BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472418.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 18,359,594 number of mapped reads = 18,203,419 (99.15%) number of supplementary alignments = 75,373 (0.41%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,137,266 number of mapped paired reads (second in pair) = 9,066,153 number of mapped paired reads (both in pair) = 18,100,990 number of mapped paired reads (singletons) = 102,429 number of mapped bases = 1,787,960,612 bp number of sequenced bases = 1,787,740,645 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,448,531 duplication rate = 46.86% >>>>>>> Insert size mean insert size = 22,597.6019 std insert size = 1,502,172.1777 median insert size = 229 >>>>>>> Mapping quality mean mapping quality = 55.1313 >>>>>>> ACTG content number of A's = 491,766,315 bp (27.51%) number of C's = 403,210,960 bp (22.55%) number of T's = 493,570,598 bp (27.61%) number of G's = 398,978,715 bp (22.32%) number of N's = 214,057 bp (0.01%) GC percentage = 44.87% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 9,566,742 number of insertions = 105,493 mapped reads with insertion percentage = 0.57% number of deletions = 89,950 mapped reads with deletion percentage = 0.49% homopolymer indels = 46.42% >>>>>>> Coverage mean coverageData = 0.5776X std coverageData = 17.9513X There is a 5.18% of reference with a coverageData >= 1X There is a 2.19% of reference with a coverageData >= 2X There is a 0.93% of reference with a coverageData >= 3X There is a 0.68% of reference with a coverageData >= 4X There is a 0.52% of reference with a coverageData >= 5X There is a 0.46% of reference with a coverageData >= 6X There is a 0.43% of reference with a coverageData >= 7X There is a 0.4% of reference with a coverageData >= 8X There is a 0.38% of reference with a coverageData >= 9X There is a 0.37% of reference with a coverageData >= 10X There is a 0.36% of reference with a coverageData >= 11X There is a 0.35% of reference with a coverageData >= 12X There is a 0.34% of reference with a coverageData >= 13X There is a 0.33% of reference with a coverageData >= 14X There is a 0.32% of reference with a coverageData >= 15X There is a 0.31% of reference with a coverageData >= 16X There is a 0.3% of reference with a coverageData >= 17X There is a 0.3% of reference with a coverageData >= 18X There is a 0.29% of reference with a coverageData >= 19X There is a 0.28% of reference with a coverageData >= 20X There is a 0.28% of reference with a coverageData >= 21X There is a 0.27% of reference with a coverageData >= 22X There is a 0.27% of reference with a coverageData >= 23X There is a 0.26% of reference with a coverageData >= 24X There is a 0.26% of reference with a coverageData >= 25X There is a 0.25% of reference with a coverageData >= 26X There is a 0.25% of reference with a coverageData >= 27X There is a 0.24% of reference with a coverageData >= 28X There is a 0.24% of reference with a coverageData >= 29X There is a 0.24% of reference with a coverageData >= 30X There is a 0.23% of reference with a coverageData >= 31X There is a 0.23% of reference with a coverageData >= 32X There is a 0.23% of reference with a coverageData >= 33X There is a 0.22% of reference with a coverageData >= 34X There is a 0.22% of reference with a coverageData >= 35X There is a 0.22% of reference with a coverageData >= 36X There is a 0.21% of reference with a coverageData >= 37X There is a 0.21% of reference with a coverageData >= 38X There is a 0.21% of reference with a coverageData >= 39X There is a 0.21% of reference with a coverageData >= 40X There is a 0.2% of reference with a coverageData >= 41X There is a 0.2% of reference with a coverageData >= 42X There is a 0.2% of reference with a coverageData >= 43X There is a 0.2% of reference with a coverageData >= 44X There is a 0.19% of reference with a coverageData >= 45X There is a 0.19% of reference with a coverageData >= 46X There is a 0.19% of reference with a coverageData >= 47X There is a 0.19% of reference with a coverageData >= 48X There is a 0.18% of reference with a coverageData >= 49X There is a 0.18% of reference with a coverageData >= 50X There is a 0.18% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 197027889 0.790481035551763 20.644378430116877 chr2 243199373 149071395 0.6129596189378334 18.457320072799494 chr3 198022430 146772981 0.7411937172975809 17.789106028193416 chr4 191154276 80144309 0.41926506001885094 14.694386211067151 chr5 180915260 69325133 0.3831911857518266 13.661363517990555 chr6 171115067 170785469 0.9980738224530514 27.710319842591787 chr7 159138663 103182589 0.6483816506614738 18.374260381208877 chr8 146364022 93026781 0.6355850278560943 17.41796454828424 chr9 141213431 59397273 0.42062056405951925 10.824287079212516 chr10 135534747 63170148 0.4660808346069366 16.297166939805756 chr11 135006516 79751110 0.5907204508558683 17.98281585786579 chr12 133851895 104962339 0.7841677474943481 18.245880704653604 chr13 115169878 35715023 0.31010732684808434 9.837270015434942 chr14 107349540 63066619 0.5874884885394013 29.362391394501827 chr15 102531392 35198388 0.34329376899515807 11.357523013735806 chr16 90354753 104921590 1.1612182703880558 30.926511974008157 chr17 81195210 82864649 1.020560806481072 23.693270229513832 chr18 78077248 26601816 0.34071149638880716 12.782849276036643 chr19 59128983 28700089 0.48538106938182923 12.40452996682121 chr20 63025520 25599957 0.40618398705794095 9.585202517310348 chr21 48129895 8609214 0.17887456434301383 8.248034370713599 chr22 51304566 14601040 0.2845953321191724 9.565344821780252 chrMT 16571 4399 0.2654637619938447 0.6260471687828878 chrX 155270560 43446480 0.27981144654852796 10.03863994985913 chrY 59373566 2013932 0.03391967395052539 1.5673618443443837