BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5365360.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 = 549,833,842 number of mapped reads = 474,905,948 (86.37%) number of supplementary alignments = 16,962,567 (3.09%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 234,857,819 number of mapped paired reads (second in pair) = 240,048,129 number of mapped paired reads (both in pair) = 460,468,010 number of mapped paired reads (singletons) = 14,437,938 number of mapped bases = 59,999,332,573 bp number of sequenced bases = 59,969,037,356 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 259,078,804 duplication rate = 42.24% >>>>>>> Insert size mean insert size = 182,680.0149 std insert size = 4,274,350.3098 median insert size = 156 >>>>>>> Mapping quality mean mapping quality = 52.5863 >>>>>>> ACTG content number of A's = 15,798,582,635 bp (26.34%) number of C's = 13,519,709,720 bp (22.54%) number of T's = 15,879,561,733 bp (26.48%) number of G's = 14,769,481,800 bp (24.63%) number of N's = 1,701,468 bp (0%) GC percentage = 47.17% >>>>>>> Mismatches and indels general error rate = 0.0115 number of mismatches = 671,954,042 number of insertions = 7,535,524 mapped reads with insertion percentage = 1.49% number of deletions = 16,335,179 mapped reads with deletion percentage = 3.32% homopolymer indels = 40.62% >>>>>>> Coverage mean coverageData = 19.3815X std coverageData = 153.8487X There is a 62.77% of reference with a coverageData >= 1X There is a 58% of reference with a coverageData >= 2X There is a 51.2% of reference with a coverageData >= 3X There is a 48.04% of reference with a coverageData >= 4X There is a 44.2% of reference with a coverageData >= 5X There is a 41.76% of reference with a coverageData >= 6X There is a 39.12% of reference with a coverageData >= 7X There is a 37.16% of reference with a coverageData >= 8X There is a 35.17% of reference with a coverageData >= 9X There is a 33.56% of reference with a coverageData >= 10X There is a 31.98% of reference with a coverageData >= 11X There is a 30.62% of reference with a coverageData >= 12X There is a 29.31% of reference with a coverageData >= 13X There is a 28.15% of reference with a coverageData >= 14X There is a 27.04% of reference with a coverageData >= 15X There is a 26.04% of reference with a coverageData >= 16X There is a 25.08% of reference with a coverageData >= 17X There is a 24.2% of reference with a coverageData >= 18X There is a 23.36% of reference with a coverageData >= 19X There is a 22.58% of reference with a coverageData >= 20X There is a 21.84% of reference with a coverageData >= 21X There is a 21.15% of reference with a coverageData >= 22X There is a 20.48% of reference with a coverageData >= 23X There is a 19.86% of reference with a coverageData >= 24X There is a 19.26% of reference with a coverageData >= 25X There is a 18.7% of reference with a coverageData >= 26X There is a 18.16% of reference with a coverageData >= 27X There is a 17.65% of reference with a coverageData >= 28X There is a 17.16% of reference with a coverageData >= 29X There is a 16.69% of reference with a coverageData >= 30X There is a 16.24% of reference with a coverageData >= 31X There is a 15.81% of reference with a coverageData >= 32X There is a 15.4% of reference with a coverageData >= 33X There is a 15% of reference with a coverageData >= 34X There is a 14.62% of reference with a coverageData >= 35X There is a 14.26% of reference with a coverageData >= 36X There is a 13.91% of reference with a coverageData >= 37X There is a 13.57% of reference with a coverageData >= 38X There is a 13.25% of reference with a coverageData >= 39X There is a 12.93% of reference with a coverageData >= 40X There is a 12.63% of reference with a coverageData >= 41X There is a 12.34% of reference with a coverageData >= 42X There is a 12.06% of reference with a coverageData >= 43X There is a 11.79% of reference with a coverageData >= 44X There is a 11.53% of reference with a coverageData >= 45X There is a 11.27% of reference with a coverageData >= 46X There is a 11.03% of reference with a coverageData >= 47X There is a 10.79% of reference with a coverageData >= 48X There is a 10.56% of reference with a coverageData >= 49X There is a 10.33% of reference with a coverageData >= 50X There is a 10.12% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 5268727367 21.138271775860492 108.72628711741756 chr2 243199373 5159568218 21.215384539663265 266.0592146433687 chr3 198022430 3754141347 18.958162199100375 50.16597103404653 chr4 191154276 3200644842 16.743778423245946 96.50323499416125 chr5 180915260 3339670729 18.459861976264467 66.51859699650439 chr6 171115067 3191433849 18.650805595044414 154.18045518362985 chr7 159138663 3139476188 19.72792864295963 126.00327662816134 chr8 146364022 2862915188 19.560238567371428 99.04989483808419 chr9 141213431 2741067970 19.410816312507837 238.24008712903458 chr10 135534747 2907264740 21.450327715593108 69.75262175593653 chr11 135006516 3127779582 23.167619420680406 329.1811624449349 chr12 133851895 2710154927 20.247415451234367 52.386809009436675 chr13 115169878 1565263304 13.590908761751054 41.0604307960155 chr14 107349540 1801718304 16.783661150294634 56.506923982687944 chr15 102531392 1926196411 18.78640651830807 51.25221582536229 chr16 90354753 2180818989 24.13618450155024 114.57165204203316 chr17 81195210 2299183785 28.316741652617193 270.7116279836738 chr18 78077248 1518160074 19.444333821806833 297.6069786388778 chr19 59128983 1759596590 29.758614146974253 95.07912396738658 chr20 63025520 1639724130 26.016828262583157 73.16575952321806 chr21 48129895 815060793 16.93460567491369 124.58546096090392 chr22 51304566 1131293213 22.0505366520399 81.32957425424695 chrMT 16571 11702555 706.2069277653733 1980.1418605495992 chrX 155270560 1592980003 10.259382094068574 73.31205741580328 chrY 59373566 354789475 5.975546003081574 96.6757511646062