BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472747.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 13,463,824 number of mapped reads = 13,326,702 (98.98%) number of supplementary alignments = 36,937 (0.27%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,694,692 number of mapped paired reads (second in pair) = 6,632,010 number of mapped paired reads (both in pair) = 13,238,662 number of mapped paired reads (singletons) = 88,040 number of mapped bases = 1,315,553,342 bp number of sequenced bases = 1,315,368,037 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,790,785 duplication rate = 46.77% >>>>>>> Insert size mean insert size = 23,832.0439 std insert size = 1,542,655.9938 median insert size = 266 >>>>>>> Mapping quality mean mapping quality = 55.1483 >>>>>>> ACTG content number of A's = 364,407,479 bp (27.7%) number of C's = 295,268,275 bp (22.45%) number of T's = 362,245,249 bp (27.54%) number of G's = 293,194,686 bp (22.29%) number of N's = 252,348 bp (0.02%) GC percentage = 44.74% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 8,763,085 number of insertions = 74,303 mapped reads with insertion percentage = 0.55% number of deletions = 76,008 mapped reads with deletion percentage = 0.56% homopolymer indels = 45.23% >>>>>>> Coverage mean coverageData = 0.425X std coverageData = 12.7425X There is a 3.88% of reference with a coverageData >= 1X There is a 1.62% of reference with a coverageData >= 2X There is a 0.78% of reference with a coverageData >= 3X There is a 0.59% of reference with a coverageData >= 4X There is a 0.47% of reference with a coverageData >= 5X There is a 0.43% of reference with a coverageData >= 6X There is a 0.4% of reference with a coverageData >= 7X There is a 0.38% of reference with a coverageData >= 8X There is a 0.36% of reference with a coverageData >= 9X There is a 0.35% of reference with a coverageData >= 10X There is a 0.33% of reference with a coverageData >= 11X There is a 0.32% of reference with a coverageData >= 12X There is a 0.31% of reference with a coverageData >= 13X There is a 0.3% of reference with a coverageData >= 14X There is a 0.29% of reference with a coverageData >= 15X There is a 0.28% of reference with a coverageData >= 16X There is a 0.28% of reference with a coverageData >= 17X There is a 0.27% of reference with a coverageData >= 18X There is a 0.26% of reference with a coverageData >= 19X There is a 0.26% of reference with a coverageData >= 20X There is a 0.25% of reference with a coverageData >= 21X There is a 0.25% of reference with a coverageData >= 22X There is a 0.24% of reference with a coverageData >= 23X There is a 0.24% of reference with a coverageData >= 24X There is a 0.23% of reference with a coverageData >= 25X There is a 0.23% of reference with a coverageData >= 26X There is a 0.22% of reference with a coverageData >= 27X There is a 0.22% of reference with a coverageData >= 28X There is a 0.21% of reference with a coverageData >= 29X There is a 0.21% of reference with a coverageData >= 30X There is a 0.21% of reference with a coverageData >= 31X There is a 0.2% of reference with a coverageData >= 32X There is a 0.2% of reference with a coverageData >= 33X There is a 0.2% of reference with a coverageData >= 34X There is a 0.19% of reference with a coverageData >= 35X There is a 0.19% of reference with a coverageData >= 36X There is a 0.19% of reference with a coverageData >= 37X There is a 0.18% of reference with a coverageData >= 38X There is a 0.18% of reference with a coverageData >= 39X There is a 0.18% of reference with a coverageData >= 40X There is a 0.18% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.17% of reference with a coverageData >= 43X There is a 0.17% of reference with a coverageData >= 44X There is a 0.17% of reference with a coverageData >= 45X There is a 0.16% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.16% of reference with a coverageData >= 48X There is a 0.16% of reference with a coverageData >= 49X There is a 0.16% of reference with a coverageData >= 50X There is a 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 133753470 0.5366224142727412 15.875010644592086 chr2 243199373 90066688 0.37034095478527407 14.293147806427122 chr3 198022430 115404959 0.5827873084882353 13.87265340436744 chr4 191154276 59134509 0.3093548846377886 12.197379078530352 chr5 180915260 66659308 0.368455972149613 13.686540103611271 chr6 171115067 72097158 0.42133728644713675 11.507869725386037 chr7 159138663 78468258 0.49308104341683456 15.544390471976332 chr8 146364022 63621012 0.43467657646084634 11.930164335017022 chr9 141213431 85317806 0.6041762840533207 14.80363701832547 chr10 135534747 34180511 0.2521900232713018 8.137769526823462 chr11 135006516 61495309 0.455498821997599 13.41253616569511 chr12 133851895 65512418 0.4894396003881753 12.17103719852708 chr13 115169878 25509762 0.2214968222854243 7.181696697877367 chr14 107349540 45524775 0.4240798330388747 12.243186799188571 chr15 102531392 33522376 0.3269474386927274 9.102573895175418 chr16 90354753 50190071 0.5554779282059462 13.208929689516255 chr17 81195210 42893872 0.5282808185359703 11.564077715413157 chr18 78077248 18562288 0.2377426007637974 6.797103016125208 chr19 59128983 45455146 0.7687456082239736 18.689104497880333 chr20 63025520 28118037 0.4461373265940527 10.851811606902885 chr21 48129895 7406846 0.1538928352118782 5.520471828226153 chr22 51304566 16074811 0.3133212548762229 8.831242057199832 chrMT 16571 1795 0.1083217669422485 0.4083021735393324 chrX 155270560 75392554 0.4855560126787718 13.751334388843922 chrY 59373566 1189603 0.02003590284605779 0.5730349887147059