BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238530.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 = 1,363,841 number of mapped reads = 1,181,422 (86.62%) number of supplementary alignments = 6,737 (0.49%) number of secondary alignments = 0 number of mapped bases = 71,913,764 bp number of sequenced bases = 71,879,858 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 166,767 duplication rate = 12.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.7593 >>>>>>> ACTG content number of A's = 17,953,297 bp (24.98%) number of C's = 11,779,765 bp (16.39%) number of T's = 25,436,030 bp (35.39%) number of G's = 16,706,398 bp (23.24%) number of N's = 4,368 bp (0.01%) GC percentage = 39.63% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 454,390 number of insertions = 4,789 mapped reads with insertion percentage = 0.4% number of deletions = 20,531 mapped reads with deletion percentage = 1.72% homopolymer indels = 42.07% >>>>>>> Coverage mean coverageData = 0.0232X std coverageData = 0.39X There is a 1.82% of reference with a coverageData >= 1X There is a 0.35% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% 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 3551125 0.014247206228625605 0.24711040105946785 chr2 243199373 7956294 0.03271510901469306 0.9194309994299992 chr3 198022430 3050262 0.01540361867087481 0.16125765871626768 chr4 191154276 5072475 0.026536026847759346 0.20322401458161846 chr5 180915260 4604564 0.02545149591029524 0.20116318241300135 chr6 171115067 4953557 0.02894868983103633 0.3714909124415184 chr7 159138663 8360394 0.0525352786205072 0.6630528696048408 chr8 146364022 4948822 0.03381173824261265 0.42409289159529184 chr9 141213431 3300759 0.023374256801394478 0.2662483119528405 chr10 135534747 5360879 0.039553539728081684 0.28780116343314843 chr11 135006516 2053151 0.015207791896503722 0.1627929155427921 chr12 133851895 2360149 0.017632540801906467 0.1845825237375856 chr13 115169878 2677970 0.023252347284764857 0.2628761971550956 chr14 107349540 1092250 0.010174705918628063 0.15294229267646503 chr15 102531392 1172711 0.01143758001451887 0.21415405409954766 chr16 90354753 2349914 0.02600764123609524 0.22650307197019087 chr17 81195210 1214298 0.014955291081826132 0.15210361938613076 chr18 78077248 1470823 0.018838048697618032 0.7614239679758014 chr19 59128983 640726 0.010836073402446309 0.20939605679982604 chr20 63025520 1601670 0.02541303903561605 0.2071261942926134 chr21 48129895 1480366 0.03075772344818122 0.2268282121359947 chr22 51304566 290006 0.005652635283962835 0.08906627792176762 chrMT 16571 8457 0.5103494055880755 0.851015859182787 chrX 155270560 2185382 0.014074670690953906 0.15993665979895022 chrY 59373566 156760 0.002640232186828731 0.13163653505449116