BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081025.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 = 2,385,588 number of mapped reads = 1,615,108 (67.7%) number of supplementary alignments = 6,289 (0.26%) number of secondary alignments = 0 number of mapped bases = 96,770,050 bp number of sequenced bases = 96,739,321 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 42,171 duplication rate = 2.14% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0363 >>>>>>> ACTG content number of A's = 27,626,563 bp (28.56%) number of C's = 19,556,996 bp (20.22%) number of T's = 27,760,651 bp (28.7%) number of G's = 21,793,871 bp (22.53%) number of N's = 1,240 bp (0%) GC percentage = 42.74% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 650,512 number of insertions = 6,060 mapped reads with insertion percentage = 0.37% number of deletions = 17,757 mapped reads with deletion percentage = 1.09% homopolymer indels = 45.69% >>>>>>> Coverage mean coverageData = 0.0313X std coverageData = 0.2405X There is a 2.77% of reference with a coverageData >= 1X There is a 0.27% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 7840105 0.031454705984463725 0.3247111399127046 chr2 243199373 8069236 0.03317950988302918 0.2545670860896989 chr3 198022430 6746309 0.0340684083111191 0.20287675418649356 chr4 191154276 6209397 0.032483693956184376 0.203525794704253 chr5 180915260 5734893 0.03169933260466806 0.19674095117332782 chr6 171115067 6030380 0.035241665773359396 0.26816120138677707 chr7 159138663 5551962 0.034887574743542996 0.33621208448443657 chr8 146364022 4780009 0.032658360536170564 0.24151759242780996 chr9 141213431 4093227 0.028986102603795527 0.23041623177125475 chr10 135534747 4900883 0.036159605624969365 0.2443597971731648 chr11 135006516 4209035 0.031176532249747115 0.22836955112492704 chr12 133851895 4173745 0.031181814796122236 0.1964469863175954 chr13 115169878 2814644 0.024439063832298234 0.17218198881433888 chr14 107349540 2889432 0.02691610974765239 0.18610917849988784 chr15 102531392 2721597 0.026544036386436654 0.18881478474667396 chr16 90354753 2932291 0.03245309076324961 0.20641932652529804 chr17 81195210 2506467 0.030869641201740843 0.20922916248154744 chr18 78077248 2266841 0.029033310702754278 0.3565595282760385 chr19 59128983 1850839 0.03130172220279858 0.2812550753258883 chr20 63025520 2061613 0.03271076541692952 0.20249568026185918 chr21 48129895 1307668 0.02716955854568143 0.1920131576208617 chr22 51304566 977432 0.019051559660401375 0.1512417375810815 chrMT 16571 31186 1.881962464546497 1.7371240049958423 chrX 155270560 5837267 0.03759416466328195 0.23160697069888503 chrY 59373566 233592 0.003934276071610723 0.0883174993568905