BamQC report ----------------------------------- >>>>>>> Input bam file = SRR054618.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 14,057,382 number of mapped reads = 11,572,882 (82.33%) number of supplementary alignments = 335 (0%) number of secondary alignments = 0 number of mapped bases = 547,416,978 bp number of sequenced bases = 547,306,023 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,699,140 duplication rate = 16.95% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6514 >>>>>>> ACTG content number of A's = 158,291,004 bp (28.92%) number of C's = 107,306,353 bp (19.61%) number of T's = 160,168,353 bp (29.26%) number of G's = 120,921,321 bp (22.09%) number of N's = 618,992 bp (0.11%) GC percentage = 41.7% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 3,219,371 number of insertions = 21,303 mapped reads with insertion percentage = 0.18% number of deletions = 73,346 mapped reads with deletion percentage = 0.63% homopolymer indels = 46.39% >>>>>>> Coverage mean coverageData = 0.1768X std coverageData = 1.1875X There is a 7.22% of reference with a coverageData >= 1X There is a 3.3% of reference with a coverageData >= 2X There is a 1.92% of reference with a coverageData >= 3X There is a 1.23% of reference with a coverageData >= 4X There is a 0.84% of reference with a coverageData >= 5X There is a 0.6% of reference with a coverageData >= 6X There is a 0.45% of reference with a coverageData >= 7X There is a 0.34% of reference with a coverageData >= 8X There is a 0.27% of reference with a coverageData >= 9X There is a 0.21% of reference with a coverageData >= 10X There is a 0.17% of reference with a coverageData >= 11X There is a 0.14% of reference with a coverageData >= 12X There is a 0.12% of reference with a coverageData >= 13X There is a 0.1% of reference with a coverageData >= 14X There is a 0.08% of reference with a coverageData >= 15X There is a 0.07% of reference with a coverageData >= 16X There is a 0.06% of reference with a coverageData >= 17X There is a 0.05% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% 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 49949253 0.20039770733409729 1.3784004756635786 chr2 243199373 44796839 0.18419800366837294 1.364727466053423 chr3 198022430 38197575 0.19289519374143627 1.1344144462065702 chr4 191154276 34033448 0.17804178233501824 1.1477554341437832 chr5 180915260 26845149 0.14838521084401615 0.9371522626889294 chr6 171115067 26962548 0.15756968964048035 1.062802904519068 chr7 159138663 35167857 0.22098876751276966 1.471547632556534 chr8 146364022 31214322 0.21326499213037478 1.2690010080908998 chr9 141213431 26681704 0.18894593673600354 1.2295301633256408 chr10 135534747 22423541 0.16544496150496374 1.096662272280913 chr11 135006516 24250382 0.17962378941769003 1.1876599095901994 chr12 133851895 20042212 0.14973424171544228 0.9466698510374473 chr13 115169878 17178673 0.14915942691195697 0.9684376833797373 chr14 107349540 12546422 0.11687448311376089 0.9830105033086489 chr15 102531392 14496060 0.1413816755750278 0.9125940218443728 chr16 90354753 15916788 0.17615883472117952 1.2036874737630836 chr17 81195210 11088956 0.13657155391309414 0.8933742614623456 chr18 78077248 20258343 0.25946538228396576 1.5973029342394405 chr19 59128983 11176750 0.18902320711316817 1.2500114455311928 chr20 63025520 9695936 0.15384142804375117 1.0698688253489907 chr21 48129895 6577225 0.13665571055162284 1.186552153063112 chr22 51304566 5685192 0.11081259317153175 0.7916796378074505 chrMT 16571 22851 1.3789753183271982 3.458067061913554 chrX 155270560 40711392 0.26219646531834495 1.4660839052454981 chrY 59373566 1497560 0.025222672325256663 0.5368251845663172