BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094096.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 170 number of mapped reads = 134 (78.82%) number of supplementary alignments = 10 (5.88%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 68 number of mapped paired reads (second in pair) = 66 number of mapped paired reads (both in pair) = 122 number of mapped paired reads (singletons) = 12 number of mapped bases = 15,921 bp number of sequenced bases = 15,645 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 17 duplication rate = 11.02% >>>>>>> Insert size mean insert size = 3,856,437.0702 std insert size = 14,172,425.2146 median insert size = 167 >>>>>>> Mapping quality mean mapping quality = 6.1678 >>>>>>> ACTG content number of A's = 4,689 bp (29.97%) number of C's = 3,301 bp (21.1%) number of T's = 4,145 bp (26.49%) number of G's = 3,510 bp (22.44%) number of N's = 0 bp (0%) GC percentage = 43.53% >>>>>>> Mismatches and indels general error rate = 0.0385 number of mismatches = 567 number of insertions = 17 mapped reads with insertion percentage = 12.69% number of deletions = 41 mapped reads with deletion percentage = 27.61% homopolymer indels = 39.66% >>>>>>> Coverage mean coverageData = 0X std coverageData = 0.0031X There is a 0% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% 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 539 2.162482074618382E-6 0.0019717121318185934 chr2 243199373 893 3.6718844665771404E-6 0.0023907032291299547 chr3 198022430 938 4.736837135065962E-6 0.002878700850543402 chr4 191154276 367 1.9199151998043715E-6 0.0017131253799934024 chr5 180915260 526 2.907438543326859E-6 0.002339266367393696 chr6 171115067 0 0.0 0.0 chr7 159138663 163 1.0242639778870078E-6 0.0010120587575681125 chr8 146364022 341 2.329807526059922E-6 0.0020331070890992568 chr9 141213431 0 0.0 0.0 chr10 135534747 649 4.788439971042998E-6 0.0030210574183125415 chr11 135006516 331 2.4517335148475352E-6 0.0020384677211460747 chr12 133851895 627 4.684281832543349E-6 0.003244462736545623 chr13 115169878 907 7.875323094463988E-6 0.004586766633714995 chr14 107349540 472 4.3968516306637175E-6 0.002596979771134137 chr15 102531392 0 0.0 0.0 chr16 90354753 0 0.0 0.0 chr17 81195210 337 4.150491143504648E-6 0.002642566562109746 chr18 78077248 461 5.904408925888371E-6 0.0027372520393324174 chr19 59128983 0 0.0 0.0 chr20 63025520 449 7.124098301767284E-6 0.0028861581277155775 chr21 48129895 0 0.0 0.0 chr22 51304566 31 6.042347186018492E-7 7.773251272808915E-4 chrMT 16571 1350 0.08146762416269386 0.35319533692833716 chrX 155270560 6376 4.106380501236036E-5 0.008868016727141784 chrY 59373566 164 2.7621719739723903E-6 0.0020105211411835665