QC statistics for 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.ℵ |
% 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 |
back |
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 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 |
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.
Multiplex QC statistics
Lane |
Mx |
Yield Mrd |
Yield Mb Q20 |
% mapped |
% variants |
hets |
% exonic |
% exon cvg |
% pair dups |
most frequent kmer |
% m/f kmer |
% GC |
% GCmapped |
σpos (%GC) |
insert ± MAD |
%lowQ |
avg Q |
1.1 |
All |
16.44 |
2432.62 |
97.9 |
1.08 |
.0027 |
|
|
0.18 |
AAAAAAAAAA |
0.04 |
39.5 ± 7.5 |
39.4 ± 7.5 |
0.50 |
201 ± 44 |
0.0 |
36.1 |
1.2 |
All |
16.44 |
2376.80 |
97.6 |
1.28 |
.0025 |
|
|
0.19 |
AAAAAAAAAA |
0.05 |
39.5 ± 7.5 |
39.4 ± 7.5 |
0.59 |
199 ± 44 |
0.0 |
35.2 |
Yield (Mrd)
 |
Median insert size
 |
MAD insert size
 |
|
Mean G+C
 |
Std. dev. G+C by reads
 |
Std. dev. G+C by position
 |
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.
Lane |
Tile |
Yield (pf, Mrd) |
Variant rate (%) |
Mapped (%) |
Average Q |
N bases (%) |
LowQ (%) |
Last base lowQ (%) |
1.1 |
1 |
0.588 |
1.05 |
97.86 |
37.63 |
0.00 |
0.00 |
0.00 |
1.1 |
2 |
0.583 |
1.06 |
97.83 |
37.64 |
0.00 |
0.00 |
0.00 |
1.1 |
3 |
0.573 |
1.07 |
97.86 |
37.59 |
0.00 |
0.00 |
0.00 |
1.1 |
4 |
0.591 |
1.07 |
97.81 |
37.55 |
0.00 |
0.00 |
0.00 |
1.1 |
5 |
0.585 |
1.10 |
97.84 |
37.54 |
0.00 |
0.00 |
0.00 |
1.1 |
6 |
0.583 |
1.05 |
97.90 |
37.63 |
0.00 |
0.00 |
0.00 |
1.1 |
7 |
0.567 |
1.07 |
97.86 |
37.67 |
0.00 |
0.00 |
0.00 |
1.1 |
8 |
0.568 |
1.05 |
97.86 |
37.65 |
0.00 |
0.00 |
0.00 |
1.1 |
9 |
0.574 |
1.07 |
97.88 |
37.61 |
0.00 |
0.00 |
0.00 |
1.1 |
10 |
0.573 |
1.06 |
97.86 |
37.61 |
0.00 |
0.00 |
0.00 |
1.1 |
11 |
0.587 |
1.04 |
97.88 |
37.69 |
0.00 |
0.00 |
0.00 |
1.1 |
12 |
0.587 |
1.06 |
97.86 |
37.64 |
0.00 |
0.00 |
0.00 |
1.1 |
13 |
0.596 |
1.05 |
97.88 |
37.64 |
0.00 |
0.00 |
0.00 |
1.1 |
14 |
0.608 |
1.07 |
97.89 |
37.56 |
0.00 |
0.00 |
0.00 |
1.1 |
21 |
0.566 |
1.08 |
97.85 |
37.40 |
0.00 |
0.00 |
0.00 |
1.1 |
22 |
0.572 |
1.04 |
97.81 |
37.58 |
0.00 |
0.00 |
0.00 |
