BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240042.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 = 2,110,322 number of mapped reads = 1,755,698 (83.2%) number of supplementary alignments = 12,694 (0.6%) number of secondary alignments = 0 number of mapped bases = 113,370,510 bp number of sequenced bases = 113,325,711 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 216,155 duplication rate = 9.63% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2851 >>>>>>> ACTG content number of A's = 31,811,138 bp (28.07%) number of C's = 20,528,706 bp (18.11%) number of T's = 36,268,811 bp (32%) number of G's = 24,643,773 bp (21.75%) number of N's = 73,283 bp (0.06%) GC percentage = 39.86% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 973,952 number of insertions = 8,169 mapped reads with insertion percentage = 0.46% number of deletions = 26,115 mapped reads with deletion percentage = 1.47% homopolymer indels = 48.03% >>>>>>> Coverage mean coverageData = 0.0366X std coverageData = 0.3906X There is a 2% of reference with a coverageData >= 1X There is a 0.85% of reference with a coverageData >= 2X There is a 0.39% of reference with a coverageData >= 3X There is a 0.18% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 9769647 0.03919607887356076 0.5884408479461121 chr2 243199373 11911540 0.04897849798321643 0.4471665026897362 chr3 198022430 7038606 0.03554448857131993 0.3138411934696209 chr4 191154276 9527893 0.04984399616569393 0.3839132549882632 chr5 180915260 6251605 0.034555432195161426 0.30619848702466324 chr6 171115067 6014564 0.03514923674137942 0.3292584372682811 chr7 159138663 6078512 0.038196324421803145 0.444096026903696 chr8 146364022 6657497 0.04548588450240866 0.5423313451151388 chr9 141213431 4155714 0.02942860300589963 0.3378366710634203 chr10 135534747 5345927 0.03944322115420336 0.4065943997898358 chr11 135006516 4834836 0.03581187148033655 0.34221194742601635 chr12 133851895 5701856 0.04259824636774847 0.34544977505782043 chr13 115169878 3241022 0.028141229775375816 0.27771095350711983 chr14 107349540 3815235 0.035540301337108664 0.3373615812458152 chr15 102531392 2929010 0.02856695830287762 0.2949384485282652 chr16 90354753 2820145 0.03121191643343876 0.29256834792410097 chr17 81195210 2541007 0.031295035753956424 0.2988081260010871 chr18 78077248 2756068 0.03529924620293994 0.5541422681047099 chr19 59128983 1638104 0.027703909603857046 0.39905434876044205 chr20 63025520 1920678 0.03047460774619551 0.2952963581977399 chr21 48129895 1410830 0.02931296650449788 0.2905768351208875 chr22 51304566 937414 0.018271551113013994 0.21303680418387164 chrMT 16571 16234 0.9796632671534609 1.4332867031650693 chrX 155270560 5812077 0.037431931719702695 0.3410886257755913 chrY 59373566 244489 0.00411780892527156 0.11945598737521156