BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094083.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 404,622 number of mapped reads = 392,774 (97.07%) number of supplementary alignments = 15,073 (3.73%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 197,363 number of mapped paired reads (second in pair) = 195,411 number of mapped paired reads (both in pair) = 390,116 number of mapped paired reads (singletons) = 2,658 number of mapped bases = 52,320,467 bp number of sequenced bases = 51,197,302 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 375,404 duplication rate = 50.98% >>>>>>> Insert size mean insert size = 482,754.1056 std insert size = 6,289,074.9443 median insert size = 168 >>>>>>> Mapping quality mean mapping quality = 39.5041 >>>>>>> ACTG content number of A's = 13,326,594 bp (26.03%) number of C's = 12,228,807 bp (23.89%) number of T's = 12,817,066 bp (25.03%) number of G's = 12,824,223 bp (25.05%) number of N's = 612 bp (0%) GC percentage = 48.93% >>>>>>> Mismatches and indels general error rate = 0.04 number of mismatches = 1,969,950 number of insertions = 31,732 mapped reads with insertion percentage = 7.93% number of deletions = 156,667 mapped reads with deletion percentage = 38% homopolymer indels = 28.3% >>>>>>> Coverage mean coverageData = 0.0169X std coverageData = 4.493X There is a 0.01% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% 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 0.01% 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 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% 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 431954 0.0017330107273835038 0.6399732992375524 chr2 243199373 2519997 0.01036185648389809 4.446967501862174 chr3 198022430 869904 0.004392956898872516 1.895118012507391 chr4 191154276 710762 0.0037182636709628195 1.383164481394135 chr5 180915260 315233 0.0017424345519554292 0.6806712906678106 chr6 171115067 1134973 0.006632805748192823 3.435940086261303 chr7 159138663 1593922 0.010015931829212364 3.655894335361854 chr8 146364022 865632 0.005914240317883585 2.035552670818595 chr9 141213431 645350 0.00457003271877163 2.116294954816793 chr10 135534747 956807 0.007059495968218393 2.648120796432729 chr11 135006516 1929999 0.014295598887982562 4.081870927598634 chr12 133851895 1394098 0.010415227965207366 4.156164394524371 chr13 115169878 1319583 0.011457709454202948 3.3682865005257354 chr14 107349540 289743 0.002699061402591944 1.2653287794274846 chr15 102531392 939712 0.009165115011800484 2.9683726575733136 chr16 90354753 304692 0.003372174566179158 1.228934322123989 chr17 81195210 1098459 0.013528618252234337 3.9268820971852545 chr18 78077248 94866 0.0012150274558857402 0.45269938928219766 chr19 59128983 213018 0.003602598745863767 0.9211041589361085 chr20 63025520 384561 0.006101671196048839 1.9319202667330035 chr21 48129895 766511 0.01592588140904941 7.0855065094218865 chr22 51304566 79851 0.0015564111779056858 0.35083086232370025 chrMT 16571 1534332 92.59139460503289 438.7247562339559 chrX 155270560 31285409 0.2014896384736424 15.07667133804465 chrY 59373566 641099 0.01079771762403491 2.5887933840719417