BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063593.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 = 127,571,644 number of mapped reads = 127,036,016 (99.58%) number of supplementary alignments = 215,606 (0.17%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 63,725,498 number of mapped paired reads (second in pair) = 63,310,518 number of mapped paired reads (both in pair) = 126,577,754 number of mapped paired reads (singletons) = 458,262 number of mapped bases = 12,582,473,888 bp number of sequenced bases = 12,580,701,854 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 74,524,207 duplication rate = 53.63% >>>>>>> Insert size mean insert size = 21,175.7443 std insert size = 1,436,744.624 median insert size = 233 >>>>>>> Mapping quality mean mapping quality = 53.6548 >>>>>>> ACTG content number of A's = 3,632,189,731 bp (28.87%) number of C's = 2,648,916,685 bp (21.06%) number of T's = 3,681,872,922 bp (29.27%) number of G's = 2,616,833,838 bp (20.8%) number of N's = 888,678 bp (0.01%) GC percentage = 41.86% >>>>>>> Mismatches and indels general error rate = 0.0037 number of mismatches = 45,793,063 number of insertions = 594,786 mapped reads with insertion percentage = 0.46% number of deletions = 738,777 mapped reads with deletion percentage = 0.57% homopolymer indels = 47.6% >>>>>>> Coverage mean coverageData = 4.0645X std coverageData = 31.2568X There is a 16.77% of reference with a coverageData >= 1X There is a 10.03% of reference with a coverageData >= 2X There is a 6.62% of reference with a coverageData >= 3X There is a 5.66% of reference with a coverageData >= 4X There is a 4.96% of reference with a coverageData >= 5X There is a 4.67% of reference with a coverageData >= 6X There is a 4.41% of reference with a coverageData >= 7X There is a 4.24% of reference with a coverageData >= 8X There is a 4.09% of reference with a coverageData >= 9X There is a 3.97% of reference with a coverageData >= 10X There is a 3.86% of reference with a coverageData >= 11X There is a 3.76% of reference with a coverageData >= 12X There is a 3.66% of reference with a coverageData >= 13X There is a 3.58% of reference with a coverageData >= 14X There is a 3.5% of reference with a coverageData >= 15X There is a 3.42% of reference with a coverageData >= 16X There is a 3.35% of reference with a coverageData >= 17X There is a 3.28% of reference with a coverageData >= 18X There is a 3.22% of reference with a coverageData >= 19X There is a 3.16% of reference with a coverageData >= 20X There is a 3.1% of reference with a coverageData >= 21X There is a 3.05% of reference with a coverageData >= 22X There is a 2.99% of reference with a coverageData >= 23X There is a 2.94% of reference with a coverageData >= 24X There is a 2.89% of reference with a coverageData >= 25X There is a 2.84% of reference with a coverageData >= 26X There is a 2.8% of reference with a coverageData >= 27X There is a 2.75% of reference with a coverageData >= 28X There is a 2.71% of reference with a coverageData >= 29X There is a 2.67% of reference with a coverageData >= 30X There is a 2.63% of reference with a coverageData >= 31X There is a 2.59% of reference with a coverageData >= 32X There is a 2.55% of reference with a coverageData >= 33X There is a 2.52% of reference with a coverageData >= 34X There is a 2.48% of reference with a coverageData >= 35X There is a 2.45% of reference with a coverageData >= 36X There is a 2.41% of reference with a coverageData >= 37X There is a 2.38% of reference with a coverageData >= 38X There is a 2.35% of reference with a coverageData >= 39X There is a 2.31% of reference with a coverageData >= 40X There is a 2.28% of reference with a coverageData >= 41X There is a 2.25% of reference with a coverageData >= 42X There is a 2.22% of reference with a coverageData >= 43X There is a 2.2% of reference with a coverageData >= 44X There is a 2.17% of reference with a coverageData >= 45X There is a 2.14% of reference with a coverageData >= 46X There is a 2.11% of reference with a coverageData >= 47X There is a 2.09% of reference with a coverageData >= 48X There is a 2.06% of reference with a coverageData >= 49X There is a 2.04% of reference with a coverageData >= 50X There is a 2.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1681646796 6.746810857494313 44.848201937274105 chr2 243199373 1215388756 4.997499545362726 36.65592400478416 chr3 198022430 732927341 3.701233951123618 27.572336781138834 chr4 191154276 551331520 2.8842227939489042 23.870762037596464 chr5 180915260 435350474 2.406377847838817 18.583264509128686 chr6 171115067 776517315 4.5379832916758875 34.35642040773549 chr7 159138663 930216601 5.8453212026797035 44.64881592815048 chr8 146364022 335169772 2.2899737751125753 18.8670578351439 chr9 141213431 369638399 2.6175867010836953 20.410741474409978 chr10 135534747 610235015 4.502424865263518 33.3184634489463 chr11 135006516 645900279 4.784215592971823 31.285625450144842 chr12 133851895 583644231 4.3603733141021275 29.070523878299884 chr13 115169878 197811375 1.7175617308546598 15.767532274285873 chr14 107349540 287378274 2.677033120030137 20.073538149875482 chr15 102531392 295833431 2.885296153981797 22.75244113830809 chr16 90354753 326263935 3.6109216634126597 27.422407829861164 chr17 81195210 590723108 7.275344296787951 36.83393379062519 chr18 78077248 244290163 3.128826505257972 27.593317595486784 chr19 59128983 460683101 7.791155498142087 35.45740730608042 chr20 63025520 176936307 2.807375599598385 18.6560780329039 chr21 48129895 184383642 3.8309587419627658 33.480340614187504 chr22 51304566 177231415 3.4544959409655664 24.201436569216906 chrMT 16571 2568865 155.0217246997767 418.84326006439045 chrX 155270560 754812559 4.861272858164484 43.28057273238427 chrY 59373566 15591214 0.2625952094573535 7.774990331965336