BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013285.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 = 3,392,626 number of mapped reads = 3,097,675 (91.31%) number of supplementary alignments = 18,780 (0.55%) number of secondary alignments = 0 number of mapped bases = 206,852,062 bp number of sequenced bases = 206,772,671 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 122,764 duplication rate = 2.54% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4343 >>>>>>> ACTG content number of A's = 57,290,842 bp (27.71%) number of C's = 38,106,493 bp (18.43%) number of T's = 64,724,756 bp (31.3%) number of G's = 46,647,705 bp (22.56%) number of N's = 2,875 bp (0%) GC percentage = 40.99% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 1,437,341 number of insertions = 14,651 mapped reads with insertion percentage = 0.47% number of deletions = 46,451 mapped reads with deletion percentage = 1.48% homopolymer indels = 47.69% >>>>>>> Coverage mean coverageData = 0.0668X std coverageData = 0.6501X There is a 5.71% of reference with a coverageData >= 1X There is a 0.68% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 18952826 0.07603923281699668 1.3408006417682667 chr2 243199373 15781720 0.06489210808943985 0.7523112367310943 chr3 198022430 16241480 0.08201838549299693 0.3246181848855803 chr4 191154276 17660042 0.0923863298773395 0.3790881872308372 chr5 180915260 10427036 0.05763491703242723 0.2759952912926995 chr6 171115067 11974439 0.06997886983266062 0.4061848792957213 chr7 159138663 11474366 0.0721029433306223 1.0086394909284715 chr8 146364022 8047182 0.054980601721917696 0.7832016351563589 chr9 141213431 9884370 0.06999596235290112 0.5934527844829972 chr10 135534747 11132921 0.08214071480872724 0.5435249090617603 chr11 135006516 10107951 0.07487009738107751 0.6249276516279424 chr12 133851895 9882330 0.07383033314545155 0.32755043146877044 chr13 115169878 7106831 0.061707376298514444 0.27930062409049755 chr14 107349540 5664740 0.052769112937046586 0.3136974638394413 chr15 102531392 4089434 0.03988470184819104 0.27493604811139666 chr16 90354753 4390108 0.04858746058439228 0.3063070914463019 chr17 81195210 6040077 0.07438957298096772 0.4066410841488103 chr18 78077248 4602366 0.058946314296323556 1.0909321513233416 chr19 59128983 3245066 0.05488114010010962 0.8360836506437388 chr20 63025520 4641758 0.0736488647773156 0.3402560898827847 chr21 48129895 3007732 0.06249197094653957 0.31855648086457444 chr22 51304566 1512260 0.029476128888801047 0.18807716575700253 chrMT 16571 32148 1.9400156900609498 1.8553466021625564 chrX 155270560 10509324 0.06768394472203874 0.3932895102069893 chrY 59373566 443555 0.007470580426312949 0.15498581859605143