BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013280.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,546,117 number of mapped reads = 1,252,054 (80.98%) number of supplementary alignments = 14,933 (0.97%) number of secondary alignments = 0 number of mapped bases = 79,563,436 bp number of sequenced bases = 79,511,810 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 175,169 duplication rate = 11.06% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7216 >>>>>>> ACTG content number of A's = 21,658,974 bp (27.24%) number of C's = 14,389,253 bp (18.1%) number of T's = 25,575,039 bp (32.17%) number of G's = 17,869,702 bp (22.47%) number of N's = 18,842 bp (0.02%) GC percentage = 40.57% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 744,334 number of insertions = 5,786 mapped reads with insertion percentage = 0.46% number of deletions = 30,060 mapped reads with deletion percentage = 2.37% homopolymer indels = 43.56% >>>>>>> Coverage mean coverageData = 0.0257X std coverageData = 0.3212X There is a 1.46% of reference with a coverageData >= 1X There is a 0.59% of reference with a coverageData >= 2X There is a 0.27% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3703850 0.01485994291665175 0.3322485464418855 chr2 243199373 5986683 0.024616358694312918 0.37201524875217745 chr3 198022430 3936665 0.019879894413981285 0.2238196705618938 chr4 191154276 6681372 0.034952772911028156 0.30514871103100855 chr5 180915260 3660616 0.020233870818857403 0.22549850013002065 chr6 171115067 3812445 0.022280007639537667 0.2622601784948334 chr7 159138663 5801495 0.0364555972171263 0.5500416331732748 chr8 146364022 4877684 0.03332570349836383 0.4443194162492128 chr9 141213431 3082606 0.021829410829908948 0.2823259414464244 chr10 135534747 5387109 0.039747069436002265 0.3721792092700108 chr11 135006516 3333225 0.024689363882258838 0.28191154063089474 chr12 133851895 3733299 0.027891267434054633 0.2669617109478637 chr13 115169878 1453911 0.012624056092166738 0.17954730983038042 chr14 107349540 4313678 0.040183479128089415 0.33009704868820483 chr15 102531392 2107722 0.020556845653670632 0.22563525004289461 chr16 90354753 2354825 0.026061993661805484 0.26216012316029047 chr17 81195210 2289394 0.028196170685438216 0.28369022950006817 chr18 78077248 1834397 0.023494642126730695 0.4627393346565431 chr19 59128983 1527545 0.025834115902179478 0.30724153711696783 chr20 63025520 1908292 0.030278084179234062 0.28620709477033685 chr21 48129895 1285559 0.026710197477056618 0.2619369276833784 chr22 51304566 984436 0.019188077723920324 0.21900789598476555 chrMT 16571 33267 2.007543298533583 2.628315415292763 chrX 155270560 5247228 0.033794094643569264 0.3059106905673612 chrY 59373566 226133 0.0038086477743310885 0.10673639696557843