BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082708.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 = 2,763,601 number of mapped reads = 2,536,688 (91.79%) number of supplementary alignments = 10,736 (0.39%) number of secondary alignments = 0 number of mapped bases = 167,073,874 bp number of sequenced bases = 167,007,143 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 102,928 duplication rate = 2.79% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5935 >>>>>>> ACTG content number of A's = 45,472,901 bp (27.23%) number of C's = 28,821,363 bp (17.26%) number of T's = 55,495,509 bp (33.23%) number of G's = 37,174,474 bp (22.26%) number of N's = 42,896 bp (0.03%) GC percentage = 39.52% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 1,543,530 number of insertions = 16,626 mapped reads with insertion percentage = 0.65% number of deletions = 41,281 mapped reads with deletion percentage = 1.61% homopolymer indels = 48.26% >>>>>>> Coverage mean coverageData = 0.054X std coverageData = 0.494X There is a 4.6% of reference with a coverageData >= 1X There is a 0.56% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% 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% 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 12371608 0.04963521434917508 0.6208187711217102 chr2 243199373 11816645 0.0485883037206679 0.5720725647529807 chr3 198022430 9158301 0.04624880625896773 0.24352634336987516 chr4 191154276 11673573 0.0610688562363104 0.3208116238223246 chr5 180915260 7748724 0.04283068216578303 0.2370353743733687 chr6 171115067 7866578 0.045972444963014274 0.35723037188047335 chr7 159138663 12501188 0.0785553162527198 1.0668181133285646 chr8 146364022 9402228 0.06423865558982794 0.5013674206127198 chr9 141213431 9533389 0.06751049763814605 0.6321464457731407 chr10 135534747 7480613 0.05519332249168547 0.3923152687439446 chr11 135006516 8209211 0.060806035465725224 0.4538198704344145 chr12 133851895 6706326 0.0501025853985855 0.26973025874160056 chr13 115169878 7022817 0.06097789736305877 0.2790600601528412 chr14 107349540 6047944 0.05633879753932807 0.3361035336045827 chr15 102531392 5076392 0.04951061232056617 0.2509622418645269 chr16 90354753 4779488 0.05289691843881196 0.3452095016549595 chr17 81195210 4282326 0.05274111613234327 0.3343540326715717 chr18 78077248 3781934 0.048438361966856205 1.0485145608560347 chr19 59128983 2388547 0.04039553665247379 0.4855230010889282 chr20 63025520 3576606 0.05674853614853158 0.29651519624945494 chr21 48129895 2807310 0.05832778151707998 0.32696604146599073 chr22 51304566 1893093 0.03689911342393969 0.21505682458333697 chrMT 16571 4016 0.24235109528694707 0.49303902925770837 chrX 155270560 10472362 0.06744589573194043 0.35448573966821056 chrY 59373566 472655 0.007960697526572684 0.24194256714423804