BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524817.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,468,322 number of mapped reads = 1,340,700 (91.31%) number of supplementary alignments = 4,959 (0.34%) number of secondary alignments = 0 number of mapped bases = 76,958,114 bp number of sequenced bases = 76,934,717 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 51,419 duplication rate = 2.98% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9201 >>>>>>> ACTG content number of A's = 18,599,672 bp (24.18%) number of C's = 14,318,964 bp (18.61%) number of T's = 24,752,225 bp (32.17%) number of G's = 19,254,429 bp (25.03%) number of N's = 9,427 bp (0.01%) GC percentage = 43.64% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 382,449 number of insertions = 5,308 mapped reads with insertion percentage = 0.39% number of deletions = 14,431 mapped reads with deletion percentage = 1.07% homopolymer indels = 41% >>>>>>> Coverage mean coverageData = 0.0249X std coverageData = 0.2243X There is a 2.21% of reference with a coverageData >= 1X There is a 0.2% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% 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 6279229 0.02519243071414454 0.2662228805117429 chr2 243199373 6505493 0.026749628996781995 0.3597635171955913 chr3 198022430 5026889 0.025385452546966523 0.17792114969470296 chr4 191154276 4937131 0.025827991417780263 0.21032682106921122 chr5 180915260 4536220 0.025073727887852025 0.1743725599133778 chr6 171115067 4373192 0.02555702473587554 0.19259515164143703 chr7 159138663 4196954 0.026372937417477236 0.2576158770255668 chr8 146364022 3703483 0.025303233331480875 0.2067051377526977 chr9 141213431 3230667 0.022877901748595005 0.19533880296148853 chr10 135534747 3798805 0.028028273812323565 0.28550834962169963 chr11 135006516 3444557 0.02551400556103529 0.20365697183873696 chr12 133851895 3475006 0.02596157491830803 0.17875803025918946 chr13 115169878 2340361 0.02032094711431404 0.1573063991678912 chr14 107349540 2328625 0.021691988619606566 0.16728602768887602 chr15 102531392 2274960 0.02218793635416556 0.16563682760973045 chr16 90354753 2348125 0.025987841502925695 0.19622520532762566 chr17 81195210 2235620 0.02753389023810641 0.18979965729392323 chr18 78077248 1986315 0.02544038181263766 0.28655555650354736 chr19 59128983 1725218 0.029177197246906816 0.23915344464119398 chr20 63025520 1701055 0.026989939948135293 0.19035312876637822 chr21 48129895 1017221 0.021134910017983625 0.18296821476931377 chr22 51304566 991564 0.019327012726313677 0.15506881034846826 chrMT 16571 8311 0.5015388329008509 0.75559254645482 chrX 155270560 4227015 0.027223544501932626 0.1923331554804174 chrY 59373566 266098 0.004481758767866495 0.13349088446504384