BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085130.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 = 1,741,271 number of mapped reads = 1,552,719 (89.17%) number of supplementary alignments = 12,942 (0.74%) number of secondary alignments = 0 number of mapped bases = 103,746,418 bp number of sequenced bases = 103,709,472 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 55,278 duplication rate = 2.73% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9828 >>>>>>> ACTG content number of A's = 29,222,076 bp (28.18%) number of C's = 19,208,583 bp (18.52%) number of T's = 32,501,529 bp (31.34%) number of G's = 22,756,355 bp (21.94%) number of N's = 20,929 bp (0.02%) GC percentage = 40.46% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 906,209 number of insertions = 8,204 mapped reads with insertion percentage = 0.52% number of deletions = 22,821 mapped reads with deletion percentage = 1.45% homopolymer indels = 46.91% >>>>>>> Coverage mean coverageData = 0.0335X std coverageData = 0.3161X There is a 3.01% of reference with a coverageData >= 1X There is a 0.25% of reference with a coverageData >= 2X There is a 0.03% 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 8051574 0.03230312513444049 0.5523727565067917 chr2 243199373 8904738 0.03661497104270906 0.37196365445484575 chr3 198022430 7148957 0.03610175372557543 0.20547895791316398 chr4 191154276 7098268 0.037133712875980864 0.21304047630067585 chr5 180915260 6494651 0.035898856735468304 0.20573023407387386 chr6 171115067 6155480 0.035972752767586505 0.23865000790552934 chr7 159138663 5747506 0.036116339622634636 0.4064411420687381 chr8 146364022 5421708 0.03704262786656683 0.4863481946609009 chr9 141213431 4359181 0.03086945037119026 0.2887253278221892 chr10 135534747 4806144 0.035460604061923695 0.2830035399089255 chr11 135006516 4701025 0.03482072672699738 0.2692529447120095 chr12 133851895 4680968 0.03497124937977158 0.20583154853944127 chr13 115169878 3466795 0.030101577428084104 0.1880996461568899 chr14 107349540 3131105 0.02916738162082483 0.19584549905342172 chr15 102531392 2833208 0.02763259080692087 0.18173801498930894 chr16 90354753 2726875 0.03017965197691371 0.20701009652455094 chr17 81195210 2524407 0.031090590196145806 0.205778873719892 chr18 78077248 2824234 0.036172304638606115 0.5114812955835898 chr19 59128983 1873951 0.03169259650550729 0.4511845569955241 chr20 63025520 1991800 0.031603071263830905 0.1968144578988579 chr21 48129895 1370161 0.028467982321590354 0.19096233220101133 chr22 51304566 1023640 0.019952220237083772 0.15104278336942448 chrMT 16571 5955 0.35936274213988295 0.6678217564201179 chrX 155270560 6141979 0.03955662296832059 0.23929381947456263 chrY 59373566 262108 0.004414557144841191 0.09709016448815386