BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231784.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,444,448 number of mapped reads = 2,162,664 (88.47%) number of supplementary alignments = 15,228 (0.62%) number of secondary alignments = 0 number of mapped bases = 137,991,099 bp number of sequenced bases = 137,939,059 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 128,482 duplication rate = 2.54% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.4136 >>>>>>> ACTG content number of A's = 40,045,958 bp (29.03%) number of C's = 27,101,421 bp (19.65%) number of T's = 38,219,526 bp (27.71%) number of G's = 32,561,425 bp (23.61%) number of N's = 10,729 bp (0.01%) GC percentage = 43.25% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 893,284 number of insertions = 10,051 mapped reads with insertion percentage = 0.46% number of deletions = 30,923 mapped reads with deletion percentage = 1.41% homopolymer indels = 43.63% >>>>>>> Coverage mean coverageData = 0.0446X std coverageData = 7.0042X There is a 3.81% of reference with a coverageData >= 1X There is a 0.36% of reference with a coverageData >= 2X There is a 0.05% 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% 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 14952833 0.05999115645132134 1.1186492336945242 chr2 243199373 13390189 0.055058484875287896 24.93447955546476 chr3 198022430 12334764 0.06228973152182811 0.2751467405183003 chr4 191154276 5400092 0.0282499147442561 0.20478696002825228 chr5 180915260 5468171 0.03022504016521326 0.19565333500057905 chr6 171115067 9567090 0.05591027235491776 0.3606859964169644 chr7 159138663 7681568 0.04826965273674569 0.6184626412696723 chr8 146364022 6897812 0.047127783903068744 0.5208198860677637 chr9 141213431 5869009 0.04156126622261589 0.37279580390983885 chr10 135534747 8110641 0.05984178359812042 0.47751480286074105 chr11 135006516 4744384 0.03514188900334262 0.32615134278302516 chr12 133851895 4722961 0.035284976727449395 0.21358645253656833 chr13 115169878 3758593 0.03263520866107022 0.19721099039080764 chr14 107349540 5853798 0.05453025695312714 0.3234606691608966 chr15 102531392 2554002 0.02490946382547893 0.1761131079567603 chr16 90354753 3927416 0.04346662316701812 0.2789079108317017 chr17 81195210 3907800 0.04812845486821205 0.2656793057186063 chr18 78077248 3191167 0.04087191956355839 0.7359346510170416 chr19 59128983 3237383 0.054751203821652064 0.7182450130538572 chr20 63025520 3083505 0.04892470542091521 0.25073470852317126 chr21 48129895 2103296 0.043700406992369295 0.2469732587122331 chr22 51304566 1159821 0.022606584373016624 0.1627249376307781 chrMT 16571 298946 18.040311387363467 10.180794136956795 chrX 155270560 5403599 0.03480118188534903 0.24151344547961928 chrY 59373566 372259 0.006269776688164561 0.13009019139432532