BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124811.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 71,946,268 number of mapped reads = 71,904,414 (99.94%) number of supplementary alignments = 25,751 (0.04%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 35,953,238 number of mapped paired reads (second in pair) = 35,951,176 number of mapped paired reads (both in pair) = 71,886,856 number of mapped paired reads (singletons) = 17,558 number of mapped bases = 7,052,207,610 bp number of sequenced bases = 7,051,467,685 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 28,923,149 duplication rate = 37.83% >>>>>>> Insert size mean insert size = 84,747.2877 std insert size = 2,904,062.8353 median insert size = 193 >>>>>>> Mapping quality mean mapping quality = 55.7787 >>>>>>> ACTG content number of A's = 1,844,582,462 bp (26.16%) number of C's = 1,659,186,933 bp (23.53%) number of T's = 1,907,113,779 bp (27.05%) number of G's = 1,640,505,229 bp (23.26%) number of N's = 79,282 bp (0%) GC percentage = 46.79% >>>>>>> Mismatches and indels general error rate = 0.0018 number of mismatches = 11,716,881 number of insertions = 393,258 mapped reads with insertion percentage = 0.54% number of deletions = 335,044 mapped reads with deletion percentage = 0.46% homopolymer indels = 39.35% >>>>>>> Coverage mean coverageData = 2.2781X std coverageData = 15.9521X There is a 15.05% of reference with a coverageData >= 1X There is a 7.13% of reference with a coverageData >= 2X There is a 4.88% of reference with a coverageData >= 3X There is a 4.17% of reference with a coverageData >= 4X There is a 3.78% of reference with a coverageData >= 5X There is a 3.55% of reference with a coverageData >= 6X There is a 3.38% of reference with a coverageData >= 7X There is a 3.26% of reference with a coverageData >= 8X There is a 3.15% of reference with a coverageData >= 9X There is a 3.05% of reference with a coverageData >= 10X There is a 2.97% of reference with a coverageData >= 11X There is a 2.89% of reference with a coverageData >= 12X There is a 2.82% of reference with a coverageData >= 13X There is a 2.75% of reference with a coverageData >= 14X There is a 2.69% of reference with a coverageData >= 15X There is a 2.63% of reference with a coverageData >= 16X There is a 2.58% of reference with a coverageData >= 17X There is a 2.52% of reference with a coverageData >= 18X There is a 2.47% of reference with a coverageData >= 19X There is a 2.43% of reference with a coverageData >= 20X There is a 2.38% of reference with a coverageData >= 21X There is a 2.34% of reference with a coverageData >= 22X There is a 2.3% of reference with a coverageData >= 23X There is a 2.25% of reference with a coverageData >= 24X There is a 2.22% of reference with a coverageData >= 25X There is a 2.18% of reference with a coverageData >= 26X There is a 2.14% of reference with a coverageData >= 27X There is a 2.1% of reference with a coverageData >= 28X There is a 2.07% of reference with a coverageData >= 29X There is a 2.03% of reference with a coverageData >= 30X There is a 2% of reference with a coverageData >= 31X There is a 1.97% of reference with a coverageData >= 32X There is a 1.94% of reference with a coverageData >= 33X There is a 1.91% of reference with a coverageData >= 34X There is a 1.88% of reference with a coverageData >= 35X There is a 1.85% of reference with a coverageData >= 36X There is a 1.82% of reference with a coverageData >= 37X There is a 1.79% of reference with a coverageData >= 38X There is a 1.76% of reference with a coverageData >= 39X There is a 1.73% of reference with a coverageData >= 40X There is a 1.71% of reference with a coverageData >= 41X There is a 1.68% of reference with a coverageData >= 42X There is a 1.65% of reference with a coverageData >= 43X There is a 1.63% of reference with a coverageData >= 44X There is a 1.6% of reference with a coverageData >= 45X There is a 1.58% of reference with a coverageData >= 46X There is a 1.55% of reference with a coverageData >= 47X There is a 1.53% of reference with a coverageData >= 48X There is a 1.51% of reference with a coverageData >= 49X There is a 1.48% of reference with a coverageData >= 50X There is a 1.46% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 755811845 3.032336858249994 19.10561703090801 chr2 243199373 563039834 2.3151368650938093 16.440375698530147 chr3 198022430 461025828 2.328149533363468 17.000234365116377 chr4 191154276 297721906 1.5574954023000773 13.155485905996311 chr5 180915260 339754910 1.87797817608089 14.691463574626763 chr6 171115067 407603088 2.3820408988297914 17.151325873279106 chr7 159138663 434136255 2.728037591970972 19.67609636448169 chr8 146364022 299213492 2.0443103975374495 16.633641195026062 chr9 141213431 271623752 1.9234979992802526 14.048959072453329 chr10 135534747 275038182 2.029281701466562 14.616184230672166 chr11 135006516 354237503 2.623854858975844 16.065034442341272 chr12 133851895 409959241 3.0627824955335896 18.654615452388153 chr13 115169878 132973506 1.1545858023744715 10.894019004132028 chr14 107349540 252478944 2.3519331708361304 16.430576292787133 chr15 102531392 248683939 2.425441946599145 16.43789863739811 chr16 90354753 256588847 2.839793574556061 16.479913786136574 chr17 81195210 311598596 3.8376475163990587 18.2368629461888 chr18 78077248 96834509 1.240239781504594 10.394824364763604 chr19 59128983 333649574 5.642741631460159 22.25931396166706 chr20 63025520 164627936 2.612083740046889 16.786867593139153 chr21 48129895 63276903 1.314711012770753 11.30052620024209 chr22 51304566 106243337 2.070835897919885 12.32246390779735 chrMT 16571 1318206 79.54897109408002 19.60156593898483 chrX 155270560 200809407 1.2932870661379723 10.381187934241852 chrY 59373566 13958070 0.23508896198015122 3.6972348309526883