BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013295.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 = 1,938,030 number of mapped reads = 1,707,475 (88.1%) number of supplementary alignments = 11,054 (0.57%) number of secondary alignments = 0 number of mapped bases = 113,147,512 bp number of sequenced bases = 113,099,347 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 80,188 duplication rate = 3.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6863 >>>>>>> ACTG content number of A's = 31,716,658 bp (28.04%) number of C's = 20,510,214 bp (18.13%) number of T's = 36,330,192 bp (32.12%) number of G's = 24,517,864 bp (21.68%) number of N's = 24,419 bp (0.02%) GC percentage = 39.81% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 970,797 number of insertions = 8,677 mapped reads with insertion percentage = 0.5% number of deletions = 28,548 mapped reads with deletion percentage = 1.65% homopolymer indels = 46.56% >>>>>>> Coverage mean coverageData = 0.0365X std coverageData = 0.4345X There is a 3.12% of reference with a coverageData >= 1X There is a 0.38% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% 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 7380229 0.029609671463967986 0.8140876324735659 chr2 243199373 12302297 0.05058523321110701 0.486714323887198 chr3 198022430 12047963 0.06084140569328434 0.27764132275872616 chr4 191154276 10180316 0.05325706655915979 0.27885610128392035 chr5 180915260 4897399 0.027070126643822086 0.18701100456699352 chr6 171115067 3848466 0.022490515110513323 0.20386813279468002 chr7 159138663 4508226 0.02832891715321248 0.8866094388942931 chr8 146364022 6316557 0.04315648691315684 0.5339694059292761 chr9 141213431 6506736 0.04607731682406328 0.3900577253436358 chr10 135534747 2551482 0.01882529798797647 0.3810819410051507 chr11 135006516 3183218 0.023578254548839703 0.22104165400232217 chr12 133851895 5359448 0.04004013540488164 0.23845508741270405 chr13 115169878 4407277 0.03826761889944869 0.22002319469101705 chr14 107349540 2872610 0.026759406700764623 0.22316703523325238 chr15 102531392 1135853 0.011078099866234137 0.12270090399385518 chr16 90354753 3163834 0.035015689766757487 0.24300362957683205 chr17 81195210 3567202 0.04393365076585183 0.26176510421870985 chr18 78077248 3445428 0.04412845083884104 0.6349080831885879 chr19 59128983 2490270 0.04211589433222621 0.5678826015437114 chr20 63025520 2720339 0.04316249988893388 0.2429385913285691 chr21 48129895 2687540 0.05583930735772434 0.2858124564699023 chr22 51304566 1042056 0.02031117464281834 0.15786396397841843 chrMT 16571 132480 7.994689517832358 6.0601707288555176 chrX 155270560 6158038 0.039660048884991465 0.255614026097672 chrY 59373566 242248 0.0040800648557979486 0.10973057247512524