BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714073.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 = 455,242 number of mapped reads = 223,783 (49.16%) number of supplementary alignments = 2,766 (0.61%) number of secondary alignments = 0 number of mapped bases = 25,766,645 bp number of sequenced bases = 25,207,884 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 213,891 duplication rate = 32.88% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 36.0216 >>>>>>> ACTG content number of A's = 8,085,402 bp (32.07%) number of C's = 4,393,184 bp (17.43%) number of T's = 6,595,043 bp (26.16%) number of G's = 6,134,054 bp (24.33%) number of N's = 201 bp (0%) GC percentage = 41.76% >>>>>>> Mismatches and indels general error rate = 0.0409 number of mismatches = 1,024,276 number of insertions = 8,488 mapped reads with insertion percentage = 3.52% number of deletions = 58,602 mapped reads with deletion percentage = 25.13% homopolymer indels = 16.49% >>>>>>> Coverage mean coverageData = 0.0083X std coverageData = 27.1484X 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 269449 0.0010810364239774552 0.30660199019456164 chr2 243199373 1535615 0.006314222693329066 5.126882347462779 chr3 198022430 170735 8.622003073086215E-4 0.209970430773011 chr4 191154276 176834 9.250852437117337E-4 0.22539536862831241 chr5 180915260 159211 8.800307945277806E-4 0.22491451596432654 chr6 171115067 223917 0.0013085755914176746 0.3474215271166042 chr7 159138663 126519 7.950236455109592E-4 0.21551793459998653 chr8 146364022 228225 0.0015592971338270548 0.35993022757585885 chr9 141213431 110505 7.825388790390625E-4 0.16523047435544536 chr10 135534747 140445 0.0010362287391881876 0.24197415955544224 chr11 135006516 133449 9.884634012776094E-4 0.20594832279550365 chr12 133851895 111930 8.362227520200591E-4 0.1847726619709929 chr13 115169878 122456 0.0010632641288375769 0.345361342335492 chr14 107349540 103588 9.649598871126975E-4 0.22033373991190258 chr15 102531392 88903 8.670807863410261E-4 0.18738622180668002 chr16 90354753 66856 7.399278707562844E-4 0.1410313818423775 chr17 81195210 54488 6.71074069517155E-4 0.15790768706578037 chr18 78077248 61416 7.866055934758356E-4 0.1814888583109269 chr19 59128983 55006 9.302713696259582E-4 0.17546833311257928 chr20 63025520 84605 0.001342392732340804 0.36472547284610446 chr21 48129895 20116870 0.4179703695592937 217.40862763834195 chr22 51304566 160922 0.003136601915704735 0.47399120996924093 chrMT 16571 41362 2.4960473115684025 16.595624532656892 chrX 155270560 1415328 0.009115237299330923 0.9334801163421168 chrY 59373566 8011 1.349253639237367E-4 0.0360312843292733