BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6432725.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP127755/SRP127755.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 = 425,498,240 number of mapped reads = 425,297,788 (99.95%) number of supplementary alignments = 225,652 (0.05%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 212,656,059 number of mapped paired reads (second in pair) = 212,641,729 number of mapped paired reads (both in pair) = 425,223,044 number of mapped paired reads (singletons) = 74,744 number of mapped bases = 58,505,792,912 bp number of sequenced bases = 58,446,927,514 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 209,237,919 duplication rate = 32.68% >>>>>>> Insert size mean insert size = 79,319.5495 std insert size = 2,872,081.5332 median insert size = 303 >>>>>>> Mapping quality mean mapping quality = 55.4043 >>>>>>> ACTG content number of A's = 15,885,212,055 bp (27.18%) number of C's = 12,763,714,758 bp (21.84%) number of T's = 15,679,588,906 bp (26.83%) number of G's = 14,118,145,307 bp (24.16%) number of N's = 266,488 bp (0%) GC percentage = 45.99% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 599,807,031 number of insertions = 12,515,642 mapped reads with insertion percentage = 2.86% number of deletions = 39,571,798 mapped reads with deletion percentage = 8.86% homopolymer indels = 51.22% >>>>>>> Coverage mean coverageData = 18.8991X std coverageData = 55.2867X There is a 64.37% of reference with a coverageData >= 1X There is a 55.64% of reference with a coverageData >= 2X There is a 49.69% of reference with a coverageData >= 3X There is a 45.22% of reference with a coverageData >= 4X There is a 41.66% of reference with a coverageData >= 5X There is a 38.71% of reference with a coverageData >= 6X There is a 36.22% of reference with a coverageData >= 7X There is a 34.06% of reference with a coverageData >= 8X There is a 32.17% of reference with a coverageData >= 9X There is a 30.5% of reference with a coverageData >= 10X There is a 29.01% of reference with a coverageData >= 11X There is a 27.66% of reference with a coverageData >= 12X There is a 26.43% of reference with a coverageData >= 13X There is a 25.31% of reference with a coverageData >= 14X There is a 24.29% of reference with a coverageData >= 15X There is a 23.34% of reference with a coverageData >= 16X There is a 22.46% of reference with a coverageData >= 17X There is a 21.65% of reference with a coverageData >= 18X There is a 20.9% of reference with a coverageData >= 19X There is a 20.19% of reference with a coverageData >= 20X There is a 19.52% of reference with a coverageData >= 21X There is a 18.9% of reference with a coverageData >= 22X There is a 18.31% of reference with a coverageData >= 23X There is a 17.75% of reference with a coverageData >= 24X There is a 17.23% of reference with a coverageData >= 25X There is a 16.73% of reference with a coverageData >= 26X There is a 16.26% of reference with a coverageData >= 27X There is a 15.82% of reference with a coverageData >= 28X There is a 15.39% of reference with a coverageData >= 29X There is a 14.98% of reference with a coverageData >= 30X There is a 14.59% of reference with a coverageData >= 31X There is a 14.22% of reference with a coverageData >= 32X There is a 13.87% of reference with a coverageData >= 33X There is a 13.53% of reference with a coverageData >= 34X There is a 13.21% of reference with a coverageData >= 35X There is a 12.89% of reference with a coverageData >= 36X There is a 12.59% of reference with a coverageData >= 37X There is a 12.31% of reference with a coverageData >= 38X There is a 12.03% of reference with a coverageData >= 39X There is a 11.76% of reference with a coverageData >= 40X There is a 11.51% of reference with a coverageData >= 41X There is a 11.26% of reference with a coverageData >= 42X There is a 11.02% of reference with a coverageData >= 43X There is a 10.79% of reference with a coverageData >= 44X There is a 10.57% of reference with a coverageData >= 45X There is a 10.36% of reference with a coverageData >= 46X There is a 10.15% of reference with a coverageData >= 47X There is a 9.95% of reference with a coverageData >= 48X There is a 9.75% of reference with a coverageData >= 49X There is a 9.57% of reference with a coverageData >= 50X There is a 9.38% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 5594947078 22.44707377479312 63.869874304989125 chr2 243199373 4669310719 19.199517915697918 59.39452937072438 chr3 198022430 3975271841 20.074856373593637 53.597863062767026 chr4 191154276 2805251068 14.6753246995113 44.840697226922025 chr5 180915260 3476855390 19.21814328984741 53.5489297477294 chr6 171115067 2898542948 16.939145095855295 47.01388333517723 chr7 159138663 2727909300 17.14171307320836 47.39899595007596 chr8 146364022 2994409201 20.45864250027237 56.302935088790605 chr9 141213431 2436369797 17.253102482865103 55.92787895509345 chr10 135534747 2891528558 21.334223304375225 56.21376756317014 chr11 135006516 3344253525 24.77105271718885 65.4930581502564 chr12 133851895 2952330359 22.056694520462337 59.04788122039197 chr13 115169878 1499942057 13.02373574625129 42.3735252932204 chr14 107349540 2064125201 19.228076813370603 55.591225676994405 chr15 102531392 1843002888 17.97501089227385 52.40382761953141 chr16 90354753 1895744907 20.981130976031775 65.15748384796122 chr17 81195210 2102446147 25.89372140302365 66.55839913047959 chr18 78077248 1587500196 20.332430210654966 57.58069546852004 chr19 59128983 1456320705 24.62955780923883 66.19960154897298 chr20 63025520 1842291374 29.230879396155714 71.28813466963958 chr21 48129895 753240199 15.650152550717179 57.794450667054356 chr22 51304566 1120549955 21.84113505608838 64.26068366734934 chrMT 16571 6979337 421.1777804598395 761.3182927710584 chrX 155270560 1361174576 8.766469161958327 26.33013455687483 chrY 59373566 205495586 3.4610618806355675 26.658739383265445