BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472441.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 = 14,277,274 number of mapped reads = 14,125,630 (98.94%) number of supplementary alignments = 48,122 (0.34%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,086,673 number of mapped paired reads (second in pair) = 7,038,957 number of mapped paired reads (both in pair) = 14,035,982 number of mapped paired reads (singletons) = 89,648 number of mapped bases = 1,384,486,383 bp number of sequenced bases = 1,384,338,180 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,190,698 duplication rate = 46.12% >>>>>>> Insert size mean insert size = 15,898.7786 std insert size = 1,255,771.6464 median insert size = 213 >>>>>>> Mapping quality mean mapping quality = 54.9318 >>>>>>> ACTG content number of A's = 373,034,582 bp (26.95%) number of C's = 321,298,410 bp (23.21%) number of T's = 371,721,615 bp (26.85%) number of G's = 318,118,860 bp (22.98%) number of N's = 164,713 bp (0.01%) GC percentage = 46.19% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 9,047,775 number of insertions = 78,927 mapped reads with insertion percentage = 0.55% number of deletions = 62,922 mapped reads with deletion percentage = 0.44% homopolymer indels = 45.1% >>>>>>> Coverage mean coverageData = 0.4472X std coverageData = 12.8391X There is a 4.03% of reference with a coverageData >= 1X There is a 1.74% of reference with a coverageData >= 2X There is a 0.76% 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 0.34% of reference with a coverageData >= 11X There is a 0.33% of reference with a coverageData >= 12X There is a 0.32% of reference with a coverageData >= 13X There is a 0.31% of reference with a coverageData >= 14X There is a 0.3% of reference with a coverageData >= 15X There is a 0.3% of reference with a coverageData >= 16X There is a 0.29% of reference with a coverageData >= 17X There is a 0.28% of reference with a coverageData >= 18X There is a 0.28% of reference with a coverageData >= 19X There is a 0.27% of reference with a coverageData >= 20X There is a 0.26% of reference with a coverageData >= 21X There is a 0.26% of reference with a coverageData >= 22X There is a 0.25% of reference with a coverageData >= 23X There is a 0.25% of reference with a coverageData >= 24X There is a 0.24% of reference with a coverageData >= 25X There is a 0.24% of reference with a coverageData >= 26X There is a 0.23% of reference with a coverageData >= 27X There is a 0.23% of reference with a coverageData >= 28X There is a 0.23% of reference with a coverageData >= 29X There is a 0.22% of reference with a coverageData >= 30X There is a 0.22% of reference with a coverageData >= 31X There is a 0.22% of reference with a coverageData >= 32X There is a 0.21% of reference with a coverageData >= 33X There is a 0.21% of reference with a coverageData >= 34X There is a 0.21% of reference with a coverageData >= 35X There is a 0.2% of reference with a coverageData >= 36X There is a 0.2% of reference with a coverageData >= 37X There is a 0.2% of reference with a coverageData >= 38X There is a 0.19% of reference with a coverageData >= 39X There is a 0.19% of reference with a coverageData >= 40X There is a 0.19% of reference with a coverageData >= 41X There is a 0.19% of reference with a coverageData >= 42X There is a 0.18% of reference with a coverageData >= 43X There is a 0.18% of reference with a coverageData >= 44X There is a 0.18% of reference with a coverageData >= 45X There is a 0.18% of reference with a coverageData >= 46X There is a 0.17% of reference with a coverageData >= 47X There is a 0.17% of reference with a coverageData >= 48X There is a 0.17% of reference with a coverageData >= 49X There is a 0.17% of reference with a coverageData >= 50X There is a 0.17% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 130547551 0.523760183530295 15.814749664607673 chr2 243199373 116459934 0.47886609477401904 13.24086333348508 chr3 198022430 156679309 0.7912200097736403 17.87799153324832 chr4 191154276 40637730 0.21259126842655615 9.19676649214561 chr5 180915260 47352478 0.26173844041680067 7.73657153172989 chr6 171115067 113794079 0.6650149574496558 15.185882933273362 chr7 159138663 82599583 0.5190415794809085 15.730775064083485 chr8 146364022 111399693 0.7611139095371402 18.976394492878757 chr9 141213431 36479812 0.25833103651450834 7.428181549750908 chr10 135534747 27513502 0.20299961898331503 6.599732115690511 chr11 135006516 42009681 0.31116780318958825 9.225198112367966 chr12 133851895 73795489 0.5513219592445815 13.297336217219955 chr13 115169878 43568585 0.3782984384163366 11.657565820579732 chr14 107349540 30507211 0.28418576362786463 8.891214164953794 chr15 102531392 26120699 0.25475806473006823 8.380035148754416 chr16 90354753 64449750 0.7132967316063605 16.84026233577659 chr17 81195210 45879055 0.5650463247770404 11.855247939205217 chr18 78077248 5177402 0.06631127674991824 2.0937251783165185 chr19 59128983 35079019 0.5932626813486712 12.866363417742187 chr20 63025520 62473044 0.9912340905715653 23.449999612646582 chr21 48129895 8023361 0.1667022336117708 7.457688393326104 chr22 51304566 12742768 0.24837493021576287 6.763769473163724 chrMT 16571 3376 0.20372940679500331 0.5305357658262407 chrX 155270560 70790314 0.4559158799968262 10.232046632123124 chrY 59373566 402958 0.006786824965170527 0.9081175100246215