BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714131.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 655,936 number of mapped reads = 509,238 (77.64%) number of supplementary alignments = 77,591 (11.83%) number of secondary alignments = 0 number of mapped bases = 58,211,621 bp number of sequenced bases = 57,606,588 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 575,902 duplication rate = 34.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 23.6567 >>>>>>> ACTG content number of A's = 11,283,779 bp (19.59%) number of C's = 10,533,751 bp (18.29%) number of T's = 11,872,599 bp (20.61%) number of G's = 23,916,108 bp (41.52%) number of N's = 351 bp (0%) GC percentage = 59.8% >>>>>>> Mismatches and indels general error rate = 0.0299 number of mismatches = 1,655,204 number of insertions = 44,615 mapped reads with insertion percentage = 8.53% number of deletions = 65,553 mapped reads with deletion percentage = 12.34% homopolymer indels = 62.49% >>>>>>> Coverage mean coverageData = 0.0188X std coverageData = 62.35X There is a 0.01% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 39354701 0.15789208806023397 215.5286038307699 chr2 243199373 7769395 0.03194660785576943 24.944659134263226 chr3 198022430 1426601 0.007204239438936286 7.124190626475945 chr4 191154276 100166 5.240060651324379E-4 0.2328958032347479 chr5 180915260 89362 4.939439602828418E-4 0.10604839415923668 chr6 171115067 7482507 0.043727926074446734 41.4503098501758 chr7 159138663 102048 6.41252088438119E-4 0.2847039928062281 chr8 146364022 101078 6.905932114929173E-4 0.26688483778211447 chr9 141213431 69513 4.922548762376575E-4 0.12322384644019377 chr10 135534747 56621 4.177600302009639E-4 0.2248096283776821 chr11 135006516 115341 8.543365418006935E-4 0.6899452494654948 chr12 133851895 64985 4.8549929009223216E-4 0.18454952788049886 chr13 115169878 27992 2.4304966269044758E-4 0.047600361341950004 chr14 107349540 101809 9.483878552250899E-4 0.6163188222217706 chr15 102531392 67145 6.548726072108725E-4 0.3834689716592104 chr16 90354753 639347 0.007075964227360568 2.7457213414679704 chr17 81195210 71567 8.814189901103772E-4 0.16216039198949592 chr18 78077248 25766 3.300065084261167E-4 0.06095737873970106 chr19 59128983 60065 0.001015830087928284 0.18669320064684242 chr20 63025520 30480 4.836136219106165E-4 0.17259845085251516 chr21 48129895 23202 4.82070447068293E-4 0.22829845621598743 chr22 51304566 7323 1.427358336877852E-4 0.02593660523583339 chrMT 16571 20232 1.220928127451572 10.418271209159354 chrX 155270560 395506 0.002547205342725627 0.3593524709199489 chrY 59373566 8869 1.493762392509825E-4 0.03550691246996601