BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549087.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 = 9,261,294 number of mapped reads = 8,203,783 (88.58%) number of secondary alignments = 0 number of mapped bases = 325,831,448 bp number of sequenced bases = 325,795,940 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 278,096 duplication rate = 2.31% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.287 >>>>>>> ACTG content number of A's = 96,382,674 bp (29.58%) number of C's = 66,867,217 bp (20.52%) number of T's = 97,629,485 bp (29.97%) number of G's = 64,837,193 bp (19.9%) number of N's = 79,371 bp (0.02%) GC percentage = 40.43% >>>>>>> Mismatches and indels general error rate = 0.0041 number of mismatches = 1,316,695 number of insertions = 8,077 mapped reads with insertion percentage = 0.1% number of deletions = 28,088 mapped reads with deletion percentage = 0.34% homopolymer indels = 45.95% >>>>>>> Coverage mean coverageData = 0.1053X std coverageData = 0.7366X There is a 8.86% of reference with a coverageData >= 1X There is a 1.25% of reference with a coverageData >= 2X There is a 0.2% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% 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% 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 26391617 0.10588385655416281 1.7356432560057582 chr2 243199373 28479508 0.11710354203914827 0.6413707906898926 chr3 198022430 23098953 0.11664816455388412 0.4000962696036855 chr4 191154276 22110612 0.11566893748168103 0.39991654030444623 chr5 180915260 20874703 0.11538387087965934 0.4049062464961131 chr6 171115067 19916648 0.11639330392805211 0.533188213515333 chr7 159138663 18299303 0.11498967413091814 0.8214081315136335 chr8 146364022 17310617 0.11827098465495844 0.5742381812452948 chr9 141213431 13898105 0.09841914399771223 0.6077716821655211 chr10 135534747 15510076 0.11443616004979151 0.5538775544205469 chr11 135006516 15166160 0.11233650381734167 0.6541726200157089 chr12 133851895 15138129 0.1130961126848447 0.4129300720830801 chr13 115169878 11004150 0.095547118665872 0.344668119152249 chr14 107349540 10107537 0.09415538250094038 0.42206320234947226 chr15 102531392 9597471 0.09360519556781205 0.3440327813356465 chr16 90354753 8801701 0.09741270611408788 0.4311850208184169 chr17 81195210 8084018 0.09956274514223191 0.42550904693962543 chr18 78077248 9069600 0.11616188111548194 1.2313500119735024 chr19 59128983 5582906 0.0944191108445075 1.3266663903895954 chr20 63025520 6844514 0.10859908811541738 0.39540081671524946 chr21 48129895 4292654 0.08918893340615017 0.4041074367401273 chr22 51304566 3364257 0.06557422199030004 0.33525928048741377 chrMT 16571 3979 0.24011827892100657 0.5331092774187902 chrX 155270560 10403766 0.06700411204802766 0.42177321927424427 chrY 59373566 2480464 0.04177724477589909 0.35812576891400244