BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230340.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 = 3,191,067 number of mapped reads = 2,701,795 (84.67%) number of supplementary alignments = 19,261 (0.6%) number of secondary alignments = 0 number of mapped bases = 176,503,923 bp number of sequenced bases = 176,419,340 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 115,813 duplication rate = 2.98% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0034 >>>>>>> ACTG content number of A's = 47,737,036 bp (27.06%) number of C's = 30,503,555 bp (17.29%) number of T's = 58,020,792 bp (32.89%) number of G's = 39,822,010 bp (22.57%) number of N's = 335,947 bp (0.19%) GC percentage = 39.86% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 1,654,616 number of insertions = 15,980 mapped reads with insertion percentage = 0.59% number of deletions = 51,337 mapped reads with deletion percentage = 1.88% homopolymer indels = 48.28% >>>>>>> Coverage mean coverageData = 0.057X std coverageData = 0.5745X There is a 4.93% of reference with a coverageData >= 1X There is a 0.54% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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% 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 14348747 0.05756754764514709 1.180119144678508 chr2 243199373 15312026 0.06296079554448522 0.5470360234051338 chr3 198022430 12641278 0.06383760667920296 0.28011159226063836 chr4 191154276 12555638 0.06568327040719717 0.3192037728108419 chr5 180915260 11217044 0.062001646516717274 0.2805506843033305 chr6 171115067 10111171 0.059089893001649005 0.38640746959234606 chr7 159138663 8412735 0.05286418046631446 0.7649154778094376 chr8 146364022 9388018 0.06414156888910856 0.9831973791903363 chr9 141213431 7211194 0.051065921626109345 0.5088846746820256 chr10 135534747 7866349 0.05803935281629293 0.43767864670658413 chr11 135006516 8056698 0.05967636406527223 0.5377247811248909 chr12 133851895 7995911 0.059737002602764794 0.2817405677522327 chr13 115169878 5570937 0.04837147609030201 0.24273774207028892 chr14 107349540 5146636 0.04794278578184871 0.2723349993568408 chr15 102531392 4807421 0.046887308425501525 0.24269320953902912 chr16 90354753 4788228 0.05299364826994768 0.31414496228683036 chr17 81195210 5087598 0.06265884403772094 0.3378778044053664 chr18 78077248 4657659 0.0596544975560614 1.0095855834564376 chr19 59128983 3095861 0.052357758292578785 0.6944459929987503 chr20 63025520 3404771 0.054022100888655895 0.2815937740599047 chr21 48129895 2300597 0.047799751069475635 0.2798278171779671 chr22 51304566 1728671 0.03369429145936056 0.2017224826841312 chrMT 16571 86488 5.2192384285800495 3.8981059267204405 chrX 155270560 10238822 0.06594181150631517 0.3515304776418007 chrY 59373566 473425 0.007973666260840725 0.1856316476327062