Flowcell QC summary (lane 7)
Date |
Flowcell |
Lane |
Platform Unit |
Readgroup |
Sample |
Library |
Type |
Project |
Genome |
Centre |
2016-09-02 |
HCVKHBBXX |
7 |
160831_K00150_0116_BHCVKHBBXX_7 |
WTCHG_310912 |
9 samples |
215/16_MPX_10nM |
Our indexes RNA-Seq PolyA |
P160524 |
GRCh37.EBVB95-8wt.ERCC |
WTCHG |
Lane |
Length |
Tiles |
Clusters |
% PF |
Yield (Mrd) |
Yield (Mb) |
Yield (Mb Q20) |
% Mapped |
% Coverage⊥ |
% Primer |
% Broken |
% Variants |
Hets⊄ |
Mean cov.* |
% high cov.ℵ |
% dups |
% pair dups |
Link |
7.1 |
75 |
88 |
4146507 |
100.0 |
364.89 |
27366.95 |
27118.11 |
88.8 |
5.4 |
0.00 |
2.9 |
2.36 ± 0.00 |
.0023 |
16.26 |
24.67 |
63.62 |
22.28 |
lane |
7.2 |
75 |
88 |
4146507 |
100.0 |
364.89 |
27366.95 |
26681.84 |
88.0 |
5.4 |
0.00 |
2.9 |
3.49 ± 0.15 |
.0020 |
15.85 |
24.41 |
57.78 |
21.21 |
|
⊥ 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 ℵ 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 |
7.1 |
48.9 ± 10.2 |
48.7 ± 10.4 |
4.70 |
171 ± 50 |
37.6 |
61.1 |
0.0 |
1.7 |
0.0 |
0.0 |
33.9 |
7.2 |
48.8 ± 10.6 |
48.7 ± 10.9 |
2.72 |
172 ± 47 |
39.4 |
62.4 |
0.1 |
2.2 |
0.1 |
0.1 |
31.6 |
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 |