BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6432720.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP127755/SRP127755.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 = 382,757,346 number of mapped reads = 382,645,028 (99.97%) number of supplementary alignments = 4,716,030 (1.23%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 191,325,333 number of mapped paired reads (second in pair) = 191,319,695 number of mapped paired reads (both in pair) = 382,606,168 number of mapped paired reads (singletons) = 38,860 number of mapped bases = 53,170,695,284 bp number of sequenced bases = 53,115,664,555 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 190,398,768 duplication rate = 32.6% >>>>>>> Insert size mean insert size = 58,869.5438 std insert size = 2,469,976.2074 median insert size = 310 >>>>>>> Mapping quality mean mapping quality = 57.4059 >>>>>>> ACTG content number of A's = 14,823,456,611 bp (27.91%) number of C's = 11,238,485,284 bp (21.16%) number of T's = 14,655,606,677 bp (27.59%) number of G's = 12,388,004,270 bp (23.32%) number of N's = 10,111,713 bp (0.02%) GC percentage = 44.48% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 424,862,078 number of insertions = 11,899,385 mapped reads with insertion percentage = 3.05% number of deletions = 38,255,415 mapped reads with deletion percentage = 9.51% homopolymer indels = 53.12% >>>>>>> Coverage mean coverageData = 17.1757X std coverageData = 50.0662X There is a 49.6% of reference with a coverageData >= 1X There is a 43.92% of reference with a coverageData >= 2X There is a 40.14% of reference with a coverageData >= 3X There is a 37.26% of reference with a coverageData >= 4X There is a 34.88% of reference with a coverageData >= 5X There is a 32.86% of reference with a coverageData >= 6X There is a 31.1% of reference with a coverageData >= 7X There is a 29.55% of reference with a coverageData >= 8X There is a 28.17% of reference with a coverageData >= 9X There is a 26.93% of reference with a coverageData >= 10X There is a 25.8% of reference with a coverageData >= 11X There is a 24.77% of reference with a coverageData >= 12X There is a 23.83% of reference with a coverageData >= 13X There is a 22.95% of reference with a coverageData >= 14X There is a 22.14% of reference with a coverageData >= 15X There is a 21.38% of reference with a coverageData >= 16X There is a 20.68% of reference with a coverageData >= 17X There is a 20.01% of reference with a coverageData >= 18X There is a 19.39% of reference with a coverageData >= 19X There is a 18.8% of reference with a coverageData >= 20X There is a 18.24% of reference with a coverageData >= 21X There is a 17.72% of reference with a coverageData >= 22X There is a 17.22% of reference with a coverageData >= 23X There is a 16.75% of reference with a coverageData >= 24X There is a 16.3% of reference with a coverageData >= 25X There is a 15.87% of reference with a coverageData >= 26X There is a 15.46% of reference with a coverageData >= 27X There is a 15.07% of reference with a coverageData >= 28X There is a 14.69% of reference with a coverageData >= 29X There is a 14.33% of reference with a coverageData >= 30X There is a 13.99% of reference with a coverageData >= 31X There is a 13.66% of reference with a coverageData >= 32X There is a 13.34% of reference with a coverageData >= 33X There is a 13.04% of reference with a coverageData >= 34X There is a 12.75% of reference with a coverageData >= 35X There is a 12.46% of reference with a coverageData >= 36X There is a 12.19% of reference with a coverageData >= 37X There is a 11.93% of reference with a coverageData >= 38X There is a 11.67% of reference with a coverageData >= 39X There is a 11.43% of reference with a coverageData >= 40X There is a 11.19% of reference with a coverageData >= 41X There is a 10.96% of reference with a coverageData >= 42X There is a 10.74% of reference with a coverageData >= 43X There is a 10.53% of reference with a coverageData >= 44X There is a 10.32% of reference with a coverageData >= 45X There is a 10.12% of reference with a coverageData >= 46X There is a 9.92% of reference with a coverageData >= 47X There is a 9.73% of reference with a coverageData >= 48X There is a 9.55% of reference with a coverageData >= 49X There is a 9.37% of reference with a coverageData >= 50X There is a 9.2% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 5279079598 21.179805196954756 58.178466936934164 chr2 243199373 4287565185 17.62983650866567 50.88660591404452 chr3 198022430 3646078281 18.41245095820711 49.5432641270492 chr4 191154276 2575154061 13.471600609133118 38.95545943161069 chr5 180915260 3873082102 21.408266511072643 56.51423996988166 chr6 171115067 2667778930 15.590555389257451 45.60839514354218 chr7 159138663 2616210148 16.439814804778145 45.78446303413837 chr8 146364022 2490607515 17.01652824899824 46.71416203923244 chr9 141213431 2058550462 14.577582652177044 44.35245134152233 chr10 135534747 2886385570 21.296277404051967 55.305933864704045 chr11 135006516 3356431670 24.86125684481777 63.052397607290075 chr12 133851895 2795835575 20.88753076674783 56.27653661425273 chr13 115169878 641329926 5.568556094155105 21.84814466494002 chr14 107349540 1424225858 13.267181750382909 40.85232973799664 chr15 102531392 1750939111 17.077102698459413 49.56250405593236 chr16 90354753 2161468862 23.922027234140078 65.83795321276703 chr17 81195210 2433752562 29.97409036813871 74.30587577437176 chr18 78077248 1064830150 13.638161913698598 39.678602461922715 chr19 59128983 1453389604 24.579986501712703 65.26056043003915 chr20 63025520 1328637840 21.080950065941543 53.545973652439905 chr21 48129895 470474880 9.77510713455743 34.075171138607786 chr22 51304566 857035277 16.704853852579124 50.60392692443176 chrMT 16571 5650538 340.9895600748295 411.28660576786564 chrX 155270560 901293556 5.804664812183327 22.13888663743357 chrY 59373566 144908023 2.4406151215508936 19.335519182796343