BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240065.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 = 1,941,300 number of mapped reads = 1,522,147 (78.41%) number of supplementary alignments = 14,804 (0.76%) number of secondary alignments = 0 number of mapped bases = 100,610,388 bp number of sequenced bases = 100,571,426 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 112,378 duplication rate = 6.06% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2481 >>>>>>> ACTG content number of A's = 28,422,169 bp (28.26%) number of C's = 18,369,290 bp (18.26%) number of T's = 32,332,963 bp (32.15%) number of G's = 21,437,828 bp (21.32%) number of N's = 9,176 bp (0.01%) GC percentage = 39.58% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 797,287 number of insertions = 7,212 mapped reads with insertion percentage = 0.47% number of deletions = 22,776 mapped reads with deletion percentage = 1.48% homopolymer indels = 47.86% >>>>>>> Coverage mean coverageData = 0.0325X std coverageData = 0.3362X There is a 2.33% of reference with a coverageData >= 1X There is a 0.61% of reference with a coverageData >= 2X There is a 0.17% 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 6329712 0.025394969828380087 0.47447410794109507 chr2 243199373 5268118 0.021661725254530157 0.3477500913438616 chr3 198022430 7486252 0.03780507087000195 0.2563609510584316 chr4 191154276 7466315 0.03905910532705007 0.26647550403523185 chr5 180915260 7010241 0.038748754527395866 0.25995227045364194 chr6 171115067 5524055 0.0322826919735829 0.2694312535885645 chr7 159138663 5879974 0.03694874576142443 0.3848970779232433 chr8 146364022 4180008 0.028558985622846575 0.6778962617310771 chr9 141213431 5313638 0.03762841793710118 0.3197222794279102 chr10 135534747 6438014 0.04750083755274948 0.3568570466650341 chr11 135006516 2677345 0.01983122799791382 0.21534789305647772 chr12 133851895 3835241 0.028652870398286106 0.2292228657426164 chr13 115169878 3343340 0.029029639156168942 0.22504066254433372 chr14 107349540 1960362 0.018261484865235565 0.19146162460651733 chr15 102531392 1606792 0.015671219990849243 0.17150019457062807 chr16 90354753 3991478 0.044175628480772895 0.2818710668752718 chr17 81195210 1739250 0.02142059857964528 0.2016769137368648 chr18 78077248 5115344 0.06551644853056296 0.4720993317174643 chr19 59128983 2005179 0.03391194805430697 0.42345787912151434 chr20 63025520 4470726 0.07093517038812215 0.3527792553627763 chr21 48129895 1978391 0.041105242386254945 0.2704628165492611 chr22 51304566 499593 0.009737788250659796 0.1231643545184559 chrMT 16571 19016 1.1475469193168788 1.5472072678741362 chrX 155270560 6261671 0.040327483844973575 0.28933577315747694 chrY 59373566 210333 0.0035425360841557 0.08557623608897076