Flowcell QC summary (lane 1)


Date Flowcell Lane Platform Unit Readgroup Sample Library Type Project Genome Centre
2013-11-23 A5TCU 1 131122_M00113_0090_000000000-A5TCU_1 WTCHG_92654 1 sample 2821/10 gDNA Indexed P100138 arabidopsis 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
1.1 151 28 628732 93.4 16.44 2483.04 2432.62 97.9 96.9 0.00 2.9 1.08 ± 0.00 .0027 20.95 27.03 3.09 0.18 lane
1.2 151 28 628732 93.4 16.44 2483.04 2376.80 97.6 96.9 0.00 2.9 1.28 ± 0.45 .0025 20.90 26.99 3.11 0.19

  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 39.5 ± 7.5 39.4 ± 7.5 0.50 201 ± 44 0.0 0.0 0.0 0.0 36.1
1.2 39.5 ± 7.5 39.4 ± 7.5 0.59 199 ± 44 0.0 0.0 0.0 0.0 35.2

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
ApplicationVersion 2.3.0.3
FPGAVersion 9.5.12
MCSVersion 2.3.0.3
RTAVersion 1.18.42
ReagentKitVersion Version2
bclToFastq 1.8.4
startPipeline 2.02
FCdetails.pm 2.0
QCVersion 2.4