Flowcell QC summary (lanes 6,7)


Date Flowcell Lane Platform Unit Readgroup Sample Library Type Project Genome Centre
2016-10-27 HF5KTBBXX 6 161021_K00198_0118_AHF5KTBBXX_6 WTCHG_323579 30 samples 443/16_MPX_10nM_1 Our indexes RNA-Seq PolyA P160354 galGal4 WTCHG
2016-10-27 HF5KTBBXX 7 161021_K00198_0118_AHF5KTBBXX_7 WTCHG_323580 30 samples 444/16_MPX_10nM_1 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
6.1 75 88 4252388 100.0 374.21 28065.77 27159.45 93.0 7.6 0.00 2.0 5.93 ± 0.11 .0115 11.14 13.12 54.58 13.13 lane
6.2 75 88 4264901 100.0 375.31 28148.35 26631.77 92.5 7.7 0.00 2.0 6.53 ± 0.21 .0118 10.91 13.02 49.94 12.84
7.1 75 88 4365291 100.0 384.15 28810.92 27906.81 92.9 8.2 0.00 1.9 5.83 ± 0.00 .0121 10.64 10.49 53.13 13.06 lane
7.2 75 88 4378843 100.0 385.34 28900.37 27430.94 92.5 8.3 0.00 1.9 6.40 ± 0.00 .0126 10.42 10.42 48.15 12.81

  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
6.1 47.8 ± 10.0 46.8 ± 9.5 4.62 214 ± 255 19.0 76.7 0.0 0.9 0.0 0.0 33.9
6.2 47.6 ± 10.6 46.6 ± 10.0 2.67 213 ± 225 20.3 80.0 0.0 1.1 0.0 0.0 31.4
7.1 47.6 ± 10.1 46.6 ± 9.5 4.65 213 ± 245 18.6 76.2 0.0 1.0 0.0 0.0 34.0
7.2 47.4 ± 10.6 46.4 ± 10.0 2.64 213 ± 225 19.7 79.3 0.0 1.1 0.0 0.0 31.5

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