BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068190.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 = 1,438,396 number of mapped reads = 1,294,177 (89.97%) number of supplementary alignments = 5,386 (0.37%) number of secondary alignments = 0 number of mapped bases = 89,027,754 bp number of sequenced bases = 88,986,427 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 37,736 duplication rate = 2.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9139 >>>>>>> ACTG content number of A's = 25,689,278 bp (28.87%) number of C's = 16,675,282 bp (18.74%) number of T's = 27,582,333 bp (31%) number of G's = 18,935,305 bp (21.28%) number of N's = 104,229 bp (0.12%) GC percentage = 40.02% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 770,495 number of insertions = 6,357 mapped reads with insertion percentage = 0.49% number of deletions = 23,653 mapped reads with deletion percentage = 1.81% homopolymer indels = 46.67% >>>>>>> Coverage mean coverageData = 0.0288X std coverageData = 0.2795X There is a 2.52% of reference with a coverageData >= 1X There is a 0.26% of reference with a coverageData >= 2X There is a 0.04% 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 13038306 0.05231002413430296 0.47631716286265885 chr2 243199373 10452819 0.04298045209187279 0.2679492624019689 chr3 198022430 2988626 0.015092361001730966 0.1764360000753794 chr4 191154276 4511147 0.02359950870259371 0.18519630038167834 chr5 180915260 3579791 0.019787114696681752 0.15378053226032445 chr6 171115067 8421711 0.04921665372693335 0.2631946626810643 chr7 159138663 4607183 0.028950745929039255 0.23480686213036 chr8 146364022 1972566 0.013477123496920575 0.32585761727655144 chr9 141213431 1615878 0.011442806739820661 0.1844639068544715 chr10 135534747 6137803 0.04528582622432608 0.5999590281482229 chr11 135006516 5725027 0.04240556063234755 0.2970890134947145 chr12 133851895 5754779 0.04299363113237956 0.23047394834613183 chr13 115169878 2540142 0.022055610756138856 0.16161029992529444 chr14 107349540 2787164 0.02596344614052375 0.18393810130858654 chr15 102531392 1137283 0.011092046814306393 0.1144293583653593 chr16 90354753 1629050 0.01802948871986845 0.1960276570923462 chr17 81195210 2176880 0.026810448547395838 0.2010337586875962 chr18 78077248 1376521 0.01763024485699086 0.36564338810275615 chr19 59128983 476085 0.008051635185404762 0.2645038077613758 chr20 63025520 712816 0.011309958251831956 0.12157275859284275 chr21 48129895 894005 0.0185748379463533 0.1629085630379209 chr22 51304566 1299861 0.025336165985694138 0.17597500126346086 chrMT 16571 19460 1.174340715708165 1.2577302284011178 chrX 155270560 4886721 0.031472295842817855 0.22027461362056872 chrY 59373566 286130 0.004819147968980001 0.1079235423652695