BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081050.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 = 1,690,079 number of mapped reads = 1,296,798 (76.73%) number of supplementary alignments = 7,040 (0.42%) number of secondary alignments = 0 number of mapped bases = 84,254,793 bp number of sequenced bases = 84,224,950 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 29,013 duplication rate = 1.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7681 >>>>>>> ACTG content number of A's = 24,551,108 bp (29.15%) number of C's = 15,849,267 bp (18.82%) number of T's = 25,267,279 bp (30%) number of G's = 18,556,178 bp (22.03%) number of N's = 1,118 bp (0%) GC percentage = 40.85% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 652,683 number of insertions = 5,303 mapped reads with insertion percentage = 0.41% number of deletions = 17,351 mapped reads with deletion percentage = 1.32% homopolymer indels = 48.08% >>>>>>> Coverage mean coverageData = 0.0272X std coverageData = 0.2277X There is a 2.47% of reference with a coverageData >= 1X There is a 0.19% 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 6525852 0.02618188863007888 0.3128744749674784 chr2 243199373 7024576 0.028884021835039846 0.23125661043808782 chr3 198022430 4843382 0.024458754495639713 0.16767493690712162 chr4 191154276 4796471 0.025092145989975133 0.1739061246637665 chr5 180915260 5822218 0.03218201714990764 0.19359078679647623 chr6 171115067 5717514 0.03341327038138611 0.24346632097949483 chr7 159138663 4124554 0.02591798826410902 0.3554948680067462 chr8 146364022 3837123 0.02621629924873204 0.23090336517711382 chr9 141213431 3326608 0.023557305961923694 0.20390574368773648 chr10 135534747 4076083 0.03007408129813383 0.22108277142200608 chr11 135006516 3884535 0.028772944559209274 0.20926992723017915 chr12 133851895 3522655 0.02631755792474959 0.17543075993486076 chr13 115169878 2865462 0.024880307679061707 0.16972208729536112 chr14 107349540 2764999 0.025756971105791417 0.18009135952159783 chr15 102531392 2739991 0.02672343510171012 0.18028627059692606 chr16 90354753 2445319 0.02706353477608422 0.1887849395276176 chr17 81195210 2155604 0.026548413385469413 0.19652715178962446 chr18 78077248 2011814 0.02576696863086158 0.36677398481322 chr19 59128983 1601172 0.027079308974416152 0.25538588126160067 chr20 63025520 1811145 0.028736692692103136 0.18351617287175273 chr21 48129895 1056658 0.02195429680451204 0.16714168224601816 chr22 51304566 1090091 0.021247446085013173 0.15626265988236862 chrMT 16571 17142 1.034457787701406 1.2561915839032451 chrX 155270560 5994048 0.03860389245714062 0.23106220350811896 chrY 59373566 199777 0.003364746527099282 0.07774890311155258