BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524968.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 = 1,930,510 number of mapped reads = 1,787,231 (92.58%) number of supplementary alignments = 4,825 (0.25%) number of secondary alignments = 0 number of mapped bases = 104,941,696 bp number of sequenced bases = 104,906,619 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 59,387 duplication rate = 2.33% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7646 >>>>>>> ACTG content number of A's = 25,688,533 bp (24.49%) number of C's = 20,398,677 bp (19.44%) number of T's = 34,044,023 bp (32.45%) number of G's = 24,774,031 bp (23.62%) number of N's = 1,355 bp (0%) GC percentage = 43.06% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 515,096 number of insertions = 7,024 mapped reads with insertion percentage = 0.39% number of deletions = 20,585 mapped reads with deletion percentage = 1.14% homopolymer indels = 44.2% >>>>>>> Coverage mean coverageData = 0.0339X std coverageData = 0.3058X There is a 3.04% of reference with a coverageData >= 1X There is a 0.25% 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 0.01% 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 11126894 0.044641389278624904 0.5852929241473565 chr2 243199373 10032762 0.0412532395796925 0.35821439307359826 chr3 198022430 5810386 0.02934205988685221 0.1865083312162105 chr4 191154276 6810271 0.035627092119037924 0.22557287454555472 chr5 180915260 4530293 0.025040966693467427 0.1756064193019851 chr6 171115067 8585834 0.05017579194238927 0.3516179693573289 chr7 159138663 6682579 0.04199217760174345 0.4062337604335368 chr8 146364022 6632140 0.04531263837502361 0.31494580915460474 chr9 141213431 2971227 0.021040682737890563 0.23940298803950383 chr10 135534747 5306064 0.03914910469416378 0.3003103481065628 chr11 135006516 4393767 0.03254485139072843 0.26671021178977206 chr12 133851895 4463671 0.033347835680622974 0.20200098654838383 chr13 115169878 2061013 0.017895417063826358 0.14739428999705279 chr14 107349540 2383139 0.022199806352220977 0.16901379776771075 chr15 102531392 2900407 0.028287990082100905 0.19525372052570691 chr16 90354753 3254918 0.0360237606980122 0.21595546585645511 chr17 81195210 2597189 0.03198697312316823 0.25703404968556104 chr18 78077248 2078444 0.026620354241993775 0.38391404974386223 chr19 59128983 2491464 0.042136087475071235 0.3692186605622436 chr20 63025520 2496819 0.03961599999492269 0.21824310605811809 chr21 48129895 1240460 0.025773170708143035 0.1833661013228718 chr22 51304566 1371310 0.026728810063416188 0.17627429639541162 chrMT 16571 9649 0.5822823004043208 0.9306637274701315 chrX 155270560 4426114 0.02850581591255934 0.21726009962567294 chrY 59373566 284882 0.0047981285139585515 0.12213166226436405