BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068103.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 = 4,074,430 number of mapped reads = 3,896,589 (95.64%) number of supplementary alignments = 23,265 (0.57%) number of secondary alignments = 0 number of mapped bases = 256,313,135 bp number of sequenced bases = 256,198,108 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 441,238 duplication rate = 9.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7249 >>>>>>> ACTG content number of A's = 70,061,155 bp (27.35%) number of C's = 45,606,406 bp (17.8%) number of T's = 83,782,029 bp (32.7%) number of G's = 56,718,232 bp (22.14%) number of N's = 30,286 bp (0.01%) GC percentage = 39.94% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 1,410,423 number of insertions = 17,100 mapped reads with insertion percentage = 0.44% number of deletions = 65,521 mapped reads with deletion percentage = 1.66% homopolymer indels = 45.42% >>>>>>> Coverage mean coverageData = 0.0828X std coverageData = 0.9027X There is a 6.13% of reference with a coverageData >= 1X There is a 1.43% of reference with a coverageData >= 2X There is a 0.37% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% 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 23391774 0.09384840810486887 2.0233911001976455 chr2 243199373 21747659 0.08942317051121673 0.873201712172497 chr3 198022430 14133098 0.07137119769714977 0.341738178538121 chr4 191154276 19034236 0.09957525616638573 0.42878208755232183 chr5 180915260 10086137 0.05575061495641661 0.31221440127524935 chr6 171115067 17851107 0.10432223949045936 0.5244113986471873 chr7 159138663 22304148 0.1401554316187764 1.6411483012288715 chr8 146364022 10855365 0.07416689464846764 1.3209771812803226 chr9 141213431 8119711 0.057499566029239814 0.663029698085685 chr10 135534747 14556037 0.10739708688872235 0.6386783766546793 chr11 135006516 10750805 0.07963174903350591 0.4739455981174739 chr12 133851895 9332156 0.06972001404985712 0.3831552566810112 chr13 115169878 6573184 0.05707381230359556 0.31531316390123354 chr14 107349540 6795650 0.0633039508133896 0.39231758044679493 chr15 102531392 5867821 0.057229506842158155 0.32194642572440774 chr16 90354753 6047036 0.06692548869011905 0.37067936023877474 chr17 81195210 8301256 0.10223824779811519 0.4349120078723449 chr18 78077248 8436081 0.10804787842932169 1.1628831271349251 chr19 59128983 4937355 0.08350143617386417 1.2638434380816832 chr20 63025520 3473370 0.05511053300313905 0.32967173340941275 chr21 48129895 5519283 0.11467473594114427 0.4618163632575665 chr22 51304566 1750480 0.034119380329618226 0.22645732989102454 chrMT 16571 157472 9.502866453442762 6.259842224415612 chrX 155270560 15571626 0.10028704733208922 0.49556669552484023 chrY 59373566 720288 0.012131459309686739 0.48250964337701435