BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818798.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 = 1,089,878 number of mapped reads = 1,056,010 (96.89%) number of supplementary alignments = 8,665 (0.8%) number of secondary alignments = 0 number of mapped bases = 71,587,797 bp number of sequenced bases = 71,557,481 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 378,368 duplication rate = 30.94% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.9524 >>>>>>> ACTG content number of A's = 20,351,722 bp (28.44%) number of C's = 15,235,862 bp (21.29%) number of T's = 20,617,526 bp (28.81%) number of G's = 15,347,850 bp (21.45%) number of N's = 4,521 bp (0.01%) GC percentage = 42.74% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 370,051 number of insertions = 9,703 mapped reads with insertion percentage = 0.91% number of deletions = 18,516 mapped reads with deletion percentage = 1.74% homopolymer indels = 39.9% >>>>>>> Coverage mean coverageData = 0.0231X std coverageData = 0.3354X There is a 1.31% of reference with a coverageData >= 1X There is a 0.51% of reference with a coverageData >= 2X There is a 0.23% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.03% 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 5870606 0.023553024567990945 0.4217946493880848 chr2 243199373 6382309 0.026243114533029657 0.5864148598070181 chr3 198022430 4780620 0.024141810601960596 0.24558668105252476 chr4 191154276 4755233 0.02487641448313717 0.2801664026841046 chr5 180915260 4427500 0.02447278355623511 0.2567416439715549 chr6 171115067 4218355 0.02465215409698551 0.27206607930089954 chr7 159138663 3931646 0.024705787555849956 0.28887510242471515 chr8 146364022 3714586 0.02537909213782059 0.2758864308650393 chr9 141213431 3111839 0.02203642371666474 0.26967718472384045 chr10 135534747 3453100 0.025477599482293643 0.357014565183187 chr11 135006516 3330844 0.024671727696461702 0.27872749586067375 chr12 133851895 3221221 0.024065561417714706 0.2559785236268031 chr13 115169878 2295037 0.01992740671306433 0.22174831993501284 chr14 107349540 2232652 0.02079796522649282 0.25800588901708577 chr15 102531392 2061024 0.020101394897671924 0.22697277834217466 chr16 90354753 2130396 0.023578128756546985 0.3702923453878684 chr17 81195210 1883709 0.023199755256498505 0.25309683047721937 chr18 78077248 1949851 0.024973357155211207 0.3423766975944094 chr19 59128983 1437542 0.024311968971291117 0.36686733812375977 chr20 63025520 1531819 0.024304741952148906 0.26990990413713195 chr21 48129895 983651 0.02043742252086775 0.2360179646761377 chr22 51304566 862345 0.01680834801331328 0.22423821931609753 chrMT 16571 17253 1.0411562367992275 1.7968985138677944 chrX 155270560 2227410 0.014345346600153951 0.2079166152525582 chrY 59373566 777249 0.013090825637793088 0.687868157678772