BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514735.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP106579/SRP106579.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 = 131,636,473 number of mapped reads = 127,588,885 (96.93%) number of supplementary alignments = 3,513,769 (2.67%) number of secondary alignments = 0 number of mapped bases = 12,151,769,272 bp number of sequenced bases = 12,146,196,248 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 97,324,113 duplication rate = 43.45% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1767 >>>>>>> ACTG content number of A's = 3,084,858,832 bp (25.4%) number of C's = 2,936,927,677 bp (24.18%) number of T's = 3,114,615,099 bp (25.64%) number of G's = 2,939,212,775 bp (24.2%) number of N's = 70,581,865 bp (0.58%) GC percentage = 48.38% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 113,607,009 number of insertions = 4,144,711 mapped reads with insertion percentage = 3.15% number of deletions = 3,066,745 mapped reads with deletion percentage = 2.34% homopolymer indels = 46.84% >>>>>>> Coverage mean coverageData = 3.9254X std coverageData = 86.4427X There is a 11.38% of reference with a coverageData >= 1X There is a 7.57% of reference with a coverageData >= 2X There is a 5.95% of reference with a coverageData >= 3X There is a 5.1% of reference with a coverageData >= 4X There is a 4.53% of reference with a coverageData >= 5X There is a 4.12% of reference with a coverageData >= 6X There is a 3.8% of reference with a coverageData >= 7X There is a 3.54% of reference with a coverageData >= 8X There is a 3.32% of reference with a coverageData >= 9X There is a 3.13% of reference with a coverageData >= 10X There is a 2.97% of reference with a coverageData >= 11X There is a 2.83% of reference with a coverageData >= 12X There is a 2.7% of reference with a coverageData >= 13X There is a 2.58% of reference with a coverageData >= 14X There is a 2.47% of reference with a coverageData >= 15X There is a 2.38% of reference with a coverageData >= 16X There is a 2.29% of reference with a coverageData >= 17X There is a 2.21% of reference with a coverageData >= 18X There is a 2.14% of reference with a coverageData >= 19X There is a 2.07% of reference with a coverageData >= 20X There is a 2% of reference with a coverageData >= 21X There is a 1.94% of reference with a coverageData >= 22X There is a 1.89% of reference with a coverageData >= 23X There is a 1.83% of reference with a coverageData >= 24X There is a 1.78% of reference with a coverageData >= 25X There is a 1.74% of reference with a coverageData >= 26X There is a 1.69% of reference with a coverageData >= 27X There is a 1.65% of reference with a coverageData >= 28X There is a 1.61% of reference with a coverageData >= 29X There is a 1.57% of reference with a coverageData >= 30X There is a 1.54% of reference with a coverageData >= 31X There is a 1.5% of reference with a coverageData >= 32X There is a 1.47% of reference with a coverageData >= 33X There is a 1.44% of reference with a coverageData >= 34X There is a 1.41% of reference with a coverageData >= 35X There is a 1.38% of reference with a coverageData >= 36X There is a 1.35% of reference with a coverageData >= 37X There is a 1.33% of reference with a coverageData >= 38X There is a 1.3% of reference with a coverageData >= 39X There is a 1.28% of reference with a coverageData >= 40X There is a 1.25% of reference with a coverageData >= 41X There is a 1.23% of reference with a coverageData >= 42X There is a 1.21% of reference with a coverageData >= 43X There is a 1.19% of reference with a coverageData >= 44X There is a 1.17% of reference with a coverageData >= 45X There is a 1.15% of reference with a coverageData >= 46X There is a 1.13% of reference with a coverageData >= 47X There is a 1.11% of reference with a coverageData >= 48X There is a 1.09% of reference with a coverageData >= 49X There is a 1.08% of reference with a coverageData >= 50X There is a 1.06% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1302426231 5.22536804833076 129.44636194510935 chr2 243199373 641663440 2.638425552190877 52.27962096276829 chr3 198022430 447677022 2.2607389577029227 24.421404823917264 chr4 191154276 366301212 1.9162595766364128 27.59580171467082 chr5 180915260 264085875 1.4597213911087434 33.8908160558579 chr6 171115067 492912301 2.880589708678313 84.59338611870135 chr7 159138663 319974347 2.010663788220968 21.401350219015523 chr8 146364022 191421582 1.3078458721228636 17.16572672893944 chr9 141213431 212071413 1.5017793385389808 18.266393005239216 chr10 135534747 1123506156 8.289432642686085 110.31119430335127 chr11 135006516 1225201487 9.075128544165972 119.66764607728919 chr12 133851895 251412322 1.8782873563351494 22.288191996445995 chr13 115169878 190081993 1.6504488526071026 40.823159197040205 chr14 107349540 265264316 2.4710335600879145 43.38323329330134 chr15 102531392 99406188 0.9695195399278301 11.111473851936067 chr16 90354753 177595636 1.9655372861237306 48.80181510210016 chr17 81195210 887699675 10.932906941185324 196.9021623774324 chr18 78077248 123633399 1.5834753678818188 18.69106562515206 chr19 59128983 3053674569 51.644293780598254 362.6459270812166 chr20 63025520 169953241 2.6965781638929753 110.67768972230276 chr21 48129895 33994403 0.7063053638492252 62.602900366536 chr22 51304566 112276871 2.188438179167133 25.227508753892405 chrMT 16571 12455945 751.6712932231006 365.3234182773616 chrX 155270560 170610868 1.0987972736106575 15.686286368865847 chrY 59373566 16468780 0.2773756253751038 13.004612044875516