BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231841.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 = 19,070,718 number of mapped reads = 16,520,590 (86.63%) number of supplementary alignments = 213,137 (1.12%) number of secondary alignments = 0 number of mapped bases = 1,086,255,233 bp number of sequenced bases = 1,085,865,565 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,466,131 duplication rate = 11.9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.1736 >>>>>>> ACTG content number of A's = 314,652,215 bp (28.98%) number of C's = 213,653,574 bp (19.68%) number of T's = 320,223,445 bp (29.49%) number of G's = 237,253,498 bp (21.85%) number of N's = 82,833 bp (0.01%) GC percentage = 41.53% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 5,942,872 number of insertions = 70,472 mapped reads with insertion percentage = 0.42% number of deletions = 233,001 mapped reads with deletion percentage = 1.4% homopolymer indels = 47.26% >>>>>>> Coverage mean coverageData = 0.3509X std coverageData = 17.0648X There is a 9.55% of reference with a coverageData >= 1X There is a 6.49% of reference with a coverageData >= 2X There is a 4.75% of reference with a coverageData >= 3X There is a 3.51% of reference with a coverageData >= 4X There is a 2.58% of reference with a coverageData >= 5X There is a 1.89% of reference with a coverageData >= 6X There is a 1.38% of reference with a coverageData >= 7X There is a 1.01% of reference with a coverageData >= 8X There is a 0.74% of reference with a coverageData >= 9X There is a 0.55% of reference with a coverageData >= 10X There is a 0.41% of reference with a coverageData >= 11X There is a 0.31% of reference with a coverageData >= 12X There is a 0.24% of reference with a coverageData >= 13X There is a 0.18% of reference with a coverageData >= 14X There is a 0.14% of reference with a coverageData >= 15X There is a 0.11% of reference with a coverageData >= 16X There is a 0.09% of reference with a coverageData >= 17X There is a 0.07% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% 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 131689315 0.5283409705125669 4.39030618118804 chr2 243199373 71462005 0.2938412386449697 60.24880553362809 chr3 198022430 137890498 0.6963377734532397 2.2501633515903916 chr4 191154276 18958071 0.09917680837021925 1.079971267716931 chr5 180915260 72067810 0.39835119491854915 1.6014567105854418 chr6 171115067 68070804 0.3978071901757196 2.5194131700909552 chr7 159138663 135103490 0.8489671048700466 6.441768185081606 chr8 146364022 54638024 0.37330228599484644 1.858759252184329 chr9 141213431 55121485 0.3903416594983802 1.8824117115003511 chr10 135534747 38173455 0.2816506899149633 2.904400969184216 chr11 135006516 4594963 0.034035120201161256 0.6398951133130736 chr12 133851895 48255121 0.36051130243617396 1.4859897487270661 chr13 115169878 9160888 0.07954239562535614 0.7007918231581929 chr14 107349540 24860014 0.23158007011487894 1.2540153902444708 chr15 102531392 41002206 0.39989904750342214 1.5915290655697376 chr16 90354753 19877622 0.2199953111487118 1.1463384716559022 chr17 81195210 19203069 0.23650494899883873 1.1977844729239573 chr18 78077248 5279457 0.06761837968469381 0.9120313606025559 chr19 59128983 30141537 0.5097590973279551 2.511396316212397 chr20 63025520 29998938 0.47598080904370166 1.7596705869135962 chr21 48129895 6435136 0.13370351213107778 0.9586555967329831 chr22 51304566 2751699 0.053634582933612576 0.519954158795431 chrMT 16571 365612 22.063363707682097 16.244471783005064 chrX 155270560 58962632 0.37974122074397104 1.6672452398328579 chrY 59373566 2191382 0.03690837771138759 0.665800522511977