BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549097.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 = 11,073,546 number of mapped reads = 9,406,118 (84.94%) number of secondary alignments = 0 number of mapped bases = 372,493,925 bp number of sequenced bases = 372,459,520 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 527,801 duplication rate = 3.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.8551 >>>>>>> ACTG content number of A's = 109,076,389 bp (29.29%) number of C's = 76,141,170 bp (20.44%) number of T's = 110,647,273 bp (29.71%) number of G's = 76,593,182 bp (20.56%) number of N's = 1,506 bp (0%) GC percentage = 41.01% >>>>>>> Mismatches and indels general error rate = 0.0034 number of mismatches = 1,262,130 number of insertions = 10,624 mapped reads with insertion percentage = 0.11% number of deletions = 27,958 mapped reads with deletion percentage = 0.3% homopolymer indels = 43.21% >>>>>>> Coverage mean coverageData = 0.1203X std coverageData = 1.2287X There is a 9.46% of reference with a coverageData >= 1X There is a 1.69% of reference with a coverageData >= 2X There is a 0.36% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% 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 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% 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 29877720 0.11987019282090375 2.6760591754737604 chr2 243199373 32651431 0.1342578749164785 1.165504042733924 chr3 198022430 25923608 0.13091248299498193 0.44864432968973283 chr4 191154276 25917546 0.13558444279844412 0.599269098482571 chr5 180915260 24097849 0.13319964827732056 0.48519899253655113 chr6 171115067 22352748 0.130629922846011 0.5523132620610064 chr7 159138663 21047124 0.13225650890381052 1.7512317101973967 chr8 146364022 19689178 0.134521979725318 1.5009083752337675 chr9 141213431 15859480 0.11230858061936048 1.0747156515254512 chr10 135534747 17921616 0.1322289405240119 1.1482247029608827 chr11 135006516 17552026 0.1300087323192608 0.8901399747288242 chr12 133851895 16992928 0.12695321198104817 0.537468564364459 chr13 115169878 12104714 0.10510312427351881 0.3799629079067284 chr14 107349540 11456844 0.10672466784673693 0.6817786980385411 chr15 102531392 10468462 0.10210006707019056 0.3865236503854338 chr16 90354753 9796516 0.1084228075970724 0.5966538374844481 chr17 81195210 8577310 0.10563812816051588 0.48837157235674894 chr18 78077248 10400286 0.13320507915442922 2.478538457101198 chr19 59128983 6426880 0.10869255099483108 2.233725043909578 chr20 63025520 7319519 0.11613579705490729 0.5471746982186545 chr21 48129895 4840361 0.10056870059658347 0.6516358643406766 chr22 51304566 3510030 0.06841554804303383 0.32012222394181084 chrMT 16571 47653 2.875686440166556 3.454432177844312 chrX 155270560 14021525 0.09030382192219825 0.6803650642303397 chrY 59373566 3640571 0.061316360886930724 0.6343934648251112