BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080695.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 = 2,790,695 number of mapped reads = 2,481,044 (88.9%) number of supplementary alignments = 24,479 (0.88%) number of secondary alignments = 0 number of mapped bases = 175,669,203 bp number of sequenced bases = 175,602,883 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 127,331 duplication rate = 4.2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.1713 >>>>>>> ACTG content number of A's = 53,253,827 bp (30.33%) number of C's = 32,393,755 bp (18.45%) number of T's = 55,031,310 bp (31.34%) number of G's = 34,921,290 bp (19.89%) number of N's = 2,701 bp (0%) GC percentage = 38.33% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 1,374,410 number of insertions = 14,143 mapped reads with insertion percentage = 0.56% number of deletions = 36,600 mapped reads with deletion percentage = 1.46% homopolymer indels = 47.94% >>>>>>> Coverage mean coverageData = 0.0567X std coverageData = 0.5575X There is a 3.8% of reference with a coverageData >= 1X There is a 1.19% of reference with a coverageData >= 2X There is a 0.4% of reference with a coverageData >= 3X There is a 0.14% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% 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 14069950 0.05644900680107032 0.7853080246499935 chr2 243199373 15482199 0.06366052185504606 0.4418769958805202 chr3 198022430 12491903 0.06308327294034317 0.3485198932097928 chr4 191154276 12553234 0.06567069417793196 0.36745805161126405 chr5 180915260 11789626 0.06516656472206933 0.35682430756416683 chr6 171115067 11400362 0.06662395193989551 0.3754218900066697 chr7 159138663 10046496 0.06313045372261296 0.48860908665490715 chr8 146364022 9831981 0.06717484847471601 1.677367524985021 chr9 141213431 7389998 0.05233211846541708 0.40704535206228315 chr10 135534747 7889270 0.05820846812072479 0.4277253331407049 chr11 135006516 8321283 0.06163615836142309 0.3961169406273669 chr12 133851895 8424462 0.06293868308700448 0.34980724410648556 chr13 115169878 6013162 0.05221123877547218 0.32211792276525636 chr14 107349540 5445410 0.050725974233331604 0.3253651438476181 chr15 102531392 4912706 0.047914164668709465 0.3002497394226688 chr16 90354753 4298232 0.047570624203908785 0.3131660719867463 chr17 81195210 4013588 0.04943133960734876 0.32812806250159826 chr18 78077248 4964508 0.0635845669150634 0.630345287071147 chr19 59128983 2695556 0.0455877281028155 0.5136961674991959 chr20 63025520 3295438 0.052287359152292594 0.3195951509430151 chr21 48129895 2318127 0.048163973763084254 0.32069594511660776 chr22 51304566 1612556 0.03143104260934592 0.2384337196954723 chrMT 16571 176536 10.653309999396535 6.874007907929265 chrX 155270560 5872609 0.03782178025248315 0.28223667248103257 chrY 59373566 360011 0.006063489600742526 0.17247907081971953