BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708517.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 = 3,123,733 number of mapped reads = 2,148,311 (68.77%) number of supplementary alignments = 414 (0.01%) number of secondary alignments = 0 number of mapped bases = 102,939,297 bp number of sequenced bases = 102,920,632 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 110,836 duplication rate = 4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.2832 >>>>>>> ACTG content number of A's = 29,824,862 bp (28.98%) number of C's = 18,951,391 bp (18.41%) number of T's = 33,133,847 bp (32.19%) number of G's = 21,009,130 bp (20.41%) number of N's = 1,402 bp (0%) GC percentage = 38.83% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 496,526 number of insertions = 4,860 mapped reads with insertion percentage = 0.23% number of deletions = 12,341 mapped reads with deletion percentage = 0.57% homopolymer indels = 49% >>>>>>> Coverage mean coverageData = 0.0333X std coverageData = 0.3594X There is a 2.78% of reference with a coverageData >= 1X There is a 0.4% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 8553461 0.03431670888394697 0.6750516532192994 chr2 243199373 9350897 0.03844951113422484 0.3014030127438125 chr3 198022430 7482875 0.03778801724632912 0.22894557596611317 chr4 191154276 6839383 0.03577938795363385 0.22547824907603217 chr5 180915260 6606940 0.03651952853507216 0.2251849547044788 chr6 171115067 6474508 0.037837159015342584 0.27370521639117945 chr7 159138663 5717129 0.03592545577689062 0.3966596479129082 chr8 146364022 5386947 0.03680513097679155 0.7911269015319228 chr9 141213431 4372193 0.030961594580900736 0.240374306594355 chr10 135534747 4825760 0.03560533447559392 0.28307531859920504 chr11 135006516 4720055 0.034961682886476386 0.3173024079772587 chr12 133851895 4757385 0.03554215650066067 0.2232362999012821 chr13 115169878 3328621 0.028901836641695496 0.19978253762062667 chr14 107349540 3108655 0.028958251707459574 0.20396545485013812 chr15 102531392 3031549 0.02956703250454261 0.19973857019306504 chr16 90354753 2613644 0.028926469424358895 0.20449655106195863 chr17 81195210 2568176 0.031629649088905615 0.2510155106031674 chr18 78077248 2944565 0.03771348344654771 0.42067575983623334 chr19 59128983 1752307 0.029635331289225793 0.4589661085785905 chr20 63025520 2043084 0.03241677339591962 0.2105097958117307 chr21 48129895 1444068 0.030003556001940167 0.23158725018507564 chr22 51304566 1076887 0.020990081077773858 0.1876853136380283 chrMT 16571 208046 12.554824693742079 9.503090434919962 chrX 155270560 3053267 0.0196641720104571 0.18748267597922152 chrY 59373566 678895 0.011434297208963329 0.131659330178717