BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617674.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 30,013,549 (93.79%) number of supplementary alignments = 189,309 (0.59%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,240,917 number of mapped paired reads (second in pair) = 14,772,632 number of mapped paired reads (both in pair) = 29,166,878 number of mapped paired reads (singletons) = 846,671 number of mapped bases = 2,894,026,779 bp number of sequenced bases = 2,892,268,619 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,907,274 duplication rate = 10.74% >>>>>>> Insert size mean insert size = 51,866.3873 std insert size = 2,149,939.7365 median insert size = 223 >>>>>>> Mapping quality mean mapping quality = 52.4838 >>>>>>> ACTG content number of A's = 861,784,737 bp (29.8%) number of C's = 574,750,199 bp (19.87%) number of T's = 860,707,685 bp (29.76%) number of G's = 591,978,472 bp (20.47%) number of N's = 3,047,526 bp (0.11%) GC percentage = 40.34% >>>>>>> Mismatches and indels general error rate = 0.0146 number of mismatches = 41,305,299 number of insertions = 456,141 mapped reads with insertion percentage = 1.49% number of deletions = 1,060,454 mapped reads with deletion percentage = 3.46% homopolymer indels = 47.59% >>>>>>> Coverage mean coverageData = 0.9349X std coverageData = 10.4218X There is a 33.1% of reference with a coverageData >= 1X There is a 19.06% of reference with a coverageData >= 2X There is a 11.59% of reference with a coverageData >= 3X There is a 7.37% of reference with a coverageData >= 4X There is a 4.83% of reference with a coverageData >= 5X There is a 3.26% of reference with a coverageData >= 6X There is a 2.26% of reference with a coverageData >= 7X There is a 1.6% of reference with a coverageData >= 8X There is a 1.15% of reference with a coverageData >= 9X There is a 0.85% of reference with a coverageData >= 10X There is a 0.64% of reference with a coverageData >= 11X There is a 0.49% of reference with a coverageData >= 12X There is a 0.38% of reference with a coverageData >= 13X There is a 0.3% of reference with a coverageData >= 14X There is a 0.24% of reference with a coverageData >= 15X There is a 0.2% of reference with a coverageData >= 16X There is a 0.16% of reference with a coverageData >= 17X There is a 0.13% of reference with a coverageData >= 18X There is a 0.11% of reference with a coverageData >= 19X There is a 0.1% of reference with a coverageData >= 20X There is a 0.08% of reference with a coverageData >= 21X There is a 0.07% of reference with a coverageData >= 22X There is a 0.07% of reference with a coverageData >= 23X There is a 0.06% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.03% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 177522752 0.7122259165805649 10.170886096664827 chr2 243199373 299135179 1.2299997952708537 11.983542615060253 chr3 198022430 242100035 1.2225889511607346 2.482557765629778 chr4 191154276 161710022 0.8459660196144396 8.29286668486576 chr5 180915260 191166364 1.05666246175143 2.32086207524892 chr6 171115067 140686816 0.8221766701584495 5.733855529990842 chr7 159138663 226434498 1.4228754579897407 13.165075687786207 chr8 146364022 128653672 0.8789979275098084 4.044186008135408 chr9 141213431 118811718 0.8413627312829755 19.95502715364686 chr10 135534747 122646082 0.9049050868114286 21.097321721016137 chr11 135006516 158984502 1.1776061386548187 11.68933765332742 chr12 133851895 123376908 0.9217419596487596 2.2257989834237577 chr13 115169878 124564941 1.0815756963813055 2.345508998077929 chr14 107349540 82762853 0.7709660702784568 2.4887369733838156 chr15 102531392 61785998 0.6026056683205862 1.846974303775587 chr16 90354753 80328875 0.8890387315872581 16.59417133467336 chr17 81195210 71196466 0.8768554943081002 12.426881461477493 chr18 78077248 53433470 0.6843667184581096 18.007088870808555 chr19 59128983 30890400 0.522424003132271 6.012141902663509 chr20 63025520 78246114 1.2414989039360564 3.0307735268398237 chr21 48129895 42156490 0.8758899224691847 4.301238413219118 chr22 51304566 18695011 0.36439273260785404 1.2903590743845526 chrMT 16571 3044052 183.69754390199748 130.98519460955336 chrX 155270560 144093264 0.928014067831017 4.359484190341484 chrY 59373566 11600297 0.19537814184851218 16.849892118705878