BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081174.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 = 2,868,452 number of mapped reads = 2,592,274 (90.37%) number of supplementary alignments = 30,823 (1.07%) number of secondary alignments = 0 number of mapped bases = 175,406,207 bp number of sequenced bases = 175,340,415 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 124,204 duplication rate = 3.88% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.3346 >>>>>>> ACTG content number of A's = 49,799,143 bp (28.4%) number of C's = 32,350,306 bp (18.45%) number of T's = 55,306,886 bp (31.54%) number of G's = 37,831,615 bp (21.58%) number of N's = 52,465 bp (0.03%) GC percentage = 40.03% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,441,481 number of insertions = 13,503 mapped reads with insertion percentage = 0.52% number of deletions = 41,192 mapped reads with deletion percentage = 1.57% homopolymer indels = 47.62% >>>>>>> Coverage mean coverageData = 0.0567X std coverageData = 0.4343X There is a 4.69% of reference with a coverageData >= 1X There is a 0.73% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.03% 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% 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 13793968 0.05534175981050013 0.801109313988977 chr2 243199373 14815145 0.060917694060008944 0.5075706147067194 chr3 198022430 12857740 0.06493072527187956 0.29470608371688595 chr4 191154276 11458468 0.059943560980032694 0.29608427361954315 chr5 180915260 10759240 0.059471157933277716 0.28447101587176804 chr6 171115067 10713353 0.06260905709723387 0.3702292523403913 chr7 159138663 9779618 0.06145343825089193 0.5916929311986324 chr8 146364022 8888793 0.06073072383867669 0.5594236609887101 chr9 141213431 7796161 0.05520835337539529 0.3717728229469571 chr10 135534747 7866268 0.058038755183569275 0.3741004042249215 chr11 135006516 7508658 0.055617004441474514 0.37058365469809296 chr12 133851895 7844885 0.05860869582757868 0.28578917076090965 chr13 115169878 5509428 0.04783740415180435 0.2548814340442838 chr14 107349540 5158621 0.0480544304148858 0.26977010278789576 chr15 102531392 4965789 0.04843188903550632 0.25946493561283923 chr16 90354753 5442033 0.06022962621567899 0.299290823956101 chr17 81195210 4287146 0.0528004792400931 0.3204778130128058 chr18 78077248 4846594 0.06207434462854019 0.6320681448502041 chr19 59128983 2959405 0.05004998986706739 0.5826792307686003 chr20 63025520 3265290 0.051809013237812236 0.2726113627247555 chr21 48129895 2144873 0.04456425678884195 0.25943966757771664 chr22 51304566 1552285 0.030256273876286176 0.20047493581499418 chrMT 16571 10317 0.6225936877677871 0.9012459918898481 chrX 155270560 10782793 0.06944518651829426 0.3465133206619107 chrY 59373566 399336 0.006725821386574625 0.13153892784571328