Flowcell QC summary (lanes 1,2)


Date Flowcell Lane Platform Unit Readgroup Sample Library Type Project Genome Centre
2016-11-13 HFW7MBBXX 1 161111_K00198_0128_BHFW7MBBXX_1 WTCHG_328669 30 samples 394/16_MPX_10nM_2 Our indexes RNA-Seq PolyA P160354 galGal4 WTCHG
2016-11-13 HFW7MBBXX 2 161111_K00198_0128_BHFW7MBBXX_2 WTCHG_328670 30 samples 395/16_MPX_10nM_2 Our indexes RNA-Seq PolyA P160354 galGal4 WTCHG

Lane Length Tiles Clusters % PF Yield (Mrd) Yield (Mb) Yield (Mb Q20) % Mapped % Coverage % Primer % Broken % Variants Hets Mean cov.* % high cov. % dups % pair dups Link
1.1 75 88 3669324 100.0 322.90 24217.54 23882.57 92.9 7.8 0.00 1.4 6.01 ± 0.11 .0108 9.53 10.10 48.78 10.96 lane
1.2 75 88 3669324 100.0 322.90 24217.54 22697.07 92.1 8.0 0.00 1.4 6.99 ± 0.11 .0112 9.29 10.03 43.36 10.62
2.1 75 88 3713823 100.0 326.82 24511.24 24184.32 92.9 8.1 0.00 1.4 5.97 ± 0.00 .0110 9.38 10.87 48.81 11.13 lane
2.2 75 88 3713823 100.0 326.82 24511.24 23167.62 92.2 8.2 0.00 1.4 6.77 ± 0.11 .0114 9.16 10.79 43.45 10.80

  Fraction of reference that is covered at least once      Estimated heterozygosity (average over multiplexes). Sample contamination can increase this estimate. Filters: base quality >= 39, mapping quality >= 30, pairs properly mapped, no indels, maximum 2 high-quality (Q30) variants in read, insert size > read length.   *   Mean coverage is computed over regions that are covered at least once      Proportion of reads in regions with coverage in top 0.1 percentile   


Lane QC statistics and plots


Lane % GC % GCmapped σpos(%GC) insert ± MAD % exonic % exon cov'ge %N maxpos %N %lowQ %lowQend avgQ
1.1 47.4 ± 10.1 46.5 ± 9.5 4.69 200 ± 192 18.8 78.6 0.0 1.1 0.0 0.0 32.4
1.2 47.1 ± 10.7 46.1 ± 10.1 2.74 199 ± 173 20.0 82.1 0.1 0.7 0.1 0.1 30.0
2.1 47.4 ± 10.0 46.4 ± 9.4 4.69 200 ± 193 18.7 79.0 0.0 0.2 0.0 0.0 32.4
2.2 47.1 ± 10.7 46.0 ± 10.0 2.69 199 ± 171 19.9 82.5 0.1 0.6 0.1 0.1 30.4

G+C histogram
Insert size histogram
Mapped coverage by G+C

Coverage histogram
Exon/genome coverage distribution
Genomic coverage by G+C

(Predicted) variants by cycle (read 1)
Fraction N/lowQ, read 1
G+C by cycle (PF), read 1

Mean Q by cycle, read 1
Q score histogram, read 1
Variants by Q, read 1

(Predicted) variants by cycle (read 2)
Fraction N/lowQ, read 2
G+C by cycle (PF), read 2

Mean Q by cycle, read 2
Q score histogram, read 2
Variants by Q, read 2

Variants by GC
Indel rate by homopolymer content
Legend


  The Fraction N/Low Q plots, and dotted lines on the GC histogram plots, refer to all reads that have passed chastity filters. If a reference genome was available, all others refer to mapped reads, otherwise they too refer to chastity-filtered reads. The dotted lines in the fraction N/lowQ plot correspond to the fraction of bases with quality score 4 or less.      "Predicted variants" (dashed line) is the expected error frequency expressed as a Phred score, and may be compared with the "Variants by cycle" graph (solid line). "Mean Q" (solid) is the numerical mean Q score and is a measure of the average information content per read. These graphs use mapped reads only; the dashed line in the Mean Q plot uses all (PF) reads. All four graphs are calculated on called bases with Q Phred score above 4 only.      Mapped coverage by G+C. The coverage was averaged over those genomic regions that were covered at least once. Regions with coverage in the top 0.1 percentile were excluded; the dotted line shows results for all reads. The G+C fraction was computed from read bases, excluding Ns and bases with quality below 4.      Genomic coverage by G+C. The G+C fraction was computed from the reference genome, over the approximate fragment Regions with coverage in the top 0.1 percentile were excluded. The G+C histogram is shown as a dotted line (arbitrary Y scale).      The insert size distribution is summarized by the median and median absolute deviation.   







Tile QC statistics and plots


Variant rate by tile (read 1)
Raw/mapped yield by tile (read 1)
Fraction N/lowQ by tile (read 1)

Variant rate by tile (read 2)
Raw/mapped yield by tile (read 2)
Fraction N/lowQ by tile (read 2)

  HiSeq tiles are grouped in order: swathe 1 top; swathe 1 bottom; swathe 2 top; etc.   





Component Version
RunMode HiSeq4000
ApplicationVersion 3.3.52
FPGAVersion 10.37.13
CPLDVersion 3.0.0
RTAVersion 2.7.3
BaseSpaceBrokerVersion 2.5.2.28
ChemistryVersion Illumina_Bruno Fluidics Controller_0_v2.0420
RecipeFragmentVersion 3.3.7
bclToFastq 2.17.1.14
startPipeline 2.2
FCdetails.pm 2.2
QCVersion 2.4