BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549033.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 10,275,295 number of mapped reads = 8,408,039 (81.83%) number of secondary alignments = 0 number of mapped bases = 333,083,827 bp number of sequenced bases = 333,053,376 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 466,128 duplication rate = 4.93% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.9554 >>>>>>> ACTG content number of A's = 94,447,387 bp (28.36%) number of C's = 70,421,566 bp (21.14%) number of T's = 96,650,911 bp (29.02%) number of G's = 71,533,173 bp (21.48%) number of N's = 339 bp (0%) GC percentage = 42.62% >>>>>>> Mismatches and indels general error rate = 0.0024 number of mismatches = 803,802 number of insertions = 8,969 mapped reads with insertion percentage = 0.11% number of deletions = 23,080 mapped reads with deletion percentage = 0.27% homopolymer indels = 42.47% >>>>>>> Coverage mean coverageData = 0.1076X std coverageData = 0.5792X There is a 7.27% of reference with a coverageData >= 1X There is a 2.13% of reference with a coverageData >= 2X There is a 0.74% of reference with a coverageData >= 3X There is a 0.29% of reference with a coverageData >= 4X There is a 0.13% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% 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 26211741 0.10516218934515714 0.6213844464321148 chr2 243199373 31030125 0.12759130345290817 0.558318043909501 chr3 198022430 20349723 0.10276473730778882 0.4539314461622003 chr4 191154276 21957086 0.11486578516297485 0.48664846472105044 chr5 180915260 19084315 0.10548759126234017 0.4516991259092583 chr6 171115067 20827130 0.12171417961692409 0.5011291932418139 chr7 159138663 18796100 0.11811146107215945 0.602908015783254 chr8 146364022 17148054 0.11716030869936056 1.3495407148455159 chr9 141213431 14931062 0.10573400769506125 0.4990500453179314 chr10 135534747 15387626 0.11353270169161861 0.5215308935766235 chr11 135006516 15683315 0.1161670967051694 0.5111211759961493 chr12 133851895 16592356 0.12396056103650979 0.505631283943859 chr13 115169878 12050469 0.10463212438238408 0.4672437871552229 chr14 107349540 11700936 0.10899847358451653 0.497000189506269 chr15 102531392 9037385 0.08814261489788415 0.42107521371240314 chr16 90354753 9371964 0.10372408411099303 0.4705764134562018 chr17 81195210 8743973 0.10769074924493699 0.46213917203311733 chr18 78077248 8874675 0.11366531515045203 0.6653506017873045 chr19 59128983 6169615 0.10434163902328575 0.6112007643499134 chr20 63025520 6182238 0.09809102725372199 0.45216461360868704 chr21 48129895 4322243 0.0898037072385053 0.46948247980304914 chr22 51304566 3751234 0.07311696194837707 0.5270714572945006 chrMT 16571 19876 1.1994448132279283 1.6623755715002067 chrX 155270560 12101134 0.07793579156280495 0.4003637800118726 chrY 59373566 2759452 0.046476103523915 0.35107732339353487