BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524981.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 = 2,269,611 number of mapped reads = 2,094,206 (92.27%) number of supplementary alignments = 4,696 (0.21%) number of secondary alignments = 0 number of mapped bases = 120,625,827 bp number of sequenced bases = 120,588,628 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 109,914 duplication rate = 4.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6582 >>>>>>> ACTG content number of A's = 30,723,907 bp (25.48%) number of C's = 21,943,144 bp (18.2%) number of T's = 39,165,081 bp (32.48%) number of G's = 28,755,292 bp (23.85%) number of N's = 1,204 bp (0%) GC percentage = 42.04% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 588,317 number of insertions = 7,676 mapped reads with insertion percentage = 0.36% number of deletions = 21,756 mapped reads with deletion percentage = 1.03% homopolymer indels = 42.21% >>>>>>> Coverage mean coverageData = 0.039X std coverageData = 0.3236X There is a 3.36% of reference with a coverageData >= 1X There is a 0.38% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 9636998 0.03866388762176845 0.5484176124197415 chr2 243199373 10190215 0.041900663123831325 0.37716195244462436 chr3 198022430 7964376 0.04021956502604276 0.23015197110568236 chr4 191154276 7880555 0.041226150755842884 0.2694474470254892 chr5 180915260 7340959 0.040576781637988966 0.23035113301196639 chr6 171115067 7037420 0.04112682841657655 0.3035176277740733 chr7 159138663 6710331 0.04216656639876382 0.40347172800637937 chr8 146364022 6209373 0.04242417579915917 0.34807620830915614 chr9 141213431 5017272 0.03552970821876001 0.2859233250950923 chr10 135534747 5830584 0.04301910859803353 0.3463927940382226 chr11 135006516 5379440 0.039845780480699165 0.3100256017204327 chr12 133851895 5443989 0.04067173647410819 0.232915144638386 chr13 115169878 3887774 0.03375686479410875 0.20898235119668576 chr14 107349540 3691622 0.03438880129341961 0.21739726295428394 chr15 102531392 3328651 0.03246470115220907 0.2228272534819616 chr16 90354753 3520209 0.03895986523254621 0.2395465867333698 chr17 81195210 3183834 0.03921209145219281 0.25015526444953495 chr18 78077248 3278181 0.04198637995027694 0.48156449414625746 chr19 59128983 2319324 0.03922482482068058 0.38452754767701125 chr20 63025520 2501098 0.039683893127736194 0.232464654902125 chr21 48129895 1618515 0.033628060065371015 0.23554924701775087 chr22 51304566 1338287 0.026085144156564936 0.18149356493378108 chrMT 16571 4258 0.2569549212479633 0.5082082830909421 chrX 155270560 6938079 0.044683802261033904 0.2684833836617578 chrY 59373566 374483 0.006307234434933553 0.17081407223826184