BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472586.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 = 8,044,008 number of mapped reads = 7,196,117 (89.46%) number of supplementary alignments = 240,776 (2.99%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,637,885 number of mapped paired reads (second in pair) = 3,558,232 number of mapped paired reads (both in pair) = 6,995,350 number of mapped paired reads (singletons) = 200,767 number of mapped bases = 579,010,513 bp number of sequenced bases = 578,759,268 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,079,827 duplication rate = 13.3% >>>>>>> Insert size mean insert size = 251,401.265 std insert size = 4,882,239.5171 median insert size = 123 >>>>>>> Mapping quality mean mapping quality = 50.063 >>>>>>> ACTG content number of A's = 148,689,179 bp (25.69%) number of C's = 115,916,391 bp (20.03%) number of T's = 172,121,307 bp (29.74%) number of G's = 141,678,279 bp (24.48%) number of N's = 354,112 bp (0.06%) GC percentage = 44.51% >>>>>>> Mismatches and indels general error rate = 0.0125 number of mismatches = 7,089,533 number of insertions = 57,839 mapped reads with insertion percentage = 0.79% number of deletions = 132,630 mapped reads with deletion percentage = 1.8% homopolymer indels = 42.2% >>>>>>> Coverage mean coverageData = 0.187X std coverageData = 1.7709X There is a 10.82% of reference with a coverageData >= 1X There is a 4.7% of reference with a coverageData >= 2X There is a 1.44% of reference with a coverageData >= 3X There is a 0.65% of reference with a coverageData >= 4X There is a 0.27% of reference with a coverageData >= 5X There is a 0.14% of reference with a coverageData >= 6X There is a 0.07% 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 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% 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 38486811 0.15441009071748713 2.355582624746082 chr2 243199373 57281366 0.23553253979811864 1.99270414058301 chr3 198022430 30481647 0.15393027446436244 0.5657043514436934 chr4 191154276 29554366 0.15461001772202052 1.0388915415207511 chr5 180915260 27386259 0.15137616915234237 0.589436566619764 chr6 171115067 38523128 0.2251299588948529 1.0396657000119154 chr7 159138663 49431110 0.310616597300431 3.33963544108885 chr8 146364022 28412062 0.19411916679906488 1.4551230879572379 chr9 141213431 20085681 0.14223633586241524 1.633881289733369 chr10 135534747 22800569 0.168226742622687 1.6670857195249935 chr11 135006516 21344602 0.15810053197728619 1.2745514586087094 chr12 133851895 29798774 0.2226249691870257 0.7099114667064411 chr13 115169878 27126595 0.23553550173943918 0.736659260435498 chr14 107349540 15082166 0.14049586053186627 4.516659591000646 chr15 102531392 13771906 0.13431892156501687 0.5385356676579282 chr16 90354753 21498762 0.23793725605115648 1.0793283356444148 chr17 81195210 22735100 0.2800054338180787 1.4780393918560775 chr18 78077248 12747473 0.16326744764364645 3.017854662597068 chr19 59128983 13389671 0.22644852525199022 1.6695125065151055 chr20 63025520 16280409 0.2583145525812401 0.9875080256658344 chr21 48129895 8789504 0.1826204690452784 0.7777691375393174 chr22 51304566 5984480 0.1166461480251095 0.49947749368917227 chrMT 16571 395271 23.853177237342344 13.848882448205957 chrX 155270560 26221225 0.16887441508551268 0.8425328031501622 chrY 59373566 1401576 0.023606060649953214 0.8374717622323531