BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231872.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 = 5,582,463 number of mapped reads = 5,274,314 (94.48%) number of supplementary alignments = 42,465 (0.76%) number of secondary alignments = 0 number of mapped bases = 346,969,703 bp number of sequenced bases = 346,831,660 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 653,576 duplication rate = 10.3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.364 >>>>>>> ACTG content number of A's = 93,948,724 bp (27.09%) number of C's = 62,750,014 bp (18.09%) number of T's = 112,542,623 bp (32.45%) number of G's = 77,450,622 bp (22.33%) number of N's = 139,677 bp (0.04%) GC percentage = 40.42% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 2,117,259 number of insertions = 23,640 mapped reads with insertion percentage = 0.44% number of deletions = 77,722 mapped reads with deletion percentage = 1.46% homopolymer indels = 45.65% >>>>>>> Coverage mean coverageData = 0.1121X std coverageData = 1.0952X There is a 7.7% of reference with a coverageData >= 1X There is a 2.22% of reference with a coverageData >= 2X There is a 0.68% of reference with a coverageData >= 3X There is a 0.22% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% 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 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 53900383 0.21624974406783926 2.41402130108503 chr2 243199373 17792742 0.07316113434223369 1.1843235846177063 chr3 198022430 9681394 0.04889039085117782 0.31114300344727036 chr4 191154276 7718600 0.04037890316406001 0.33244150637730896 chr5 180915260 25141456 0.1389681334786242 0.5104895683275877 chr6 171115067 31974165 0.18685768331552008 0.863617463607004 chr7 159138663 32398609 0.2035872891554958 2.1732144778297875 chr8 146364022 10443108 0.07135023933682282 1.1170361653680938 chr9 141213431 19321263 0.13682312555666182 0.7586530427065057 chr10 135534747 15350915 0.11326184126052931 0.7755675178610388 chr11 135006516 14409414 0.10673124843840871 0.6344236804774372 chr12 133851895 12658261 0.09456915794879109 0.44547144338211636 chr13 115169878 19266727 0.16728963627103954 0.573050165103977 chr14 107349540 11483920 0.10697689063222814 0.5015784879169207 chr15 102531392 3025149 0.029504612597086362 0.26726550386986014 chr16 90354753 5651869 0.06255198329190276 0.4504011538594836 chr17 81195210 8750736 0.10777404233574862 0.4971411926705216 chr18 78077248 6026483 0.07718616055729834 1.5602348175161165 chr19 59128983 12147573 0.2054419403763464 1.3923950959870601 chr20 63025520 9952842 0.15791764986627638 0.5632543320940682 chr21 48129895 5302406 0.11016865920858543 0.4892295401204365 chr22 51304566 2306447 0.04495597916177675 0.2715698949379771 chrMT 16571 635743 38.364793917084064 19.79748695588562 chrX 155270560 10947981 0.07050905851051223 0.4400751863519401 chrY 59373566 681517 0.011478458275522815 0.2708030643828775