BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231739.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 = 2,041,067 number of mapped reads = 1,237,606 (60.64%) number of supplementary alignments = 11,978 (0.59%) number of secondary alignments = 0 number of mapped bases = 81,520,090 bp number of sequenced bases = 81,465,242 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 204,567 duplication rate = 11.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9038 >>>>>>> ACTG content number of A's = 23,315,139 bp (28.62%) number of C's = 14,063,534 bp (17.26%) number of T's = 27,059,287 bp (33.22%) number of G's = 17,025,073 bp (20.9%) number of N's = 2,209 bp (0%) GC percentage = 38.16% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 738,747 number of insertions = 7,696 mapped reads with insertion percentage = 0.61% number of deletions = 31,409 mapped reads with deletion percentage = 2.49% homopolymer indels = 44.52% >>>>>>> Coverage mean coverageData = 0.0263X std coverageData = 0.6543X There is a 1.28% of reference with a coverageData >= 1X There is a 0.57% of reference with a coverageData >= 2X There is a 0.3% of reference with a coverageData >= 3X There is a 0.17% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 7960796 0.031938921428003184 0.5168422251534655 chr2 243199373 2948618 0.0121242829026537 0.31157718900463305 chr3 198022430 6756384 0.03411928638589073 0.33952884522000754 chr4 191154276 2279146 0.01192307097540418 0.19853804471667216 chr5 180915260 2550184 0.014096013791208105 0.2139317930105481 chr6 171115067 2399018 0.014019910940981019 0.22271898610040466 chr7 159138663 15751635 0.09898056640076208 1.6723779379753823 chr8 146364022 5317886 0.03633328687838327 1.8370836855454613 chr9 141213431 3139294 0.022230845733080446 0.35172179900690975 chr10 135534747 1748856 0.01290337746378794 0.2938846635543674 chr11 135006516 1878398 0.013913387706412629 0.28859954155127626 chr12 133851895 1571097 0.011737577566608228 0.19066896388429347 chr13 115169878 7837311 0.06805000696449466 0.496723787118146 chr14 107349540 2776101 0.02586039027274826 0.3306134048043288 chr15 102531392 1199422 0.011698095350153833 0.1991269942104816 chr16 90354753 2747553 0.030408505460692258 0.34393036803839605 chr17 81195210 1602761 0.01973960040253606 0.24922554426758453 chr18 78077248 1568852 0.02009358731496274 0.8920877526091128 chr19 59128983 2358213 0.03988252258625859 0.393924666609928 chr20 63025520 893738 0.014180573202728038 0.21201562619094994 chr21 48129895 1322117 0.02746976697123482 0.305999319131677 chr22 51304566 777387 0.015152394038378572 0.19860913889718285 chrMT 16571 786603 47.46865005129443 27.11187278595366 chrX 155270560 3035116 0.01954727283781291 0.2703836367613536 chrY 59373566 313604 0.005281879144668522 0.12440837187981997