BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8438294.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP178894/SRP178894.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 = 657,211,676 number of mapped reads = 654,856,490 (99.64%) number of supplementary alignments = 10,928,532 (1.66%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 327,621,246 number of mapped paired reads (second in pair) = 327,235,244 number of mapped paired reads (both in pair) = 653,120,456 number of mapped paired reads (singletons) = 1,736,034 number of mapped bases = 94,459,245,984 bp number of sequenced bases = 94,432,443,876 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 269,986,945 duplication rate = 38.51% >>>>>>> Insert size mean insert size = 38,597.4019 std insert size = 1,906,485.0168 median insert size = 258 >>>>>>> Mapping quality mean mapping quality = 55.0604 >>>>>>> ACTG content number of A's = 28,554,097,904 bp (30.24%) number of C's = 18,883,033,298 bp (20%) number of T's = 27,209,466,848 bp (28.81%) number of G's = 19,785,139,397 bp (20.95%) number of N's = 706,429 bp (0%) GC percentage = 40.95% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 487,116,514 number of insertions = 11,999,288 mapped reads with insertion percentage = 1.8% number of deletions = 10,714,016 mapped reads with deletion percentage = 1.61% homopolymer indels = 48.44% >>>>>>> Coverage mean coverageData = 30.5131X std coverageData = 106.3788X There is a 91.52% of reference with a coverageData >= 1X There is a 90.85% of reference with a coverageData >= 2X There is a 90.04% of reference with a coverageData >= 3X There is a 89.14% of reference with a coverageData >= 4X There is a 88.11% of reference with a coverageData >= 5X There is a 86.95% of reference with a coverageData >= 6X There is a 85.65% of reference with a coverageData >= 7X There is a 84.24% of reference with a coverageData >= 8X There is a 82.71% of reference with a coverageData >= 9X There is a 81.07% of reference with a coverageData >= 10X There is a 79.33% of reference with a coverageData >= 11X There is a 77.51% of reference with a coverageData >= 12X There is a 75.61% of reference with a coverageData >= 13X There is a 73.66% of reference with a coverageData >= 14X There is a 71.65% of reference with a coverageData >= 15X There is a 69.6% of reference with a coverageData >= 16X There is a 67.53% of reference with a coverageData >= 17X There is a 65.44% of reference with a coverageData >= 18X There is a 63.34% of reference with a coverageData >= 19X There is a 61.25% of reference with a coverageData >= 20X There is a 59.17% of reference with a coverageData >= 21X There is a 57.1% of reference with a coverageData >= 22X There is a 55.06% of reference with a coverageData >= 23X There is a 53.05% of reference with a coverageData >= 24X There is a 51.07% of reference with a coverageData >= 25X There is a 49.13% of reference with a coverageData >= 26X There is a 47.24% of reference with a coverageData >= 27X There is a 45.39% of reference with a coverageData >= 28X There is a 43.6% of reference with a coverageData >= 29X There is a 41.85% of reference with a coverageData >= 30X There is a 40.15% of reference with a coverageData >= 31X There is a 38.51% of reference with a coverageData >= 32X There is a 36.91% of reference with a coverageData >= 33X There is a 35.37% of reference with a coverageData >= 34X There is a 33.89% of reference with a coverageData >= 35X There is a 32.45% of reference with a coverageData >= 36X There is a 31.07% of reference with a coverageData >= 37X There is a 29.74% of reference with a coverageData >= 38X There is a 28.46% of reference with a coverageData >= 39X There is a 27.23% of reference with a coverageData >= 40X There is a 26.05% of reference with a coverageData >= 41X There is a 24.91% of reference with a coverageData >= 42X There is a 23.82% of reference with a coverageData >= 43X There is a 22.78% of reference with a coverageData >= 44X There is a 21.78% of reference with a coverageData >= 45X There is a 20.82% of reference with a coverageData >= 46X There is a 19.9% of reference with a coverageData >= 47X There is a 19.02% of reference with a coverageData >= 48X There is a 18.18% of reference with a coverageData >= 49X There is a 17.38% of reference with a coverageData >= 50X There is a 16.61% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 7800836952 31.297161550502214 31.890825858757893 chr2 243199373 8267042544 33.99286125626648 95.33099249624765 chr3 198022430 6776718108 34.22197226849504 57.4803513702083 chr4 191154276 6222482418 32.55214870526883 24.573436939998043 chr5 180915260 6082286700 33.619533808259185 25.212051442008477 chr6 171115067 5574596625 32.57805827817605 26.032197577948413 chr7 159138663 5093565959 32.00709282696437 25.327003636283667 chr8 146364022 4921890568 33.627735154749985 26.13536217364363 chr9 141213431 4084829251 28.92663411740205 31.067907543562878 chr10 135534747 4489081358 33.121258255641266 36.22617864440572 chr11 135006516 4447172465 32.94042833458498 26.50636407127609 chr12 133851895 4469118195 33.38853136894326 25.878807056370007 chr13 115169878 3200978421 27.79353835036623 25.108752963643195 chr14 107349540 3002685452 27.971106834738183 27.528498895660626 chr15 102531392 2716231622 26.491707261713564 27.097032564822925 chr16 90354753 2557695152 28.307256310024997 49.510197162681806 chr17 81195210 2434817785 29.987209651899416 36.480257399992716 chr18 78077248 2614118471 33.48118098373549 27.0921985688833 chr19 59128983 1498813837 25.34820930371828 70.27339331859316 chr20 63025520 2092326154 33.19807839744916 29.145784962796633 chr21 48129895 1203351545 25.002164351283128 40.400871844120886 chr22 51304566 1026228864 20.002680930972108 26.419713303647562 chrMT 16571 651854095 39337.04031138736 15572.011830041729 chrX 155270560 2752294919 17.725800171004728 17.885147453549244 chrY 59373566 478228524 8.054569671627943 26.788684755610415