BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5365358.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP102259/SRP102259.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 = 1,121,462,854 number of mapped reads = 1,088,890,431 (97.1%) number of supplementary alignments = 4,475,086 (0.4%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 545,616,706 number of mapped paired reads (second in pair) = 543,273,725 number of mapped paired reads (both in pair) = 1,083,749,012 number of mapped paired reads (singletons) = 5,141,419 number of mapped bases = 113,735,783,762 bp number of sequenced bases = 113,696,820,818 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 713,357,793 duplication rate = 34.47% >>>>>>> Insert size mean insert size = 37,039.046 std insert size = 1,854,651.5893 median insert size = 161 >>>>>>> Mapping quality mean mapping quality = 53.754 >>>>>>> ACTG content number of A's = 34,217,939,428 bp (30.1%) number of C's = 22,290,298,620 bp (19.61%) number of T's = 33,321,656,369 bp (29.31%) number of G's = 23,837,321,980 bp (20.97%) number of N's = 29,604,421 bp (0.03%) GC percentage = 40.57% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 661,174,992 number of insertions = 34,756,428 mapped reads with insertion percentage = 3.12% number of deletions = 18,555,185 mapped reads with deletion percentage = 1.66% homopolymer indels = 49.89% >>>>>>> Coverage mean coverageData = 36.74X std coverageData = 469.1561X There is a 86.8% of reference with a coverageData >= 1X There is a 85.69% of reference with a coverageData >= 2X There is a 84.3% of reference with a coverageData >= 3X There is a 83.17% of reference with a coverageData >= 4X There is a 81.83% of reference with a coverageData >= 5X There is a 80.63% of reference with a coverageData >= 6X There is a 79.28% of reference with a coverageData >= 7X There is a 78.02% of reference with a coverageData >= 8X There is a 76.63% of reference with a coverageData >= 9X There is a 75.32% of reference with a coverageData >= 10X There is a 73.9% of reference with a coverageData >= 11X There is a 72.55% of reference with a coverageData >= 12X There is a 71.11% of reference with a coverageData >= 13X There is a 69.73% of reference with a coverageData >= 14X There is a 68.27% of reference with a coverageData >= 15X There is a 66.87% of reference with a coverageData >= 16X There is a 65.4% of reference with a coverageData >= 17X There is a 63.99% of reference with a coverageData >= 18X There is a 62.52% of reference with a coverageData >= 19X There is a 61.11% of reference with a coverageData >= 20X There is a 59.66% of reference with a coverageData >= 21X There is a 58.25% of reference with a coverageData >= 22X There is a 56.82% of reference with a coverageData >= 23X There is a 55.43% of reference with a coverageData >= 24X There is a 54.03% of reference with a coverageData >= 25X There is a 52.67% of reference with a coverageData >= 26X There is a 51.31% of reference with a coverageData >= 27X There is a 49.99% of reference with a coverageData >= 28X There is a 48.66% of reference with a coverageData >= 29X There is a 47.38% of reference with a coverageData >= 30X There is a 46.1% of reference with a coverageData >= 31X There is a 44.86% of reference with a coverageData >= 32X There is a 43.62% of reference with a coverageData >= 33X There is a 42.42% of reference with a coverageData >= 34X There is a 41.23% of reference with a coverageData >= 35X There is a 40.08% of reference with a coverageData >= 36X There is a 38.94% of reference with a coverageData >= 37X There is a 37.83% of reference with a coverageData >= 38X There is a 36.74% of reference with a coverageData >= 39X There is a 35.68% of reference with a coverageData >= 40X There is a 34.63% of reference with a coverageData >= 41X There is a 33.61% of reference with a coverageData >= 42X There is a 32.61% of reference with a coverageData >= 43X There is a 31.63% of reference with a coverageData >= 44X There is a 30.67% of reference with a coverageData >= 45X There is a 29.75% of reference with a coverageData >= 46X There is a 28.83% of reference with a coverageData >= 47X There is a 27.94% of reference with a coverageData >= 48X There is a 27.07% of reference with a coverageData >= 49X There is a 26.23% of reference with a coverageData >= 50X There is a 25.4% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 9392268050 37.682024671866316 1272.3385408395268 chr2 243199373 9939176144 40.86842832444309 263.7549524420345 chr3 198022430 7747238009 39.1230327241212 75.9184901224973 chr4 191154276 7893319721 41.292927818156684 213.99392447428295 chr5 180915260 7094644656 39.215291490612785 45.02813481518722 chr6 171115067 6766783975 39.54522587423585 165.09168484585186 chr7 159138663 6237053325 39.192570852502385 265.98832530621485 chr8 146364022 5836821514 39.878799682069406 145.63526363119158 chr9 141213431 4849124835 34.33897753677552 415.51638015433537 chr10 135534747 6159652105 45.44703289260576 1002.2835609621774 chr11 135006516 5234465574 38.771947673992265 257.3243188637736 chr12 133851895 5103932085 38.13119033540765 76.38437264864024 chr13 115169878 3790712434 32.9140961146108 34.12531303452285 chr14 107349540 3469657938 32.321125344365704 46.997111741011366 chr15 102531392 3104433184 30.2778800077151 45.422885028551306 chr16 90354753 3257603569 36.05348319639588 148.63237798745018 chr17 81195210 2983301867 36.74233821182309 208.22484713631536 chr18 78077248 3230533298 41.376116355945335 475.55004773537433 chr19 59128983 2135748958 36.12017067839641 638.2815383252749 chr20 63025520 2280575144 36.18494768468392 72.45344060898472 chr21 48129895 1611878522 33.49017324887162 136.85368216924718 chr22 51304566 1283326261 25.013880070635427 113.29348815098533 chrMT 16571 25165995 1518.6769054372096 291.548429749267 chrX 155270560 3160968425 20.357809136516284 102.47348553876674 chrY 59373566 1147398174 19.325067556157904 408.66347051276887