BamQC report ----------------------------------- >>>>>>> Input bam file = SRR630877.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017516/SRP017516.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 = 54,204,428 number of mapped reads = 53,943,794 (99.52%) number of supplementary alignments = 311,660 (0.57%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 27,026,962 number of mapped paired reads (second in pair) = 26,916,832 number of mapped paired reads (both in pair) = 53,818,358 number of mapped paired reads (singletons) = 125,436 number of mapped bases = 5,261,886,584 bp number of sequenced bases = 5,260,518,942 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,021,934 duplication rate = 18.9% >>>>>>> Insert size mean insert size = 173,023.537 std insert size = 3,869,795.4571 median insert size = 193 >>>>>>> Mapping quality mean mapping quality = 53.4955 >>>>>>> ACTG content number of A's = 1,632,364,648 bp (31.03%) number of C's = 999,545,730 bp (19%) number of T's = 1,600,091,500 bp (30.42%) number of G's = 1,026,282,546 bp (19.51%) number of N's = 2,234,518 bp (0.04%) GC percentage = 38.51% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 35,546,260 number of insertions = 12,232,921 mapped reads with insertion percentage = 22.5% number of deletions = 747,408 mapped reads with deletion percentage = 1.36% homopolymer indels = 23.39% >>>>>>> Coverage mean coverageData = 1.6997X std coverageData = 6.6149X There is a 26.93% of reference with a coverageData >= 1X There is a 19.09% of reference with a coverageData >= 2X There is a 14.1% of reference with a coverageData >= 3X There is a 11.21% of reference with a coverageData >= 4X There is a 9.18% of reference with a coverageData >= 5X There is a 7.73% of reference with a coverageData >= 6X There is a 6.61% of reference with a coverageData >= 7X There is a 5.74% of reference with a coverageData >= 8X There is a 5.04% of reference with a coverageData >= 9X There is a 4.47% of reference with a coverageData >= 10X There is a 3.99% of reference with a coverageData >= 11X There is a 3.59% of reference with a coverageData >= 12X There is a 3.24% of reference with a coverageData >= 13X There is a 2.95% of reference with a coverageData >= 14X There is a 2.69% of reference with a coverageData >= 15X There is a 2.46% of reference with a coverageData >= 16X There is a 2.26% of reference with a coverageData >= 17X There is a 2.08% of reference with a coverageData >= 18X There is a 1.92% of reference with a coverageData >= 19X There is a 1.78% of reference with a coverageData >= 20X There is a 1.65% of reference with a coverageData >= 21X There is a 1.54% of reference with a coverageData >= 22X There is a 1.43% of reference with a coverageData >= 23X There is a 1.34% of reference with a coverageData >= 24X There is a 1.25% of reference with a coverageData >= 25X There is a 1.17% of reference with a coverageData >= 26X There is a 1.1% of reference with a coverageData >= 27X There is a 1.03% of reference with a coverageData >= 28X There is a 0.97% of reference with a coverageData >= 29X There is a 0.91% of reference with a coverageData >= 30X There is a 0.86% of reference with a coverageData >= 31X There is a 0.81% of reference with a coverageData >= 32X There is a 0.77% of reference with a coverageData >= 33X There is a 0.72% of reference with a coverageData >= 34X There is a 0.68% of reference with a coverageData >= 35X There is a 0.65% of reference with a coverageData >= 36X There is a 0.61% of reference with a coverageData >= 37X There is a 0.58% of reference with a coverageData >= 38X There is a 0.55% of reference with a coverageData >= 39X There is a 0.53% of reference with a coverageData >= 40X There is a 0.5% of reference with a coverageData >= 41X There is a 0.48% of reference with a coverageData >= 42X There is a 0.45% of reference with a coverageData >= 43X There is a 0.43% of reference with a coverageData >= 44X There is a 0.41% of reference with a coverageData >= 45X There is a 0.39% of reference with a coverageData >= 46X There is a 0.37% of reference with a coverageData >= 47X There is a 0.36% of reference with a coverageData >= 48X There is a 0.34% of reference with a coverageData >= 49X There is a 0.33% of reference with a coverageData >= 50X There is a 0.31% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 387094876 1.5530347505132194 5.894864652222801 chr2 243199373 416162644 1.7111994939230373 6.578731169946213 chr3 198022430 399804130 2.0189840615530272 7.122607607006346 chr4 191154276 376198764 1.9680373982322006 6.321682559313017 chr5 180915260 354133245 1.9574536995939424 6.4451899231273755 chr6 171115067 339826535 1.9859533176000217 6.64901017636917 chr7 159138663 278441128 1.7496761802001566 7.14684194162543 chr8 146364022 258921165 1.7690219321794804 5.998562467333061 chr9 141213431 215593495 1.5267208896014997 6.307856179754477 chr10 135534747 245817844 1.8136887362175842 8.981870748566092 chr11 135006516 228963986 1.6959476681851415 6.632302889825286 chr12 133851895 264133616 1.9733274302915174 6.85223529696578 chr13 115169878 187159076 1.6250696731657561 6.429829420190555 chr14 107349540 153861189 1.43327292320023 6.245694675338592 chr15 102531392 261475576 2.550200196248189 9.28540464851974 chr16 90354753 103822375 1.1490527233249146 5.184316195739702 chr17 81195210 62720131 0.7724609739909534 2.998243834077201 chr18 78077248 131507003 1.6843191373753337 5.746434207735641 chr19 59128983 33703777 0.5700043411874681 2.8778510776477284 chr20 63025520 77397750 1.228038261326523 5.233978275253005 chr21 48129895 54469518 1.1317190282671508 4.217742568171421 chr22 51304566 20404213 0.39770754517249013 2.119905751082509 chrMT 16571 260 0.01569006094985215 0.16477585460668237 chrX 155270560 405444506 2.611213007797486 9.374050542206621 chrY 59373566 4829782 0.08134566146827024 1.4312359543922357