BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2971296.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 10,646,085 number of mapped reads = 8,488,234 (79.73%) number of secondary alignments = 0 number of mapped bases = 335,588,193 bp number of sequenced bases = 335,558,543 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 549,927 duplication rate = 5.37% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.8013 >>>>>>> ACTG content number of A's = 97,725,359 bp (29.12%) number of C's = 68,182,459 bp (20.32%) number of T's = 99,561,134 bp (29.67%) number of G's = 70,083,814 bp (20.89%) number of N's = 5,777 bp (0%) GC percentage = 41.2% >>>>>>> Mismatches and indels general error rate = 0.0026 number of mismatches = 854,131 number of insertions = 9,412 mapped reads with insertion percentage = 0.11% number of deletions = 22,386 mapped reads with deletion percentage = 0.26% homopolymer indels = 41.03% >>>>>>> Coverage mean coverageData = 0.1084X std coverageData = 0.7698X There is a 7.98% of reference with a coverageData >= 1X There is a 1.91% of reference with a coverageData >= 2X There is a 0.52% of reference with a coverageData >= 3X There is a 0.16% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% 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 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 26061853 0.10456083477521205 1.4990232771985572 chr2 243199373 28149084 0.11574488722057684 0.6485923266484536 chr3 198022430 22612896 0.11419360927951444 0.4380420651552551 chr4 191154276 22631714 0.11839501827309372 0.501648982662996 chr5 180915260 20871384 0.11536552527409794 0.44891003924859924 chr6 171115067 19983743 0.11678540849941636 0.5204763475529054 chr7 159138663 18518753 0.11636866020421448 1.0065315835934208 chr8 146364022 17110955 0.11690683793862948 1.1653258602706362 chr9 141213431 13892526 0.09837963642424352 0.6198351353195498 chr10 135534747 17137655 0.12644473376262694 0.6948851358395125 chr11 135006516 15167796 0.11234862175096794 0.6244274255489163 chr12 133851895 14926846 0.11151762924238016 0.44908052950461763 chr13 115169878 10932922 0.09492865834241832 0.39435488335052227 chr14 107349540 11371044 0.10592540964777306 0.5068184824257259 chr15 102531392 9298820 0.09069241935191907 0.38806815639973236 chr16 90354753 8666286 0.09591400244323617 0.4615562486803044 chr17 81195210 8000710 0.09853672402596163 0.46370462122436734 chr18 78077248 9022361 0.11555685210626276 1.4177590799103374 chr19 59128983 5875639 0.09936986401406565 1.3266446144130812 chr20 63025520 6495049 0.10305427071446614 0.44174544545803174 chr21 48129895 4274916 0.08882038907419183 0.469162519308944 chr22 51304566 3319932 0.06471026379991207 0.374126226882212 chrMT 16571 37047 2.2356526461891257 2.488324122725421 chrX 155270560 20065438 0.12922886347547147 0.5555284188051667 chrY 59373566 1162824 0.01958487721623458 0.3203938515543152