BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094051.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 516,500 number of mapped reads = 485,731 (94.04%) number of supplementary alignments = 16,495 (3.19%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 243,675 number of mapped paired reads (second in pair) = 242,056 number of mapped paired reads (both in pair) = 482,554 number of mapped paired reads (singletons) = 3,177 number of mapped bases = 63,731,614 bp number of sequenced bases = 62,046,038 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 465,081 duplication rate = 51.69% >>>>>>> Insert size mean insert size = 494,698.0241 std insert size = 6,560,359.6663 median insert size = 163 >>>>>>> Mapping quality mean mapping quality = 41.2732 >>>>>>> ACTG content number of A's = 17,235,605 bp (27.78%) number of C's = 13,807,996 bp (22.25%) number of T's = 16,595,646 bp (26.75%) number of G's = 14,406,122 bp (23.22%) number of N's = 669 bp (0%) GC percentage = 45.47% >>>>>>> Mismatches and indels general error rate = 0.0452 number of mismatches = 2,736,273 number of insertions = 41,223 mapped reads with insertion percentage = 8.31% number of deletions = 230,710 mapped reads with deletion percentage = 44.46% homopolymer indels = 29.86% >>>>>>> Coverage mean coverageData = 0.0206X std coverageData = 5.067X There is a 0.02% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% 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 1254559 0.005033323467627388 2.2412283144460825 chr2 243199373 2821483 0.011601522508859428 3.4291926092216856 chr3 198022430 1682781 0.008497931269705154 2.965593096768289 chr4 191154276 1355921 0.007093333345051617 2.227664855100612 chr5 180915260 692617 0.003828405630348706 2.1388415107508503 chr6 171115067 1218186 0.007119104245799699 3.619945581926348 chr7 159138663 1769286 0.01111788905754474 3.606994143327423 chr8 146364022 895630 0.006119195057375507 2.9238505028218387 chr9 141213431 908456 0.0064332124328882 2.9813984438733954 chr10 135534747 1662880 0.012269030907624006 4.4229236537770324 chr11 135006516 1813278 0.013431040617328426 3.5454329599711087 chr12 133851895 1856678 0.01387113719981327 4.421271273234072 chr13 115169878 948368 0.008234514236439497 2.575628744990958 chr14 107349540 446325 0.004157679669610136 1.3979801849874445 chr15 102531392 1230461 0.012000822148206082 3.3265796719627194 chr16 90354753 612151 0.006774972867227029 2.254391373034327 chr17 81195210 1463951 0.018030016795325735 5.470407735550052 chr18 78077248 345622 0.00442666729237178 1.181967149441505 chr19 59128983 203315 0.0034384998639330564 0.826800026199157 chr20 63025520 453779 0.007199924728903466 2.5318435047276555 chr21 48129895 150588 0.0031287830567675247 0.6385263918690613 chr22 51304566 122962 0.0023967067570555027 0.602356496526871 chrMT 16571 3165234 191.0104399251705 769.9318386380664 chrX 155270560 36316587 0.23389229097904973 16.41812512349938 chrY 59373566 340516 0.005735144828592576 1.7900270989591542