BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081030.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 3,131,038 number of mapped reads = 2,487,720 (79.45%) number of supplementary alignments = 13,114 (0.42%) number of secondary alignments = 0 number of mapped bases = 153,211,538 bp number of sequenced bases = 153,160,387 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 104,451 duplication rate = 3.5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.634 >>>>>>> ACTG content number of A's = 43,851,605 bp (28.63%) number of C's = 30,906,887 bp (20.18%) number of T's = 44,724,803 bp (29.2%) number of G's = 33,675,132 bp (21.99%) number of N's = 1,960 bp (0%) GC percentage = 42.17% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 1,117,174 number of insertions = 10,194 mapped reads with insertion percentage = 0.41% number of deletions = 29,635 mapped reads with deletion percentage = 1.18% homopolymer indels = 45.94% >>>>>>> Coverage mean coverageData = 0.0495X std coverageData = 0.3319X There is a 3.97% of reference with a coverageData >= 1X There is a 0.7% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% 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 12550284 0.05035206712684579 0.4282067539134538 chr2 243199373 12744249 0.05240247473828808 0.3815324025572229 chr3 198022430 10174075 0.05137839688160579 0.2724406393463359 chr4 191154276 10101311 0.05284376165354522 0.288706828133975 chr5 180915260 9508645 0.05255855697302704 0.2767774954863669 chr6 171115067 8783814 0.051332791167945487 0.3364988172026726 chr7 159138663 8482606 0.05330323781845522 0.47683738384302565 chr8 146364022 7842557 0.05358254639927837 0.35494700055905937 chr9 141213431 6668401 0.047222144188253594 0.3152428579955974 chr10 135534747 7009769 0.05171934987269353 0.3170428093307367 chr11 135006516 7045484 0.052186251513963965 0.327938197319132 chr12 133851895 7179861 0.053640338823742466 0.2829630420003863 chr13 115169878 4822424 0.04187226802480419 0.24595887217487677 chr14 107349540 4626122 0.043094008600316314 0.2648951969301872 chr15 102531392 4511115 0.04399740325382494 0.26326887694192674 chr16 90354753 4363282 0.048290564194226726 0.2791974701174397 chr17 81195210 3997364 0.04923152486458253 0.28447371273558103 chr18 78077248 3998263 0.05120906669251457 0.4930499859977385 chr19 59128983 2795418 0.047276612215704776 0.34832640158418393 chr20 63025520 3172348 0.050334340755935056 0.27624132698686615 chr21 48129895 1956922 0.0406591786663985 0.25846687511013366 chr22 51304566 1612228 0.031424649416194265 0.23092678886752319 chrMT 16571 58856 3.5517470279403778 2.7816069144250775 chrX 155270560 8823856 0.056828905621258786 0.3094226331467425 chrY 59373566 382284 0.006438622871329642 0.1299483059397953