BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524319.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 = 3,984,628 number of mapped reads = 3,623,851 (90.95%) number of supplementary alignments = 15,451 (0.39%) number of secondary alignments = 0 number of mapped bases = 209,996,620 bp number of sequenced bases = 209,939,949 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 208,386 duplication rate = 4.16% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0683 >>>>>>> ACTG content number of A's = 52,500,003 bp (25.01%) number of C's = 39,603,611 bp (18.86%) number of T's = 67,224,940 bp (32.02%) number of G's = 50,582,650 bp (24.09%) number of N's = 28,745 bp (0.01%) GC percentage = 42.96% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 1,078,226 number of insertions = 13,132 mapped reads with insertion percentage = 0.36% number of deletions = 35,772 mapped reads with deletion percentage = 0.98% homopolymer indels = 43.25% >>>>>>> Coverage mean coverageData = 0.0678X std coverageData = 0.5706X There is a 5.62% of reference with a coverageData >= 1X There is a 0.8% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% 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 0.01% 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 17639095 0.07076850974024253 1.115029372798629 chr2 243199373 13659275 0.05616492687257051 0.89288563247334 chr3 198022430 14573489 0.07359514273206323 0.3209798925748534 chr4 191154276 10824783 0.05662851612066475 0.3436542838955116 chr5 180915260 12282283 0.06788970150997765 0.30932423559959993 chr6 171115067 13451097 0.07860848980645287 0.38547501268483725 chr7 159138663 9529911 0.0598843223912218 0.7006733386078672 chr8 146364022 21825759 0.1491196996485926 0.6805099367198428 chr9 141213431 8632150 0.061128392241953246 0.40632108669635475 chr10 135534747 10746627 0.07929056745869013 0.5401671546630268 chr11 135006516 10187271 0.07545762457865367 0.4380862415797184 chr12 133851895 8196769 0.061237601454951385 0.3005863161322794 chr13 115169878 5308563 0.04609332832670015 0.25584131766247814 chr14 107349540 4404666 0.041031065433536094 0.2625877785386061 chr15 102531392 6505160 0.06344554456063563 0.3072302747851382 chr16 90354753 6729492 0.07447856118869585 0.35400566799461014 chr17 81195210 6622542 0.08156321044061589 0.39091945603751993 chr18 78077248 4855708 0.06219107517723985 0.7829136906689881 chr19 59128983 3781215 0.06394858846126272 0.7554352203236376 chr20 63025520 4881513 0.07745295873798423 0.33980264342092675 chr21 48129895 3055821 0.06349112126673037 0.33862854687523686 chr22 51304566 1621950 0.03161414522052482 0.208679905660798 chrMT 16571 18190 1.097700802606964 1.3203634638886586 chrX 155270560 10053809 0.06475025916052599 0.35761247864193807 chrY 59373566 609482 0.010265207920979515 0.2919445849920304