BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5365369.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP102259/SRP102259.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 = 637,397,960 number of mapped reads = 593,936,696 (93.18%) number of supplementary alignments = 6,666,331 (1.05%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 297,110,111 number of mapped paired reads (second in pair) = 296,826,585 number of mapped paired reads (both in pair) = 590,313,268 number of mapped paired reads (singletons) = 3,623,428 number of mapped bases = 81,603,193,623 bp number of sequenced bases = 81,543,996,764 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 296,853,460 duplication rate = 43.71% >>>>>>> Insert size mean insert size = 58,624.094 std insert size = 2,458,138.4362 median insert size = 178 >>>>>>> Mapping quality mean mapping quality = 54.5123 >>>>>>> ACTG content number of A's = 21,381,190,412 bp (26.22%) number of C's = 19,149,094,083 bp (23.48%) number of T's = 20,973,982,162 bp (25.72%) number of G's = 20,038,668,020 bp (24.57%) number of N's = 1,062,087 bp (0%) GC percentage = 48.06% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 780,404,775 number of insertions = 12,034,065 mapped reads with insertion percentage = 1.96% number of deletions = 40,720,116 mapped reads with deletion percentage = 6.6% homopolymer indels = 51.76% >>>>>>> Coverage mean coverageData = 26.3602X std coverageData = 87.4743X There is a 66.23% of reference with a coverageData >= 1X There is a 62.55% of reference with a coverageData >= 2X There is a 56.53% of reference with a coverageData >= 3X There is a 53.75% of reference with a coverageData >= 4X There is a 49.99% of reference with a coverageData >= 5X There is a 47.66% of reference with a coverageData >= 6X There is a 44.98% of reference with a coverageData >= 7X There is a 43.03% of reference with a coverageData >= 8X There is a 40.97% of reference with a coverageData >= 9X There is a 39.32% of reference with a coverageData >= 10X There is a 37.66% of reference with a coverageData >= 11X There is a 36.24% of reference with a coverageData >= 12X There is a 34.85% of reference with a coverageData >= 13X There is a 33.63% of reference with a coverageData >= 14X There is a 32.45% of reference with a coverageData >= 15X There is a 31.37% of reference with a coverageData >= 16X There is a 30.35% of reference with a coverageData >= 17X There is a 29.4% of reference with a coverageData >= 18X There is a 28.49% of reference with a coverageData >= 19X There is a 27.65% of reference with a coverageData >= 20X There is a 26.85% of reference with a coverageData >= 21X There is a 26.09% of reference with a coverageData >= 22X There is a 25.37% of reference with a coverageData >= 23X There is a 24.69% of reference with a coverageData >= 24X There is a 24.03% of reference with a coverageData >= 25X There is a 23.41% of reference with a coverageData >= 26X There is a 22.82% of reference with a coverageData >= 27X There is a 22.26% of reference with a coverageData >= 28X There is a 21.71% of reference with a coverageData >= 29X There is a 21.2% of reference with a coverageData >= 30X There is a 20.7% of reference with a coverageData >= 31X There is a 20.22% of reference with a coverageData >= 32X There is a 19.76% of reference with a coverageData >= 33X There is a 19.32% of reference with a coverageData >= 34X There is a 18.9% of reference with a coverageData >= 35X There is a 18.49% of reference with a coverageData >= 36X There is a 18.09% of reference with a coverageData >= 37X There is a 17.71% of reference with a coverageData >= 38X There is a 17.34% of reference with a coverageData >= 39X There is a 16.99% of reference with a coverageData >= 40X There is a 16.65% of reference with a coverageData >= 41X There is a 16.31% of reference with a coverageData >= 42X There is a 15.99% of reference with a coverageData >= 43X There is a 15.68% of reference with a coverageData >= 44X There is a 15.38% of reference with a coverageData >= 45X There is a 15.09% of reference with a coverageData >= 46X There is a 14.81% of reference with a coverageData >= 47X There is a 14.53% of reference with a coverageData >= 48X There is a 14.26% of reference with a coverageData >= 49X There is a 14% of reference with a coverageData >= 50X There is a 13.75% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 7495911278 30.07379178405337 100.91003950590127 chr2 243199373 6841262159 28.130262321852285 144.57712554581576 chr3 198022430 5108842818 25.799313835306435 60.797712120027306 chr4 191154276 3941880613 20.621461865702653 66.08962488165996 chr5 180915260 4527523501 25.025658427044796 61.05875485884439 chr6 171115067 4268442821 24.94486836159203 59.844263296158324 chr7 159138663 4111122055 25.833584230879204 64.4897669325084 chr8 146364022 3959496048 27.052386193650786 68.38677200601329 chr9 141213431 3653744363 25.873915371406845 98.16657116790726 chr10 135534747 4268100242 31.490819413268245 112.0565129525147 chr11 135006516 4335479372 32.11311202194122 89.29974099280402 chr12 133851895 3734126905 27.897452665873725 67.04724366682873 chr13 115169878 2060791486 17.893493696329173 47.64114159883295 chr14 107349540 2522834342 23.501119259570185 62.14117972565572 chr15 102531392 2678777031 26.12640849545864 65.06786364264944 chr16 90354753 3132373505 34.66750116620871 143.50956598040736 chr17 81195210 3003984746 36.99706849702095 88.14001966115968 chr18 78077248 2023186729 25.912628593159432 106.55316197809678 chr19 59128983 2099692051 35.51036977923331 91.56955090827326 chr20 63025520 2496062865 39.60400271191733 88.97913769742924 chr21 48129895 1097093244 22.79442421389035 99.74178904564573 chr22 51304566 1730994552 33.739580839646905 84.14531475195759 chrMT 16571 6588005 397.5623076458874 362.174104508693 chrX 155270560 2062715299 13.284651636472491 36.621830704679745 chrY 59373566 442167593 7.44721300721604 89.47503482254417