BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6003999.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 = 3,449,033 number of mapped reads = 3,150,053 (91.33%) number of supplementary alignments = 22,101 (0.64%) number of secondary alignments = 0 number of mapped bases = 207,559,045 bp number of sequenced bases = 207,472,484 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 127,512 duplication rate = 2.81% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.2225 >>>>>>> ACTG content number of A's = 55,694,254 bp (26.84%) number of C's = 40,117,005 bp (19.34%) number of T's = 62,834,868 bp (30.29%) number of G's = 48,784,951 bp (23.51%) number of N's = 41,406 bp (0.02%) GC percentage = 42.85% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,692,418 number of insertions = 16,704 mapped reads with insertion percentage = 0.52% number of deletions = 52,228 mapped reads with deletion percentage = 1.64% homopolymer indels = 45.69% >>>>>>> Coverage mean coverageData = 0.067X std coverageData = 0.579X There is a 5.55% of reference with a coverageData >= 1X There is a 0.81% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.04% 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 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 15577857 0.06249876906023837 1.07809152593722 chr2 243199373 13428612 0.05521647459181566 0.7777598772842864 chr3 198022430 8269205 0.04175893104634662 0.23796135943818633 chr4 191154276 15006910 0.0785067973054393 0.3573927069048319 chr5 180915260 13283430 0.07342349119692833 0.31793694126134675 chr6 171115067 14492482 0.08469436534189008 0.39427302546351395 chr7 159138663 11604299 0.07291941996521611 0.7710080302650898 chr8 146364022 14937841 0.10205951432518028 0.5534280289180894 chr9 141213431 9006403 0.06377865714487173 0.5694359702816391 chr10 135534747 11131757 0.08213212660514281 0.4931114745073371 chr11 135006516 10536776 0.07804642555178595 0.5212267279318767 chr12 133851895 9007997 0.0672982403424322 0.31186691162839497 chr13 115169878 8387641 0.07282842654396143 0.3140398483899772 chr14 107349540 4843725 0.045121059671052156 0.33422910929936483 chr15 102531392 3042122 0.029670152142282434 0.2213594847209638 chr16 90354753 5138098 0.05686582973670461 0.3714907728294252 chr17 81195210 4538703 0.05589865461275363 0.3077102721376481 chr18 78077248 6580121 0.0842770610972354 1.2538244995714196 chr19 59128983 5544364 0.09376728160536771 0.7826019904058168 chr20 63025520 6146980 0.09753160307126384 0.39479312778830056 chr21 48129895 3399325 0.07062814078443345 0.3597165065768157 chr22 51304566 2699777 0.05262254825428209 0.26588335790354856 chrMT 16571 99180 5.985154788485909 4.778224997339315 chrX 155270560 10340277 0.0665952193384245 0.37060370698387224 chrY 59373566 515163 0.008676639028216698 0.1876773240504326