BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472548.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 9,916,194 number of mapped reads = 9,764,895 (98.47%) number of supplementary alignments = 45,626 (0.46%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,899,175 number of mapped paired reads (second in pair) = 4,865,720 number of mapped paired reads (both in pair) = 9,689,310 number of mapped paired reads (singletons) = 75,585 number of mapped bases = 959,254,914 bp number of sequenced bases = 959,135,640 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,742,498 duplication rate = 32.79% >>>>>>> Insert size mean insert size = 35,839.1891 std insert size = 1,831,006.172 median insert size = 237 >>>>>>> Mapping quality mean mapping quality = 49.9469 >>>>>>> ACTG content number of A's = 279,842,821 bp (29.18%) number of C's = 201,750,851 bp (21.03%) number of T's = 276,700,630 bp (28.85%) number of G's = 200,692,774 bp (20.92%) number of N's = 148,564 bp (0.02%) GC percentage = 41.96% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 5,674,878 number of insertions = 49,529 mapped reads with insertion percentage = 0.5% number of deletions = 56,747 mapped reads with deletion percentage = 0.58% homopolymer indels = 48.67% >>>>>>> Coverage mean coverageData = 0.3099X std coverageData = 58.764X There is a 1.58% of reference with a coverageData >= 1X There is a 1% of reference with a coverageData >= 2X There is a 0.68% of reference with a coverageData >= 3X There is a 0.53% of reference with a coverageData >= 4X There is a 0.42% of reference with a coverageData >= 5X There is a 0.34% of reference with a coverageData >= 6X There is a 0.29% of reference with a coverageData >= 7X There is a 0.25% of reference with a coverageData >= 8X There is a 0.21% of reference with a coverageData >= 9X There is a 0.18% of reference with a coverageData >= 10X There is a 0.16% of reference with a coverageData >= 11X There is a 0.14% of reference with a coverageData >= 12X There is a 0.13% of reference with a coverageData >= 13X There is a 0.12% of reference with a coverageData >= 14X There is a 0.1% of reference with a coverageData >= 15X There is a 0.1% of reference with a coverageData >= 16X There is a 0.09% of reference with a coverageData >= 17X There is a 0.08% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.06% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.04% of reference with a coverageData >= 30X There is a 0.04% of reference with a coverageData >= 31X There is a 0.04% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.03% of reference with a coverageData >= 35X There is a 0.03% of reference with a coverageData >= 36X There is a 0.03% of reference with a coverageData >= 37X There is a 0.03% of reference with a coverageData >= 38X There is a 0.03% of reference with a coverageData >= 39X There is a 0.03% of reference with a coverageData >= 40X There is a 0.03% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 148371220 0.5952692089782196 107.92808992682063 chr2 243199373 79876711 0.3284412702823868 51.928707258826705 chr3 198022430 288697698 1.4579040263267147 137.13279448493665 chr4 191154276 100237176 0.5243784135909154 50.47257182706098 chr5 180915260 11434654 0.06320447484640046 8.781084621381389 chr6 171115067 31367666 0.18331329058241258 23.90577745302138 chr7 159138663 14964306 0.09403312631827251 1.564056224008562 chr8 146364022 5854671 0.040000752370688474 4.256996201265841 chr9 141213431 141877148 1.0047000982505694 124.66628599265064 chr10 135534747 7367357 0.05435769913673871 1.7820110461390932 chr11 135006516 15202465 0.11260541676373606 10.892150996115024 chr12 133851895 11999351 0.0896464782960301 2.760022640639293 chr13 115169878 29947160 0.26002597658391197 48.52023521447679 chr14 107349540 1227877 0.011438120740899308 0.4034269858801101 chr15 102531392 40121162 0.3913061279807847 55.12139314242898 chr16 90354753 5027923 0.055646469422588093 1.3884551429373015 chr17 81195210 7835271 0.09649917772242969 6.221098062926641 chr18 78077248 2255860 0.028892667938296184 0.548692310350965 chr19 59128983 1377080 0.023289424747927764 0.5118270370157708 chr20 63025520 3790766 0.06014652477282218 1.7920727292023042 chr21 48129895 3113418 0.06468782032456127 3.738763284206686 chr22 51304566 488151 0.009514767165168105 0.2864095669389469 chrMT 16571 24187 1.4595980930541308 1.7585759229280058 chrX 155270560 2381623 0.01533853552147941 0.33150481862429054 chrY 59373566 4414013 0.07434306708140118 9.792776021511235