BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2971289.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 9,069,122 number of mapped reads = 7,597,359 (83.77%) number of secondary alignments = 0 number of mapped bases = 299,631,670 bp number of sequenced bases = 299,600,852 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 426,550 duplication rate = 4.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.1913 >>>>>>> ACTG content number of A's = 88,041,627 bp (29.39%) number of C's = 60,060,546 bp (20.05%) number of T's = 90,079,957 bp (30.07%) number of G's = 61,401,102 bp (20.49%) number of N's = 17,620 bp (0.01%) GC percentage = 40.54% >>>>>>> Mismatches and indels general error rate = 0.003 number of mismatches = 875,905 number of insertions = 10,177 mapped reads with insertion percentage = 0.13% number of deletions = 24,770 mapped reads with deletion percentage = 0.33% homopolymer indels = 40.91% >>>>>>> Coverage mean coverageData = 0.0968X std coverageData = 0.8463X There is a 7.82% of reference with a coverageData >= 1X There is a 1.32% of reference with a coverageData >= 2X There is a 0.25% of reference with a coverageData >= 3X There is a 0.06% 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 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 23811774 0.09553345907210398 1.6343890594941641 chr2 243199373 25684113 0.10560928954368645 0.6505487921949767 chr3 198022430 20870916 0.10539672702733725 0.3861713060844271 chr4 191154276 20655915 0.10805886968492402 0.41405709844086513 chr5 180915260 19113160 0.10564703054899846 0.39598366884204805 chr6 171115067 17978366 0.10506594372545815 0.5569455878665365 chr7 159138663 16797574 0.10555306726436428 1.1950965090198238 chr8 146364022 15574662 0.10641045379307765 1.8193893382355235 chr9 141213431 12312528 0.08719091316462667 0.6360118604911175 chr10 135534747 14021517 0.10345330116711694 0.7092893040440359 chr11 135006516 13637477 0.10101347256453903 0.558983634972172 chr12 133851895 13496548 0.1008319531075746 0.4009464379655626 chr13 115169878 9993532 0.08677209851694034 0.34213713952737274 chr14 107349540 9188878 0.08559773986921602 0.4819373807112568 chr15 102531392 7991545 0.07794242177069048 0.32812954195776206 chr16 90354753 7469761 0.08267147827851402 0.42846630418988146 chr17 81195210 6787778 0.08359825659666377 0.38498917380110453 chr18 78077248 8099344 0.10373500869292934 1.234260679732623 chr19 59128983 5052231 0.08544423975633067 1.5218561228762597 chr20 63025520 5693359 0.09033418526336633 0.3866562703302783 chr21 48129895 3619029 0.07519295439975508 0.403299086268853 chr22 51304566 2796160 0.05450119196018537 0.27504520973127633 chrMT 16571 24024 1.4497616317663389 1.7141181016722056 chrX 155270560 17973930 0.11575877616465091 0.5384742561502145 chrY 59373566 987549 0.016632805919051585 0.23074988907299954