BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234035.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 = 1,102,861 number of mapped reads = 824,320 (74.74%) number of supplementary alignments = 5,130 (0.47%) number of secondary alignments = 0 number of mapped bases = 53,981,859 bp number of sequenced bases = 53,952,298 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 29,460 duplication rate = 3.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4497 >>>>>>> ACTG content number of A's = 15,007,398 bp (27.82%) number of C's = 9,373,086 bp (17.37%) number of T's = 17,804,356 bp (33%) number of G's = 11,756,241 bp (21.79%) number of N's = 11,217 bp (0.02%) GC percentage = 39.16% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 439,190 number of insertions = 4,379 mapped reads with insertion percentage = 0.53% number of deletions = 16,953 mapped reads with deletion percentage = 2.03% homopolymer indels = 45.17% >>>>>>> Coverage mean coverageData = 0.0174X std coverageData = 0.1826X There is a 1.52% of reference with a coverageData >= 1X There is a 0.17% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% 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 5277947 0.02117526118420383 0.24850124688436734 chr2 243199373 4253378 0.017489263839508336 0.20087924048438408 chr3 198022430 4009960 0.020250029251736787 0.16095038636652004 chr4 191154276 3155114 0.016505589443366678 0.14644797976740984 chr5 180915260 2910006 0.01608491179793236 0.14205749734934212 chr6 171115067 3053498 0.017844705633081392 0.15981724795833085 chr7 159138663 4075174 0.02560769283326202 0.24479943828829906 chr8 146364022 2054760 0.014038695930342772 0.2690684366146376 chr9 141213431 2955040 0.020926054831144212 0.1793501758739684 chr10 135534747 2850813 0.02103381651643914 0.18418864535128526 chr11 135006516 2638737 0.01954525661561402 0.1750953016782278 chr12 133851895 1161583 0.008678121441612762 0.10520365068863724 chr13 115169878 3654760 0.0317336447990333 0.20101201113986691 chr14 107349540 3084439 0.028732670861933828 0.19407379669677383 chr15 102531392 348548 0.0033994271725092742 0.06748011276390072 chr16 90354753 1994874 0.022078240864650475 0.17249311316223145 chr17 81195210 892067 0.010986694904785639 0.11996744255809311 chr18 78077248 572666 0.007334607900114512 0.25627638550544546 chr19 59128983 928159 0.015697192018337268 0.1930478831833054 chr20 63025520 1317869 0.020910085311473828 0.16302266189898013 chr21 48129895 634345 0.013179854225736415 0.1308412750936554 chr22 51304566 419177 0.008170364407721528 0.09929833938614918 chrMT 16571 25504 1.5390742864039588 1.8872774542601725 chrX 155270560 1609897 0.010368333829671252 0.11720167012308355 chrY 59373566 103544 0.0017439410662987633 0.05118991377583423