BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081033.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 = 3,764,002 number of mapped reads = 2,366,095 (62.86%) number of supplementary alignments = 10,150 (0.27%) number of secondary alignments = 0 number of mapped bases = 146,790,283 bp number of sequenced bases = 146,743,332 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 98,544 duplication rate = 3.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6142 >>>>>>> ACTG content number of A's = 41,058,088 bp (27.98%) number of C's = 29,691,302 bp (20.23%) number of T's = 42,962,846 bp (29.28%) number of G's = 33,029,341 bp (22.51%) number of N's = 1,755 bp (0%) GC percentage = 42.74% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 1,061,932 number of insertions = 9,655 mapped reads with insertion percentage = 0.4% number of deletions = 27,108 mapped reads with deletion percentage = 1.13% homopolymer indels = 45.22% >>>>>>> Coverage mean coverageData = 0.0474X std coverageData = 0.3731X There is a 3.94% of reference with a coverageData >= 1X There is a 0.58% of reference with a coverageData >= 2X There is a 0.11% 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 12576400 0.05045684520079892 0.5618649846567945 chr2 243199373 11446394 0.047065886144369296 0.4137696970064976 chr3 198022430 10194641 0.05148225380326865 0.2634937722211778 chr4 191154276 9296625 0.04863414616997634 0.2832747910748047 chr5 180915260 8217814 0.04542355354656097 0.24974839619440387 chr6 171115067 8770462 0.05125476180306203 0.32353088651917417 chr7 159138663 7563725 0.04752914758370189 0.6174581556993471 chr8 146364022 7274415 0.049700841098777676 0.3441322047373626 chr9 141213431 6316188 0.04472795509090067 0.3640769576795305 chr10 135534747 6347422 0.04683243330951878 0.34888965526854304 chr11 135006516 6658379 0.04931894546482482 0.40086530341587456 chr12 133851895 6557290 0.04898914580178338 0.2605799437113425 chr13 115169878 4714665 0.04093661538827019 0.23377422295986156 chr14 107349540 4215329 0.039267322431004364 0.24502182083127166 chr15 102531392 4662528 0.045474150980023754 0.2599452847641525 chr16 90354753 4553858 0.0503997614823871 0.2849253428799804 chr17 81195210 4166022 0.05130871636393329 0.3134386046261204 chr18 78077248 4233506 0.054222018685904504 0.6638799736759513 chr19 59128983 2955122 0.049977555000396336 0.429588509054724 chr20 63025520 3365380 0.053397100095326465 0.2801586332777137 chr21 48129895 1893966 0.03935113508973996 0.2591870177923722 chr22 51304566 1845219 0.03596598010399309 0.22123798578859066 chrMT 16571 36133 2.180496047311568 2.1547529862500263 chrX 155270560 8538118 0.054988646914134916 0.31713025115632304 chrY 59373566 390682 0.006580066287411472 0.15106049769117486