 0.322X There is a 1.38% of reference with a coverageData >= 1X There is a 0.63% of reference with a coverageData >= 2X There is a 0.31% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.07% 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% 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 6585366 0.026420660352136093 0.42759583175147464 chr2 243199373 8859744 0.036429962342049295 0.3950275526695186 chr3 198022430 5089108 0.025699654327037597 0.27052867608349346 chr4 191154276 5258372 0.027508524057290772 0.2841288981472411 chr5 180915260 4289549 0.02371026634237488 0.2618815785138104 chr6 171115067 4296732 0.025110190910307157 0.28823107706549034 chr7 159138663 4744902 0.029816148449104414 0.41066213157176773 chr8 146364022 4504662 0.030777112697818593 0.40616496073847574 chr9 141213431 3075814 0.021781313421950634 0.2876488477542747 chr10 135534747 3863125 0.0285028384639992 0.3180541398382685 chr11 135006516 3608992 0.02673198381032216 0.3055376123339937 chr12 133851895 4105856 0.030674619884910857 0.299885518174173 chr13 115169878 2003986 0.017400261551028126 0.227054772982905 chr14 107349540 2722590 0.025361915849849006 0.2797060436227577 chr15 102531392 2328260 0.022707777145949605 0.2696069995585828 chr16 90354753 2473763 0.02737833835924492 0.28187340102910785 chr17 81195210 1995045 0.024570969149534806 0.2681769086040786 chr18 78077248 2075649 0.02658455636141274 0.40872128150255743 chr19 59128983 1448786 0.024502129522505064 0.3306349526161376 chr20 63025520 1726163 0.02738831825584303 0.28126018673837805 chr21 48129895 1370064 0.028465966942167648 0.2934824674594756 chr22 51304566 733177 0.014290677363882193 0.1934011054709792 chrMT 16571 16954 1.0231126667068975 1.8329637363725866 chrX 155270560 4458993 0.028717568868174365 0.2980119280700045 chrY 59373566 220287 0.003710186448966195 0.09677517709655839