BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063599.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 = 1,768,183 number of mapped reads = 857,898 (48.52%) number of supplementary alignments = 7,680 (0.43%) number of secondary alignments = 0 number of mapped bases = 54,920,219 bp number of sequenced bases = 54,897,741 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 176,531 duplication rate = 13.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.45 >>>>>>> ACTG content number of A's = 15,138,801 bp (27.58%) number of C's = 9,985,492 bp (18.19%) number of T's = 17,607,719 bp (32.07%) number of G's = 12,164,384 bp (22.16%) number of N's = 1,345 bp (0%) GC percentage = 40.35% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 446,443 number of insertions = 4,393 mapped reads with insertion percentage = 0.51% number of deletions = 13,360 mapped reads with deletion percentage = 1.54% homopolymer indels = 46.33% >>>>>>> Coverage mean coverageData = 0.0177X std coverageData = 0.4172X There is a 0.61% of reference with a coverageData >= 1X There is a 0.34% of reference with a coverageData >= 2X There is a 0.23% of reference with a coverageData >= 3X There is a 0.16% of reference with a coverageData >= 4X There is a 0.11% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 4708378 0.01889013548335352 0.4723308374478443 chr2 243199373 4393355 0.018064828645754774 0.40105574135233574 chr3 198022430 3404358 0.01719177973929519 0.31198213289788235 chr4 191154276 3906446 0.020436090061621223 0.7434597692144564 chr5 180915260 3444172 0.01903748749552691 0.33915024412843536 chr6 171115067 3172205 0.018538431802735407 0.3536095349399033 chr7 159138663 3480052 0.021868048495543788 0.48493642170702195 chr8 146364022 2754323 0.018818306318474906 0.4234459166505668 chr9 141213431 1998467 0.014152102854862297 0.2916668922795473 chr10 135534747 2659120 0.019619470717719346 0.3585047024579375 chr11 135006516 2658888 0.019694516078023968 0.34463561844989027 chr12 133851895 2324327 0.017364916649106835 0.3282217285743928 chr13 115169878 1860391 0.016153451165416707 0.3402548408050247 chr14 107349540 1697479 0.015812634129591985 0.3835990569496815 chr15 102531392 1381004 0.01346908466823507 0.6860313361208797 chr16 90354753 1454282 0.016095246256718782 0.30541305955689946 chr17 81195210 1240013 0.015271996956470708 0.2900689805603089 chr18 78077248 1413103 0.01809878083817708 0.44965594480349513 chr19 59128983 955009 0.01615128404965125 0.3380761000405015 chr20 63025520 1071092 0.01699457616533747 0.30888321306935046 chr21 48129895 859498 0.017857882299556233 0.33334080088368495 chr22 51304566 594520 0.011588052416231336 0.23784844545733252 chrMT 16571 10198 0.6154124675638163 2.62750656071609 chrX 155270560 3313966 0.02134317027001126 0.3752828614322672 chrY 59373566 165573 0.002788665245405674 0.18405000472709263