BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237289.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 = 3,073,428 number of mapped reads = 2,655,467 (86.4%) number of supplementary alignments = 20,182 (0.66%) number of secondary alignments = 0 number of mapped bases = 176,875,485 bp number of sequenced bases = 176,803,581 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 181,688 duplication rate = 5.31% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3067 >>>>>>> ACTG content number of A's = 48,560,227 bp (27.47%) number of C's = 32,844,184 bp (18.58%) number of T's = 55,661,323 bp (31.48%) number of G's = 39,735,044 bp (22.47%) number of N's = 2,803 bp (0%) GC percentage = 41.05% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 1,374,432 number of insertions = 13,597 mapped reads with insertion percentage = 0.51% number of deletions = 40,711 mapped reads with deletion percentage = 1.52% homopolymer indels = 47.17% >>>>>>> Coverage mean coverageData = 0.0571X std coverageData = 0.5429X There is a 4.25% of reference with a coverageData >= 1X There is a 0.99% of reference with a coverageData >= 2X There is a 0.25% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 17666629 0.07087897686722314 1.0291323266784789 chr2 243199373 9906850 0.04073550798175783 0.5899384034928744 chr3 198022430 13966325 0.07052900522430716 0.3372569853399197 chr4 191154276 11816155 0.061814756369875816 0.3818251466443333 chr5 180915260 10732209 0.0593217454403791 0.314842301701507 chr6 171115067 16790070 0.09812151725949417 0.5816303942361356 chr7 159138663 10680550 0.06711474005534407 0.7580900858157006 chr8 146364022 10122667 0.06916089665805986 0.6448822313713037 chr9 141213431 9224382 0.0653222709389449 0.549425417160021 chr10 135534747 4986708 0.036792838075685494 0.4659865015600246 chr11 135006516 5702462 0.042238420551493974 0.4207400704964811 chr12 133851895 4543735 0.0339459893339575 0.26302749633382133 chr13 115169878 6349277 0.05512966680402318 0.30002470187469266 chr14 107349540 6809520 0.06343315490685847 0.36873185566313865 chr15 102531392 3137178 0.030597243817776315 0.2411095306067874 chr16 90354753 4446171 0.0492079370744337 0.3260179866082246 chr17 81195210 5009362 0.061695289660560024 0.34334293102799995 chr18 78077248 4624847 0.05923424708821704 0.9387975749773351 chr19 59128983 4661625 0.07883824079977834 0.6557003647041668 chr20 63025520 2819050 0.044728706720706154 0.28210198831942546 chr21 48129895 3684715 0.07655771947975369 0.4047333219057348 chr22 51304566 1935354 0.0377228412769343 0.24326362588080533 chrMT 16571 101706 6.1375897652525495 5.177165985794343 chrX 155270560 6729796 0.04334238248383982 0.3042359596085809 chrY 59373566 428142 0.0072109867882956535 0.234932984451917