BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819121.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,384,388 number of mapped reads = 1,263,100 (91.24%) number of supplementary alignments = 4,616 (0.33%) number of secondary alignments = 0 number of mapped bases = 73,479,161 bp number of sequenced bases = 73,456,544 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 55,212 duplication rate = 3.33% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7435 >>>>>>> ACTG content number of A's = 18,596,648 bp (25.32%) number of C's = 14,406,846 bp (19.61%) number of T's = 22,972,674 bp (31.27%) number of G's = 17,479,372 bp (23.8%) number of N's = 1,004 bp (0%) GC percentage = 43.41% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 375,253 number of insertions = 4,834 mapped reads with insertion percentage = 0.38% number of deletions = 13,618 mapped reads with deletion percentage = 1.07% homopolymer indels = 43.74% >>>>>>> Coverage mean coverageData = 0.0237X std coverageData = 0.2379X There is a 2.12% of reference with a coverageData >= 1X There is a 0.18% of reference with a coverageData >= 2X There is a 0.02% 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 7095229 0.028466244021915596 0.41147961129261956 chr2 243199373 6321754 0.025994121292409748 0.28713544083092 chr3 198022430 4345747 0.021945731097229745 0.16252810624032393 chr4 191154276 4462256 0.023343741470894432 0.18875352817338092 chr5 180915260 4254412 0.023516048342190704 0.16839772265163852 chr6 171115067 3383015 0.019770409814350246 0.18588843417788986 chr7 159138663 4027403 0.025307508081804105 0.3025094624383596 chr8 146364022 4540950 0.031025042479360127 0.24643644720537222 chr9 141213431 3396872 0.024054879029176763 0.21944111472571465 chr10 135534747 3429281 0.025301858570629124 0.23720256745361115 chr11 135006516 2412168 0.01786704872822583 0.2133070550485119 chr12 133851895 3004595 0.02244716072193076 0.1663565161093871 chr13 115169878 1780704 0.015461542817645427 0.13662980978036876 chr14 107349540 1815058 0.016907925269172088 0.14663152383148748 chr15 102531392 2140627 0.020877771755990593 0.15935870213497394 chr16 90354753 2096820 0.023206526833181647 0.17776356643286967 chr17 81195210 2692044 0.03315520706209147 0.2074478120228053 chr18 78077248 1867230 0.02391516155897298 0.3584932492401262 chr19 59128983 1451390 0.02454616883906155 0.30709481200178657 chr20 63025520 2197729 0.03487046199698154 0.20585452891022565 chr21 48129895 1079829 0.022435723161249366 0.18026666715465414 chr22 51304566 693173 0.01351094169669031 0.12750264413753268 chrMT 16571 12094 0.7298292197211997 0.9376785956293454 chrX 155270560 4708024 0.030321420879785583 0.20715363780878432 chrY 59373566 270757 0.004560228031444162 0.14882062653413666