BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2046434.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP058890/SRP058890.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 = 6,928,254 number of mapped reads = 6,897,971 (99.56%) number of supplementary alignments = 26,075 (0.38%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,453,073 number of mapped paired reads (second in pair) = 3,444,898 number of mapped paired reads (both in pair) = 6,877,932 number of mapped paired reads (singletons) = 20,039 number of mapped bases = 641,501,083 bp number of sequenced bases = 641,345,346 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,022,377 duplication rate = 41.74% >>>>>>> Insert size mean insert size = 20,508.8399 std insert size = 1,242,230.162 median insert size = 117 >>>>>>> Mapping quality mean mapping quality = 52.3549 >>>>>>> ACTG content number of A's = 185,604,922 bp (28.94%) number of C's = 135,399,840 bp (21.11%) number of T's = 181,980,232 bp (28.37%) number of G's = 138,309,916 bp (21.57%) number of N's = 50,436 bp (0.01%) GC percentage = 42.68% >>>>>>> Mismatches and indels general error rate = 0.0033 number of mismatches = 1,990,630 number of insertions = 48,555 mapped reads with insertion percentage = 0.69% number of deletions = 58,403 mapped reads with deletion percentage = 0.83% homopolymer indels = 45.93% >>>>>>> Coverage mean coverageData = 0.2072X std coverageData = 21.1901X There is a 2.12% of reference with a coverageData >= 1X There is a 1.4% of reference with a coverageData >= 2X There is a 0.31% of reference with a coverageData >= 3X There is a 0.24% of reference with a coverageData >= 4X There is a 0.11% of reference with a coverageData >= 5X There is a 0.09% of reference with a coverageData >= 6X There is a 0.07% of reference with a coverageData >= 7X There is a 0.07% of reference with a coverageData >= 8X There is a 0.06% of reference with a coverageData >= 9X There is a 0.06% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.05% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.04% of reference with a coverageData >= 30X There is a 0.04% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.03% of reference with a coverageData >= 35X There is a 0.03% of reference with a coverageData >= 36X There is a 0.03% of reference with a coverageData >= 37X There is a 0.03% of reference with a coverageData >= 38X There is a 0.03% of reference with a coverageData >= 39X There is a 0.03% of reference with a coverageData >= 40X There is a 0.03% of reference with a coverageData >= 41X There is a 0.03% of reference with a coverageData >= 42X There is a 0.03% of reference with a coverageData >= 43X There is a 0.03% of reference with a coverageData >= 44X There is a 0.03% of reference with a coverageData >= 45X There is a 0.03% of reference with a coverageData >= 46X There is a 0.03% of reference with a coverageData >= 47X There is a 0.03% of reference with a coverageData >= 48X There is a 0.03% of reference with a coverageData >= 49X There is a 0.03% of reference with a coverageData >= 50X There is a 0.03% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 141286907 0.5668467602333476 48.23398696295825 chr2 243199373 70118455 0.28831675894164416 24.591589816402273 chr3 198022430 22121170 0.11171042593508221 7.32438351529336 chr4 191154276 19207846 0.10048347545204796 5.322312012106035 chr5 180915260 37583669 0.20774184001946547 15.33394818529801 chr6 171115067 52193616 0.3050205742548668 22.840192614665106 chr7 159138663 45588828 0.28647235775758656 19.263522944503453 chr8 146364022 72200033 0.4932908512175212 30.505651648716675 chr9 141213431 5923848 0.041949607470411224 2.5981336118269973 chr10 135534747 21732322 0.16034502207762266 32.19440880231803 chr11 135006516 14583383 0.10801984550138306 8.154487561953031 chr12 133851895 10266241 0.07669851069347954 3.7790383895913497 chr13 115169878 9098593 0.07900149898569833 5.716794942924112 chr14 107349540 26468406 0.246562826445274 21.690197905102814 chr15 102531392 8575543 0.08363821881985178 4.999028191043928 chr16 90354753 26710366 0.29561661244317716 19.10656666430472 chr17 81195210 14224305 0.17518650422851298 9.363743962772539 chr18 78077248 2995117 0.03836094479149675 0.8584805603427448 chr19 59128983 4188533 0.07083722376892564 8.56453319605812 chr20 63025520 3854535 0.06115832126414824 1.132359565661618 chr21 48129895 6648373 0.13813396019251653 18.16474184053737 chr22 51304566 2272621 0.04429666162656946 3.333679962622623 chrMT 16571 126438 7.630076639913101 4.425580471639497 chrX 155270560 23372919 0.15053026794003962 17.89243559195622 chrY 59373566 159016 0.002678228893982888 0.3215906404695685