BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514720.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP106579/SRP106579.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 = 184,682,202 number of mapped reads = 173,706,600 (94.06%) number of supplementary alignments = 10,162,713 (5.5%) number of secondary alignments = 0 number of mapped bases = 16,027,084,290 bp number of sequenced bases = 16,012,250,510 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 167,688,757 duplication rate = 52.34% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.9708 >>>>>>> ACTG content number of A's = 4,315,618,934 bp (26.95%) number of C's = 3,570,835,133 bp (22.3%) number of T's = 4,338,648,543 bp (27.1%) number of G's = 3,591,492,762 bp (22.43%) number of N's = 195,655,138 bp (1.22%) GC percentage = 44.73% >>>>>>> Mismatches and indels general error rate = 0.0108 number of mismatches = 158,215,578 number of insertions = 8,385,902 mapped reads with insertion percentage = 4.58% number of deletions = 6,040,932 mapped reads with deletion percentage = 3.19% homopolymer indels = 37.7% >>>>>>> Coverage mean coverageData = 5.1772X std coverageData = 322.4512X There is a 7.04% of reference with a coverageData >= 1X There is a 3.74% of reference with a coverageData >= 2X There is a 2.46% of reference with a coverageData >= 3X There is a 1.92% of reference with a coverageData >= 4X There is a 1.61% of reference with a coverageData >= 5X There is a 1.41% of reference with a coverageData >= 6X There is a 1.28% of reference with a coverageData >= 7X There is a 1.18% of reference with a coverageData >= 8X There is a 1.11% of reference with a coverageData >= 9X There is a 1.05% of reference with a coverageData >= 10X There is a 1% of reference with a coverageData >= 11X There is a 0.96% of reference with a coverageData >= 12X There is a 0.93% of reference with a coverageData >= 13X There is a 0.9% of reference with a coverageData >= 14X There is a 0.87% of reference with a coverageData >= 15X There is a 0.85% of reference with a coverageData >= 16X There is a 0.82% of reference with a coverageData >= 17X There is a 0.8% of reference with a coverageData >= 18X There is a 0.79% of reference with a coverageData >= 19X There is a 0.77% of reference with a coverageData >= 20X There is a 0.75% of reference with a coverageData >= 21X There is a 0.74% of reference with a coverageData >= 22X There is a 0.73% of reference with a coverageData >= 23X There is a 0.71% of reference with a coverageData >= 24X There is a 0.7% of reference with a coverageData >= 25X There is a 0.69% of reference with a coverageData >= 26X There is a 0.68% of reference with a coverageData >= 27X There is a 0.67% of reference with a coverageData >= 28X There is a 0.66% of reference with a coverageData >= 29X There is a 0.65% of reference with a coverageData >= 30X There is a 0.64% of reference with a coverageData >= 31X There is a 0.63% of reference with a coverageData >= 32X There is a 0.63% of reference with a coverageData >= 33X There is a 0.62% of reference with a coverageData >= 34X There is a 0.61% of reference with a coverageData >= 35X There is a 0.6% of reference with a coverageData >= 36X There is a 0.6% of reference with a coverageData >= 37X There is a 0.59% of reference with a coverageData >= 38X There is a 0.58% of reference with a coverageData >= 39X There is a 0.58% of reference with a coverageData >= 40X There is a 0.57% of reference with a coverageData >= 41X There is a 0.57% of reference with a coverageData >= 42X There is a 0.56% of reference with a coverageData >= 43X There is a 0.55% of reference with a coverageData >= 44X There is a 0.55% of reference with a coverageData >= 45X There is a 0.54% of reference with a coverageData >= 46X There is a 0.54% of reference with a coverageData >= 47X There is a 0.53% of reference with a coverageData >= 48X There is a 0.53% of reference with a coverageData >= 49X There is a 0.52% of reference with a coverageData >= 50X There is a 0.52% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1078907155 4.328603678784816 180.27802640286146 chr2 243199373 1482778117 6.096965212981861 443.11600882499715 chr3 198022430 1267496744 6.400773609333044 186.87589462135614 chr4 191154276 719197571 3.762393319414942 161.55117772201768 chr5 180915260 724931805 4.007024089620743 152.65430694006054 chr6 171115067 1324599272 7.740985614083884 330.5038820642954 chr7 159138663 915167938 5.7507579914756475 303.7799159923977 chr8 146364022 860663971 5.8802973520364175 225.09464654638006 chr9 141213431 984558148 6.972128224828699 738.6510600133726 chr10 135534747 683760995 5.044912910782945 185.0988821212804 chr11 135006516 689890718 5.1100549694949535 229.97050035906696 chr12 133851895 732414412 5.471826992064625 259.7375757786712 chr13 115169878 297393302 2.5822142661295517 145.5729985649611 chr14 107349540 377659076 3.5180316189524428 132.12196564429075 chr15 102531392 388680316 3.7908420866850223 189.1854951488442 chr16 90354753 691758377 7.656026429511683 582.1853112619912 chr17 81195210 390020468 4.803491092639578 178.37358841618808 chr18 78077248 295310778 3.7822897907467232 135.22567708854754 chr19 59128983 310546345 5.2520156654816805 457.1594226586232 chr20 63025520 401283554 6.367001081466682 274.11938727620367 chr21 48129895 353101026 7.336417958111066 574.9987374687662 chr22 51304566 364214153 7.099059233831157 703.2058225939713 chrMT 16571 2252071 135.90435097459417 228.02903304838725 chrX 155270560 613536710 3.951403987980722 245.54273186218006 chrY 59373566 76961268 1.2962210826279157 121.81582195730533