BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085087.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,369,219 number of mapped reads = 1,050,694 (76.74%) number of supplementary alignments = 6,276 (0.46%) number of secondary alignments = 0 number of mapped bases = 68,540,513 bp number of sequenced bases = 68,517,340 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 21,403 duplication rate = 1.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2496 >>>>>>> ACTG content number of A's = 20,387,882 bp (29.76%) number of C's = 12,605,860 bp (18.4%) number of T's = 20,390,934 bp (29.76%) number of G's = 15,131,228 bp (22.08%) number of N's = 1,436 bp (0%) GC percentage = 40.48% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 635,097 number of insertions = 5,687 mapped reads with insertion percentage = 0.54% number of deletions = 14,250 mapped reads with deletion percentage = 1.34% homopolymer indels = 46.32% >>>>>>> Coverage mean coverageData = 0.0221X std coverageData = 0.1956X There is a 2.06% of reference with a coverageData >= 1X There is a 0.11% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 5572346 0.022356397659687274 0.2612101137729657 chr2 243199373 6010246 0.024713246279627538 0.20939083225920543 chr3 198022430 4598057 0.02321987968736673 0.1601626585028223 chr4 191154276 4673558 0.02444914180209079 0.1675544985110268 chr5 180915260 4318064 0.023867881570631466 0.1623497363143516 chr6 171115067 4151660 0.02426238713391615 0.1800805185691757 chr7 159138663 3553337 0.022328558836767404 0.18339205686978263 chr8 146364022 3635869 0.024841275542428043 0.34852154782355965 chr9 141213431 2817024 0.01994869737284409 0.18075648861788654 chr10 135534747 2970843 0.02191941967472002 0.1906797087805624 chr11 135006516 3094707 0.02292264915568964 0.1845450070167649 chr12 133851895 3025405 0.022602631064730164 0.1580385869289256 chr13 115169878 2245392 0.019496347821085648 0.14615350647879263 chr14 107349540 2150988 0.020037235371479 0.15309295554267366 chr15 102531392 1940207 0.018923053341556115 0.14451210060075312 chr16 90354753 1710747 0.018933669156286664 0.15165646266093655 chr17 81195210 1801734 0.022190151364840364 0.1673734665366595 chr18 78077248 1765392 0.022610837922975975 0.2940022987428325 chr19 59128983 1023164 0.017303933673271533 0.1891907753703191 chr20 63025520 1442684 0.022890473573244616 0.16176885348388303 chr21 48129895 925883 0.0192371705776628 0.15263660109160548 chr22 51304566 667467 0.013009894674871628 0.11922361274207596 chrMT 16571 10897 0.6575945929636111 0.9138279956855717 chrX 155270560 4258579 0.0274268283697824 0.18335813109707583 chrY 59373566 176263 0.002968711699074972 0.07390807245109912