BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013257.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 = 2,075,344 number of mapped reads = 1,260,018 (60.71%) number of supplementary alignments = 5,549 (0.27%) number of secondary alignments = 0 number of mapped bases = 73,748,172 bp number of sequenced bases = 73,714,756 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 76,922 duplication rate = 5.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9016 >>>>>>> ACTG content number of A's = 20,175,780 bp (27.37%) number of C's = 12,257,010 bp (16.63%) number of T's = 23,490,435 bp (31.87%) number of G's = 17,767,548 bp (24.1%) number of N's = 23,983 bp (0.03%) GC percentage = 40.73% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 773,302 number of insertions = 4,792 mapped reads with insertion percentage = 0.38% number of deletions = 20,557 mapped reads with deletion percentage = 1.62% homopolymer indels = 47.64% >>>>>>> Coverage mean coverageData = 0.0238X std coverageData = 0.2152X There is a 2.02% of reference with a coverageData >= 1X There is a 0.26% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.02% 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 4317245 0.01732089967390693 0.2382068817355816 chr2 243199373 8778459 0.03609573039483124 0.2772353502300528 chr3 198022430 4489335 0.022670840873935342 0.17343485141270856 chr4 191154276 3417911 0.01788037951084076 0.15510728400524573 chr5 180915260 2590221 0.014317316294932776 0.13919866398188863 chr6 171115067 3527209 0.020613082540533966 0.20833283783342785 chr7 159138663 5415057 0.034027287259539185 0.3645748435638915 chr8 146364022 3789361 0.02588997588492068 0.23013377987680894 chr9 141213431 3083248 0.021833957139671793 0.19997746311308032 chr10 135534747 3243436 0.023930660378921133 0.20643257685583657 chr11 135006516 3717156 0.02753315995503506 0.20585611713521562 chr12 133851895 3999068 0.029876812726484 0.20144758673957192 chr13 115169878 1079411 0.009372337791310328 0.11117340889666874 chr14 107349540 2604879 0.024265395082270498 0.18551686938706852 chr15 102531392 1473205 0.014368331213137143 0.14066424860866225 chr16 90354753 2566681 0.02840670706055718 0.2010716222223464 chr17 81195210 2892700 0.03562648584811838 0.24445084281826993 chr18 78077248 1178302 0.01509148990497206 0.22103132644883347 chr19 59128983 1415574 0.023940442202430575 0.22209440508933762 chr20 63025520 2461613 0.039057400875074096 0.23526699001576032 chr21 48129895 1684956 0.03500851186149481 0.22506302280414056 chr22 51304566 686899 0.01338865238622231 0.13237173739565622 chrMT 16571 6452 0.389354897109408 0.747332352426834 chrX 155270560 5170683 0.033301116451180446 0.2266091536988799 chrY 59373566 159111 0.0026798289326263477 0.059694822932767004