BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080673.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 = 1,512,233 number of mapped reads = 1,352,089 (89.41%) number of supplementary alignments = 15,594 (1.03%) number of secondary alignments = 0 number of mapped bases = 88,807,567 bp number of sequenced bases = 88,774,508 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 58,989 duplication rate = 3.76% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1914 >>>>>>> ACTG content number of A's = 23,959,576 bp (26.99%) number of C's = 16,345,181 bp (18.41%) number of T's = 28,145,954 bp (31.7%) number of G's = 20,319,654 bp (22.89%) number of N's = 4,143 bp (0%) GC percentage = 41.3% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 622,760 number of insertions = 6,537 mapped reads with insertion percentage = 0.48% number of deletions = 20,588 mapped reads with deletion percentage = 1.51% homopolymer indels = 47.33% >>>>>>> Coverage mean coverageData = 0.0287X std coverageData = 0.2476X There is a 2.47% of reference with a coverageData >= 1X There is a 0.31% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% 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 11227133 0.04504355076411224 0.317183471950584 chr2 243199373 6003064 0.02468371495349209 0.3674130665246222 chr3 198022430 5794382 0.029261240759443263 0.19273798162845632 chr4 191154276 3820158 0.019984685040474848 0.16380926236990367 chr5 180915260 4186338 0.023139772731167067 0.17164703046322136 chr6 171115067 5668008 0.03312395629076895 0.2574038328810758 chr7 159138663 5802401 0.03646129036537149 0.46144380605816904 chr8 146364022 8515779 0.05818218769637254 0.2979388724426408 chr9 141213431 2892237 0.020481316681555596 0.17844214527519897 chr10 135534747 4266461 0.031478724787821384 0.2097377994751762 chr11 135006516 3288550 0.024358453928253358 0.1848094941745907 chr12 133851895 2911595 0.021752362938156387 0.16745733965725285 chr13 115169878 1995492 0.017326509627803896 0.15013469273341645 chr14 107349540 1851100 0.01724366960491866 0.15032805205582586 chr15 102531392 1626783 0.015866194423655146 0.14959484396455933 chr16 90354753 2182972 0.024160012921511723 0.1779412879167685 chr17 81195210 1495133 0.01841405422807577 0.1558113894933913 chr18 78077248 2935924 0.0376028110007156 0.27228964551147217 chr19 59128983 1516144 0.025641300138715392 0.20989294475674064 chr20 63025520 2355765 0.03737795420013988 0.22206822131889786 chr21 48129895 1372943 0.028525784234517862 0.19344161877370553 chr22 51304566 879058 0.017134108492409816 0.14644537568164082 chrMT 16571 142811 8.618128055035907 5.5733488424209 chrX 155270560 5891908 0.03794607297094826 0.22748757437787193 chrY 59373566 185428 0.003123073321888734 0.06793101211960373