BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548920.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 = 9,886,925 number of mapped reads = 8,579,420 (86.78%) number of secondary alignments = 0 number of mapped bases = 339,422,926 bp number of sequenced bases = 339,384,988 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 338,358 duplication rate = 2.89% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.0587 >>>>>>> ACTG content number of A's = 99,095,207 bp (29.2%) number of C's = 70,334,031 bp (20.72%) number of T's = 99,695,919 bp (29.38%) number of G's = 70,256,467 bp (20.7%) number of N's = 3,364 bp (0%) GC percentage = 41.43% >>>>>>> Mismatches and indels general error rate = 0.0028 number of mismatches = 923,724 number of insertions = 11,430 mapped reads with insertion percentage = 0.13% number of deletions = 28,467 mapped reads with deletion percentage = 0.33% homopolymer indels = 39.94% >>>>>>> Coverage mean coverageData = 0.1096X std coverageData = 1.3972X There is a 8.67% of reference with a coverageData >= 1X There is a 1.66% of reference with a coverageData >= 2X There is a 0.35% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.03% 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 0.01% 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 26772992 0.10741394301280396 1.141311716831194 chr2 243199373 28596196 0.11758334590772156 0.595531535742228 chr3 198022430 22985659 0.11607603744686902 0.4116726217354421 chr4 191154276 22441264 0.11739870260605627 0.42653168601657265 chr5 180915260 21190215 0.11712784759008167 0.4205366438173365 chr6 171115067 19902895 0.11631293111085303 0.46899160845364285 chr7 159138663 18849036 0.1184441017956774 0.8891185867203749 chr8 146364022 17861717 0.12203625423739722 5.785918196661729 chr9 141213431 14251303 0.10092030835225581 0.5737156036574897 chr10 135534747 15700197 0.11583890734676326 0.5330793427684759 chr11 135006516 15432763 0.11431124554017823 0.6603665637817621 chr12 133851895 15413908 0.1151564421258287 0.42397337723929057 chr13 115169878 11038692 0.09584704083823029 0.3692951564319838 chr14 107349540 10429371 0.09715338323759934 0.46308541237991413 chr15 102531392 9712886 0.09473085082079058 0.3703254877258308 chr16 90354753 9271412 0.10261122621850341 0.42429374183867086 chr17 81195210 8695646 0.10709555403576147 0.43807150322814603 chr18 78077248 9055196 0.11597739715416198 1.0269464713560028 chr19 59128983 6426134 0.10867993450859792 1.0091411308043787 chr20 63025520 6870209 0.10900678011065994 0.41229332530223795 chr21 48129895 4308092 0.08950969039097217 0.41003198352142445 chr22 51304566 3720292 0.07251385773344228 0.40391102701772136 chrMT 16571 19677 1.1874358819624646 1.6120252974908436 chrX 155270560 19480615 0.12546238643049912 0.5236232124193028 chrY 59373566 996559 0.016784556952499703 0.2213870209033862