BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004142.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 = 1,779,050 number of mapped reads = 1,366,424 (76.81%) number of supplementary alignments = 10,174 (0.57%) number of secondary alignments = 0 number of mapped bases = 87,106,086 bp number of sequenced bases = 87,062,807 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 191,102 duplication rate = 10.82% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3336 >>>>>>> ACTG content number of A's = 22,984,051 bp (26.4%) number of C's = 16,616,511 bp (19.09%) number of T's = 27,083,177 bp (31.11%) number of G's = 20,367,111 bp (23.39%) number of N's = 11,957 bp (0.01%) GC percentage = 42.48% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 851,838 number of insertions = 6,970 mapped reads with insertion percentage = 0.5% number of deletions = 26,351 mapped reads with deletion percentage = 1.91% homopolymer indels = 47.51% >>>>>>> Coverage mean coverageData = 0.0281X std coverageData = 0.3306X There is a 1.53% of reference with a coverageData >= 1X There is a 0.64% of reference with a coverageData >= 2X There is a 0.31% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% 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 8544853 0.03428217336317088 0.3897538732257211 chr2 243199373 9061608 0.037259997376720214 0.4486958223323175 chr3 198022430 5677847 0.028672746819640584 0.27857829438112075 chr4 191154276 5750878 0.03008500840441571 0.28641431246933274 chr5 180915260 4821055 0.026648139023761733 0.26967372548242435 chr6 171115067 5225869 0.030540086806032107 0.31764073028435763 chr7 159138663 4475897 0.028125767275046166 0.33423517073817843 chr8 146364022 5241458 0.0358111093722199 0.4440926184404611 chr9 141213431 3201247 0.022669564625194896 0.29617662833360553 chr10 135534747 3874776 0.028588801659842993 0.2982228180771032 chr11 135006516 3406882 0.025234944956286406 0.31496900327935684 chr12 133851895 3587642 0.026803072156729644 0.2732080193279456 chr13 115169878 2121348 0.01841929536471333 0.22028878710960087 chr14 107349540 1841370 0.017153031116854345 0.23472596729555267 chr15 102531392 1878856 0.018324690256814224 0.22174636137565318 chr16 90354753 2951340 0.032663915311682605 0.3066969348973659 chr17 81195210 2201041 0.02710801536198995 0.28169585090703114 chr18 78077248 2673565 0.03424256193046148 0.5113875904296673 chr19 59128983 1705336 0.028840949285395285 0.3510916098412718 chr20 63025520 1875500 0.02975778700437537 0.2939926901285905 chr21 48129895 1555124 0.03231097844697147 0.30554827993718015 chr22 51304566 1279737 0.02494392019610886 0.26292387185647137 chrMT 16571 343388 20.72222557479935 15.881197383101062 chrX 155270560 3582838 0.023074805681128477 0.2654956816015861 chrY 59373566 226631 0.0038170353453252245 0.09820366698268583