BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231770.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,400,287 number of mapped reads = 341,377 (24.38%) number of supplementary alignments = 2,647 (0.19%) number of secondary alignments = 0 number of mapped bases = 21,458,506 bp number of sequenced bases = 21,447,268 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 21,056 duplication rate = 5.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.215 >>>>>>> ACTG content number of A's = 5,587,720 bp (26.05%) number of C's = 4,076,692 bp (19.01%) number of T's = 6,676,779 bp (31.13%) number of G's = 5,101,009 bp (23.78%) number of N's = 5,068 bp (0.02%) GC percentage = 42.79% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 202,495 number of insertions = 1,784 mapped reads with insertion percentage = 0.52% number of deletions = 6,989 mapped reads with deletion percentage = 2.02% homopolymer indels = 45.33% >>>>>>> Coverage mean coverageData = 0.0069X std coverageData = 0.1153X There is a 0.53% of reference with a coverageData >= 1X There is a 0.11% 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 1860485 0.0074643144018485715 0.12945208116655912 chr2 243199373 1766884 0.0072651667568238345 0.1504725551914357 chr3 198022430 1392357 0.0070313095339755195 0.10785791177743048 chr4 191154276 1302293 0.006812785082558132 0.1062047616058466 chr5 180915260 1306773 0.007223122029617623 0.10856716443122244 chr6 171115067 1257764 0.007350398898537672 0.11967371486147822 chr7 159138663 1162421 0.007304453726622046 0.12242996324665364 chr8 146364022 1120867 0.007658077338158964 0.118610446793012 chr9 141213431 930340 0.006588183527670254 0.10735018066059594 chr10 135534747 1001066 0.00738604691533456 0.11599418197321529 chr11 135006516 985722 0.007301292035415535 0.11268069703898585 chr12 133851895 931055 0.006955859683570412 0.10643939517882205 chr13 115169878 637563 0.0055358485315057816 0.09698722695224736 chr14 107349540 651826 0.006071996209764848 0.10091562721568667 chr15 102531392 582729 0.005683420351885986 0.09727003363751015 chr16 90354753 675317 0.00747406171316743 0.11374430291335315 chr17 81195210 614635 0.007569843097887178 0.11254145150762504 chr18 78077248 549988 0.0070441519660119165 0.1297513597813653 chr19 59128983 475181 0.008036346574741527 0.12265467256337337 chr20 63025520 500230 0.00793694363806915 0.11516930038599678 chr21 48129895 293978 0.006108012494105794 0.09944867672367394 chr22 51304566 256659 0.005002654149730065 0.09189330593836742 chrMT 16571 16498 0.9955947136563876 1.5413475391159475 chrX 155270560 1112392 0.0071642170930535706 0.10893026927709411 chrY 59373566 73483 0.0012376383119720314 0.04529503245257488