BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231851.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 = 4,135,278 number of mapped reads = 3,794,868 (91.77%) number of supplementary alignments = 17,710 (0.43%) number of secondary alignments = 0 number of mapped bases = 238,312,760 bp number of sequenced bases = 238,209,061 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 295,393 duplication rate = 6.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.9279 >>>>>>> ACTG content number of A's = 57,159,043 bp (24%) number of C's = 43,552,785 bp (18.28%) number of T's = 77,173,016 bp (32.4%) number of G's = 60,238,534 bp (25.29%) number of N's = 85,683 bp (0.04%) GC percentage = 43.57% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 1,496,803 number of insertions = 15,920 mapped reads with insertion percentage = 0.42% number of deletions = 58,537 mapped reads with deletion percentage = 1.53% homopolymer indels = 43.64% >>>>>>> Coverage mean coverageData = 0.077X std coverageData = 0.7189X There is a 6.14% of reference with a coverageData >= 1X There is a 1.08% of reference with a coverageData >= 2X There is a 0.24% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% 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 26021327 0.10439824340497832 1.1527574474993567 chr2 243199373 11207878 0.046085143484313175 1.5873728566628276 chr3 198022430 31431359 0.15872625641448798 0.4961125317296646 chr4 191154276 5838220 0.030541927296462885 0.23658804497431696 chr5 180915260 9183118 0.05075922285383776 0.2792542321144532 chr6 171115067 20293249 0.11859416798171256 0.6826008889097511 chr7 159138663 18043997 0.113385375117799 1.0157555596986945 chr8 146364022 10644642 0.07272717608156463 0.5060616987508653 chr9 141213431 7762715 0.05497150621600576 0.37523348017557157 chr10 135534747 11577331 0.08541965257071679 0.5226713302131233 chr11 135006516 4105267 0.03040791749636736 0.26693025809748744 chr12 133851895 7341140 0.05484524518685372 0.291613923161721 chr13 115169878 8979866 0.07797061311465486 0.38848707217667405 chr14 107349540 9005361 0.08388821228297764 0.36199988511512593 chr15 102531392 6051886 0.059024713133710306 0.35694781490933514 chr16 90354753 7715702 0.08539342695120865 0.38632327864306987 chr17 81195210 8323430 0.10251134272575932 0.399931853666992 chr18 78077248 5766559 0.0738570985493751 0.9531433406285158 chr19 59128983 8027403 0.13576088396446798 0.7595425352259982 chr20 63025520 7353587 0.11667633999687746 0.43290404096353335 chr21 48129895 4150880 0.08624327977445204 0.37600319092292145 chr22 51304566 3100724 0.06043758366458065 0.29882721713672916 chrMT 16571 264316 15.950515961619697 9.308142462513132 chrX 155270560 5620952 0.036201015826825125 0.2738987930322334 chrY 59373566 501851 0.008452431507987915 0.1958364166925301