BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231801.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 = 3,494,920 number of mapped reads = 3,238,693 (92.67%) number of supplementary alignments = 28,274 (0.81%) number of secondary alignments = 0 number of mapped bases = 213,433,504 bp number of sequenced bases = 213,351,628 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 198,644 duplication rate = 4.07% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1911 >>>>>>> ACTG content number of A's = 63,564,475 bp (29.79%) number of C's = 42,443,064 bp (19.89%) number of T's = 61,864,601 bp (29%) number of G's = 45,462,404 bp (21.31%) number of N's = 17,084 bp (0.01%) GC percentage = 41.2% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 1,253,588 number of insertions = 15,532 mapped reads with insertion percentage = 0.48% number of deletions = 48,242 mapped reads with deletion percentage = 1.47% homopolymer indels = 45.67% >>>>>>> Coverage mean coverageData = 0.0689X std coverageData = 3.2805X There is a 5.11% of reference with a coverageData >= 1X There is a 1.18% of reference with a coverageData >= 2X There is a 0.29% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% 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% 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 30578827 0.12268305241253541 1.8352767871554103 chr2 243199373 10741856 0.04416892966249547 11.398337328525448 chr3 198022430 18366871 0.09275146759889775 0.38198149120498043 chr4 191154276 11859524 0.06204163594017641 0.353926157181021 chr5 180915260 7800406 0.04311635182128915 0.26916117909821313 chr6 171115067 19390846 0.11332050613637665 0.5536982230053623 chr7 159138663 12216422 0.07676589566421077 0.9084802414747376 chr8 146364022 11248011 0.07684956211438354 1.3644325130054415 chr9 141213431 7494356 0.05307112749069881 0.5058034089957703 chr10 135534747 6014406 0.04437538072801361 0.44831140551584486 chr11 135006516 6706073 0.04967221730245968 0.44026767411456597 chr12 133851895 6245247 0.04665789005079084 0.2862289271468627 chr13 115169878 9392514 0.08155356385807755 0.3591607804573318 chr14 107349540 8439185 0.07861407696763302 0.39186528389683184 chr15 102531392 4084371 0.039835321849526824 0.24731632110238083 chr16 90354753 4415579 0.04886936053048587 0.34687893183298524 chr17 81195210 6089783 0.07500175195063846 0.39339457234660097 chr18 78077248 6351129 0.08134417083962796 1.0988823903912448 chr19 59128983 6303550 0.10660677184317545 0.9665925021097272 chr20 63025520 5877712 0.09325923847990465 0.4082279165321447 chr21 48129895 6218497 0.12920238035009218 0.4901516122122872 chr22 51304566 2294827 0.044729488599513735 0.2615935050908331 chrMT 16571 135120 8.154003982861626 5.330911957117792 chrX 155270560 4590597 0.029565147443275788 0.28231513642976686 chrY 59373566 577795 0.00973151924208157 0.255975442541819