BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238540.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 = 4,509,900 number of mapped reads = 4,095,544 (90.81%) number of supplementary alignments = 26,680 (0.59%) number of secondary alignments = 0 number of mapped bases = 253,237,303 bp number of sequenced bases = 253,127,596 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 375,438 duplication rate = 7.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.8432 >>>>>>> ACTG content number of A's = 63,157,428 bp (24.95%) number of C's = 45,024,141 bp (17.79%) number of T's = 82,844,039 bp (32.73%) number of G's = 62,084,645 bp (24.53%) number of N's = 17,343 bp (0.01%) GC percentage = 42.31% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 1,452,711 number of insertions = 19,022 mapped reads with insertion percentage = 0.46% number of deletions = 62,842 mapped reads with deletion percentage = 1.52% homopolymer indels = 43.02% >>>>>>> Coverage mean coverageData = 0.0818X std coverageData = 0.799X There is a 6.42% of reference with a coverageData >= 1X There is a 1.17% of reference with a coverageData >= 2X There is a 0.26% 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 0.02% 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% 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 19290799 0.07739518931830465 1.2345881387348987 chr2 243199373 23780789 0.09778310160363778 1.5831450060491499 chr3 198022430 14981888 0.07565753031108648 0.35306000649058494 chr4 191154276 19862906 0.10391034098551895 0.4613423151827707 chr5 180915260 14071975 0.07778213402230415 0.359469020627982 chr6 171115067 15182333 0.08872586889148693 0.6119108891084968 chr7 159138663 10146158 0.0637567125972398 0.8761185145172569 chr8 146364022 14028369 0.09584574684617508 0.7325973083688201 chr9 141213431 11137928 0.07887300748326127 0.7262136506348282 chr10 135534747 12735199 0.09396261314450972 0.8230240272874024 chr11 135006516 13333445 0.09876149237122747 0.7428849835563549 chr12 133851895 11674401 0.08721879507197115 0.4001707788205567 chr13 115169878 6896372 0.05987999744169217 0.39241455235034495 chr14 107349540 7263210 0.06765944222956148 0.4046582478044371 chr15 102531392 6574618 0.06412297611252561 0.4025331529245056 chr16 90354753 6630354 0.07338135272197578 0.46202727207625816 chr17 81195210 7732284 0.09523079009217415 0.45539680605908195 chr18 78077248 7437411 0.09525708436854742 1.5284043974103187 chr19 59128983 6225042 0.10527903042066528 0.8325942945357918 chr20 63025520 5518743 0.0875636250204679 0.40153883031418425 chr21 48129895 2534314 0.0526557142915022 0.36166428219523516 chr22 51304566 3206312 0.062495646099023625 0.30872089259936053 chrMT 16571 73603 4.441675215738338 3.5624425729329787 chrX 155270560 12196891 0.07855250216138848 0.44440011107626554 chrY 59373566 721959 0.01215960314729959 0.33074403754708304