BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708539.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 25,228,568 number of mapped reads = 24,342,989 (96.49%) number of supplementary alignments = 526 (0%) number of secondary alignments = 0 number of mapped bases = 1,213,940,089 bp number of sequenced bases = 1,213,835,062 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 232,830 duplication rate = 0.94% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5475 >>>>>>> ACTG content number of A's = 378,514,791 bp (31.18%) number of C's = 226,852,774 bp (18.69%) number of T's = 376,970,289 bp (31.06%) number of G's = 231,011,113 bp (19.03%) number of N's = 486,095 bp (0.04%) GC percentage = 37.72% >>>>>>> Mismatches and indels general error rate = 0.0035 number of mismatches = 4,199,821 number of insertions = 66,043 mapped reads with insertion percentage = 0.27% number of deletions = 63,673 mapped reads with deletion percentage = 0.26% homopolymer indels = 48.36% >>>>>>> Coverage mean coverageData = 0.3921X std coverageData = 0.7033X There is a 29.4% of reference with a coverageData >= 1X There is a 7.61% of reference with a coverageData >= 2X There is a 1.73% of reference with a coverageData >= 3X There is a 0.37% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.02% 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 92738041 0.3720674421108062 0.7034484080556325 chr2 243199373 112449119 0.4623742142624685 0.7472285299165109 chr3 198022430 94186899 0.4756375275265534 0.7521064293721512 chr4 191154276 102422321 0.5358097299377179 0.7959206555367891 chr5 180915260 87632831 0.48438606560883807 0.7602701132725053 chr6 171115067 82904612 0.48449627173976445 0.7638685713864368 chr7 159138663 69802956 0.4386297753425263 0.7401730987994398 chr8 146364022 67782333 0.46310788726480884 0.746115072797554 chr9 141213431 50475424 0.35744067432226045 0.679263169550294 chr10 135534747 51558978 0.3804115117431842 0.6762830842103318 chr11 135006516 53903126 0.3992631437137449 0.7161925645095393 chr12 133851895 56103370 0.4191451305190711 0.7235119823388031 chr13 115169878 51707132 0.4489640251246945 0.7532683555010996 chr14 107349540 38705656 0.36055725995658666 0.681779087046877 chr15 102531392 32228000 0.3143232464843548 0.6407092464733495 chr16 90354753 21384222 0.23666958615890413 0.5457923313013963 chr17 81195210 18883519 0.2325693720109844 0.5510163287878848 chr18 78077248 36825566 0.47165553273598987 0.7537235620409826 chr19 59128983 8217120 0.1389694120056149 0.4090761351871569 chr20 63025520 18174344 0.2883648401472927 0.6043488007213474 chr21 48129895 15708309 0.32637322395986945 0.6727952966451825 chr22 51304566 5936727 0.11571537316970969 0.3798297766452864 chrMT 16571 1113 0.06716553014302094 0.262315941770666 chrX 155270560 38698320 0.2492315349413308 0.52795824947549 chrY 59373566 5510051 0.0928031002887716 0.34424316284666406