BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038493.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 12,578,636 number of mapped reads = 12,226,776 (97.2%) number of supplementary alignments = 267,244 (2.12%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,169,815 number of mapped paired reads (second in pair) = 6,056,961 number of mapped paired reads (both in pair) = 12,096,840 number of mapped paired reads (singletons) = 129,936 number of mapped bases = 1,746,362,490 bp number of sequenced bases = 1,744,789,289 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,950,592 duplication rate = 10.45% >>>>>>> Insert size mean insert size = 109,932.6304 std insert size = 3,191,091.9088 median insert size = 255 >>>>>>> Mapping quality mean mapping quality = 53.5916 >>>>>>> ACTG content number of A's = 516,858,555 bp (29.62%) number of C's = 347,245,699 bp (19.9%) number of T's = 519,376,717 bp (29.77%) number of G's = 361,272,970 bp (20.71%) number of N's = 35,348 bp (0%) GC percentage = 40.61% >>>>>>> Mismatches and indels general error rate = 0.0146 number of mismatches = 24,316,222 number of insertions = 409,030 mapped reads with insertion percentage = 3.04% number of deletions = 756,913 mapped reads with deletion percentage = 5.85% homopolymer indels = 45.34% >>>>>>> Coverage mean coverageData = 0.5641X std coverageData = 7.9593X There is a 17.35% of reference with a coverageData >= 1X There is a 10.96% of reference with a coverageData >= 2X There is a 6.97% of reference with a coverageData >= 3X There is a 4.81% of reference with a coverageData >= 4X There is a 3.34% of reference with a coverageData >= 5X There is a 2.39% of reference with a coverageData >= 6X There is a 1.73% of reference with a coverageData >= 7X There is a 1.28% of reference with a coverageData >= 8X There is a 0.95% of reference with a coverageData >= 9X There is a 0.71% of reference with a coverageData >= 10X There is a 0.54% of reference with a coverageData >= 11X There is a 0.42% of reference with a coverageData >= 12X There is a 0.32% of reference with a coverageData >= 13X There is a 0.25% of reference with a coverageData >= 14X There is a 0.2% of reference with a coverageData >= 15X There is a 0.16% of reference with a coverageData >= 16X There is a 0.13% of reference with a coverageData >= 17X There is a 0.11% of reference with a coverageData >= 18X There is a 0.09% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 126739263 0.5084812326305097 7.97775371481981 chr2 243199373 173926464 0.7151600016666161 14.98255179538549 chr3 198022430 119916407 0.6055698185301533 1.8586807365164772 chr4 191154276 129142638 0.6755937701336067 4.976314413744634 chr5 180915260 120918336 0.6683700203067447 2.311242249833219 chr6 171115067 93618347 0.5471075612529199 6.146617828120343 chr7 159138663 95481270 0.5999878860362173 6.904091259226911 chr8 146364022 91549187 0.6254896917221912 2.8131037856942114 chr9 141213431 78645802 0.556928625294856 16.894928601838995 chr10 135534747 78452871 0.5788395428959631 11.061404896060676 chr11 135006516 81044874 0.6003034253546695 4.925893522975602 chr12 133851895 79208346 0.5917611102928352 1.9431543383098142 chr13 115169878 57211415 0.4967567561372254 1.6469345831745372 chr14 107349540 49196744 0.45828555949098615 2.179491552896729 chr15 102531392 42724584 0.4166975905291523 1.4933913286709688 chr16 90354753 52053508 0.576101491860644 9.068707616332619 chr17 81195210 37899985 0.4667761189360801 5.551585508749222 chr18 78077248 59465637 0.7616256787124465 14.093860128754306 chr19 59128983 24697350 0.41768602717215686 4.672054098268421 chr20 63025520 34829405 0.5526238418976948 2.3031976394125726 chr21 48129895 24759083 0.5144221278687602 2.923114196620689 chr22 51304566 14557966 0.2837557577233964 2.1493870181152874 chrMT 16571 10770015 649.931506849315 384.0893765776811 chrX 155270560 48673276 0.31347395153337504 1.911794496296319 chrY 59373566 20879717 0.35166688488948095 8.796652899742282