BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083612.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 = 1,936,639 number of mapped reads = 1,718,599 (88.74%) number of supplementary alignments = 20,904 (1.08%) number of secondary alignments = 0 number of mapped bases = 113,370,492 bp number of sequenced bases = 113,328,762 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 91,995 duplication rate = 4.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0666 >>>>>>> ACTG content number of A's = 30,420,460 bp (26.84%) number of C's = 21,153,213 bp (18.67%) number of T's = 35,677,970 bp (31.48%) number of G's = 26,071,717 bp (23.01%) number of N's = 5,402 bp (0%) GC percentage = 41.67% >>>>>>> Mismatches and indels general error rate = 0.0072 number of mismatches = 804,440 number of insertions = 8,388 mapped reads with insertion percentage = 0.48% number of deletions = 25,784 mapped reads with deletion percentage = 1.49% homopolymer indels = 47.93% >>>>>>> Coverage mean coverageData = 0.0366X std coverageData = 0.3164X There is a 3.01% of reference with a coverageData >= 1X There is a 0.48% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% 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 11646040 0.046724216586806415 0.5734667288003034 chr2 243199373 7456922 0.030661764905125805 0.4555116707456169 chr3 198022430 8638103 0.043621841222734214 0.24792465177321396 chr4 191154276 5488712 0.02871351933555491 0.20592207950819527 chr5 180915260 5544431 0.030646563479498633 0.20591466399653627 chr6 171115067 9230491 0.053943180818787864 0.32254595520521806 chr7 159138663 9212022 0.05788676256504681 0.412927505674276 chr8 146364022 7684603 0.05250336042282303 0.32097558193313536 chr9 141213431 4092465 0.02898070651650692 0.23207698740465477 chr10 135534747 5270003 0.03888304008122729 0.25397583516184385 chr11 135006516 3925524 0.02907655212730621 0.22917637222812764 chr12 133851895 3789804 0.0283134131197769 0.19841068776578802 chr13 115169878 4040727 0.03508492906452501 0.23481286552641809 chr14 107349540 2235690 0.020826265301183405 0.17124557357565834 chr15 102531392 2267524 0.022115412224189838 0.19184216456491776 chr16 90354753 2613106 0.02892051511667571 0.20575739672397947 chr17 81195210 2079448 0.025610476283022113 0.19556649686071245 chr18 78077248 3339965 0.04277769882463071 0.3959248922944173 chr19 59128983 3478842 0.05883480187710991 0.4242738641063745 chr20 63025520 2742203 0.04350940698307606 0.2570675321353957 chr21 48129895 1949309 0.040501002547377256 0.2401948056453963 chr22 51304566 727161 0.014173416845588363 0.1388680754094697 chrMT 16571 91189 5.50292679983103 4.073881650106756 chrX 155270560 5582936 0.035956178685772756 0.22951165462569786 chrY 59373566 243272 0.0040973115881232395 0.08737131187884847