BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038424.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 11,407,816 number of mapped reads = 10,683,054 (93.65%) number of supplementary alignments = 209,851 (1.84%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,415,814 number of mapped paired reads (second in pair) = 5,267,240 number of mapped paired reads (both in pair) = 10,514,564 number of mapped paired reads (singletons) = 168,490 number of mapped bases = 1,521,815,613 bp number of sequenced bases = 1,520,668,739 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,454,214 duplication rate = 8.05% >>>>>>> Insert size mean insert size = 99,087.1713 std insert size = 2,995,498.3711 median insert size = 264 >>>>>>> Mapping quality mean mapping quality = 53.77 >>>>>>> ACTG content number of A's = 440,750,620 bp (28.98%) number of C's = 312,787,717 bp (20.57%) number of T's = 441,641,840 bp (29.04%) number of G's = 325,457,700 bp (21.4%) number of N's = 30,862 bp (0%) GC percentage = 41.97% >>>>>>> Mismatches and indels general error rate = 0.0148 number of mismatches = 21,682,258 number of insertions = 281,567 mapped reads with insertion percentage = 2.45% number of deletions = 530,386 mapped reads with deletion percentage = 4.74% homopolymer indels = 45.77% >>>>>>> Coverage mean coverageData = 0.4916X std coverageData = 7.2575X There is a 24.05% of reference with a coverageData >= 1X There is a 11.12% of reference with a coverageData >= 2X There is a 4.99% of reference with a coverageData >= 3X There is a 2.54% of reference with a coverageData >= 4X There is a 1.27% of reference with a coverageData >= 5X There is a 0.68% of reference with a coverageData >= 6X There is a 0.37% of reference with a coverageData >= 7X There is a 0.21% of reference with a coverageData >= 8X There is a 0.13% of reference with a coverageData >= 9X There is a 0.09% of reference with a coverageData >= 10X There is a 0.06% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 119396752 0.47902288676745164 6.759313079870825 chr2 243199373 140253476 0.5767016348352181 8.19613178460964 chr3 198022430 102761082 0.5189365770332179 1.1982416226759716 chr4 191154276 101722787 0.5321502041628406 6.076215372916734 chr5 180915260 93582410 0.5172720642802603 1.2590428704426466 chr6 171115067 90690697 0.5299983139415771 7.3541506837008255 chr7 159138663 79988812 0.5026359433470922 6.522467073864703 chr8 146364022 77170254 0.5272487934227443 1.942257998891351 chr9 141213431 65611952 0.46462968525989573 12.424857089128633 chr10 135534747 87231327 0.6436085869551961 19.673597974802796 chr11 135006516 71129434 0.5268592665556973 3.801838245333363 chr12 133851895 65552837 0.48974156847013633 1.143345091351715 chr13 115169878 46588536 0.40452014718640233 0.9975471523179422 chr14 107349540 44402778 0.4136280229985149 1.1659723134440854 chr15 102531392 41870583 0.40836842437484905 1.0126923582004095 chr16 90354753 57601200 0.6375004976218572 13.081820186615328 chr17 81195210 35895435 0.4420880862307025 4.622760800792908 chr18 78077248 43561960 0.5579341116121306 10.339786939741941 chr19 59128983 20035221 0.33883926263369013 3.5553957058754895 chr20 63025520 31788326 0.5043722923666477 2.076136897421386 chr21 48129895 19801034 0.41140821105053316 2.9261742558010915 chr22 51304566 14637456 0.28530513249054673 1.0161896388194918 chrMT 16571 1637860 98.83893548971093 42.32842286790919 chrX 155270560 46151105 0.29723023475924865 1.2964734598605037 chrY 59373566 22752299 0.3832058697636588 10.756714341068953