BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237575.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 = 1,915,474 number of mapped reads = 1,543,153 (80.56%) number of supplementary alignments = 8,530 (0.45%) number of secondary alignments = 0 number of mapped bases = 97,088,448 bp number of sequenced bases = 97,031,075 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 94,516 duplication rate = 4.14% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.7811 >>>>>>> ACTG content number of A's = 24,817,878 bp (25.58%) number of C's = 18,194,607 bp (18.75%) number of T's = 29,515,764 bp (30.42%) number of G's = 24,480,158 bp (25.23%) number of N's = 22,668 bp (0.02%) GC percentage = 43.98% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 932,222 number of insertions = 9,195 mapped reads with insertion percentage = 0.59% number of deletions = 34,762 mapped reads with deletion percentage = 2.22% homopolymer indels = 46.09% >>>>>>> Coverage mean coverageData = 0.0314X std coverageData = 0.3103X There is a 2.47% of reference with a coverageData >= 1X There is a 0.36% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% 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 8291347 0.03326510067150445 0.36607375702963946 chr2 243199373 8334099 0.03426858752633379 0.44937951895356454 chr3 198022430 6764757 0.034161569474730716 0.25121358140745126 chr4 191154276 6223603 0.03255801089168416 0.25637404603801517 chr5 180915260 5404809 0.02987480989718612 0.22498468451205958 chr6 171115067 5146189 0.030074435233689852 0.2510883857726037 chr7 159138663 5669100 0.035623649797786726 0.41920671682682964 chr8 146364022 5097255 0.03482587407990196 0.30017857622053046 chr9 141213431 3962339 0.028059221930525857 0.33433234670073353 chr10 135534747 4210846 0.031068387208484625 0.30810587436289694 chr11 135006516 4111728 0.030455774445731196 0.3363787692743617 chr12 133851895 5551562 0.041475408323505616 0.28702463524482436 chr13 115169878 3122149 0.027109076211750436 0.22507316789721737 chr14 107349540 2736048 0.02548728201350467 0.250121220348 chr15 102531392 3053382 0.029779972166963264 0.24251202084254178 chr16 90354753 2685445 0.02972112601536302 0.26067946778187967 chr17 81195210 2492757 0.030700788876585207 0.25796620213043003 chr18 78077248 2525869 0.03235089689636602 0.4568998523731415 chr19 59128983 1981974 0.033519500918864104 0.3192612853921333 chr20 63025520 2012425 0.031930319654641486 0.24776475499142203 chr21 48129895 1188160 0.024686527988477848 0.23522382537850653 chr22 51304566 1088698 0.021220294505561163 0.19671020834180714 chrMT 16571 95019 5.734053466900006 5.08933664859412 chrX 155270560 4984017 0.032098918172253646 0.26778653841971 chrY 59373566 354871 0.005976919088875343 0.14391299108527267