1.1 |
23 |
0.573 |
1.05 |
97.82 |
37.52 |
0.00 |
0.00 |
0.00 |
1.1 |
24 |
0.578 |
1.06 |
97.83 |
37.46 |
0.00 |
0.00 |
0.00 |
1.1 |
25 |
0.593 |
1.05 |
97.84 |
37.50 |
0.00 |
0.00 |
0.00 |
1.1 |
26 |
0.588 |
1.03 |
97.85 |
37.65 |
0.00 |
0.00 |
0.00 |
1.1 |
27 |
0.583 |
1.03 |
97.86 |
37.70 |
0.00 |
0.00 |
0.00 |
1.1 |
28 |
0.579 |
1.05 |
97.86 |
37.49 |
0.00 |
0.00 |
0.00 |
1.1 |
29 |
0.592 |
1.06 |
97.86 |
37.48 |
0.00 |
0.00 |
0.00 |
1.1 |
30 |
0.603 |
1.06 |
97.86 |
37.48 |
0.00 |
0.00 |
0.00 |
1.1 |
31 |
0.600 |
1.05 |
97.85 |
37.58 |
0.00 |
0.00 |
0.00 |
1.1 |
32 |
0.618 |
1.05 |
97.83 |
37.50 |
0.00 |
0.00 |
0.00 |
1.1 |
33 |
0.618 |
1.03 |
97.89 |
37.63 |
0.00 |
0.00 |
0.00 |
1.1 |
34 |
0.619 |
1.04 |
97.87 |
37.53 |
0.00 |
0.00 |
0.00 |
|
Lane |
Tile |
Yield (pf, Mrd) |
Variant rate (%) |
Mapped (%) |
Average Q |
N bases (%) |
LowQ (%) |
Last base lowQ (%) |
1.2 |
1 |
0.588 |
1.18 |
97.64 |
37.10 |
0.00 |
0.00 |
0.00 |
1.2 |
2 |
0.583 |
1.19 |
97.61 |
37.11 |
0.00 |
0.00 |
0.00 |
1.2 |
3 |
0.573 |
1.20 |
97.64 |
37.05 |
0.00 |
0.00 |
0.00 |
1.2 |
4 |
0.591 |
1.26 |
97.59 |
36.92 |
0.00 |
0.00 |
0.00 |
1.2 |
5 |
0.585 |
1.27 |
97.64 |
36.90 |
0.00 |
0.00 |
0.00 |
1.2 |
6 |
0.583 |
1.19 |
97.70 |
37.11 |
0.00 |
0.00 |
0.00 |
1.2 |
7 |
0.567 |
1.21 |
97.67 |
37.11 |
0.00 |
0.00 |
0.00 |
1.2 |
8 |
0.568 |
1.17 |
97.67 |
37.19 |
0.00 |
0.00 |
0.00 |
1.2 |
9 |
0.574 |
1.23 |
97.66 |
37.00 |
0.00 |
0.00 |
0.00 |
1.2 |
10 |
0.573 |
1.19 |
97.66 |
37.17 |
0.00 |
0.00 |
0.00 |
1.2 |
11 |
0.587 |
1.21 |
97.67 |
37.06 |
0.00 |
0.00 |
0.00 |
1.2 |
12 |
0.587 |
1.21 |
97.62 |
37.01 |
0.00 |
0.00 |
0.00 |
1.2 |
13 |
0.596 |
1.18 |
97.66 |
37.07 |
0.00 |
0.00 |
0.00 |
1.2 |
14 |
0.608 |
1.22 |
97.68 |
36.95 |
0.00 |
0.00 |
0.00 |
1.2 |
21 |
0.566 |
1.40 |
97.62 |
36.29 |
0.00 |
0.00 |
0.00 |
1.2 |
22 |
0.572 |
1.33 |
97.59 |
36.52 |
0.00 |
0.00 |
0.00 |
1.2 |
23 |
0.573 |
1.31 |
97.59 |
36.56 |
0.00 |
0.00 |
0.00 |
1.2 |
24 |
0.578 |
1.33 |
97.58 |
36.49 |
0.00 |
0.00 |
0.00 |
1.2 |
25 |
0.593 |
1.36 |
97.61 |
36.38 |
0.00 |
0.00 |
0.00 |
1.2 |
26 |
0.588 |
1.26 |
97.60 |
36.71 |
0.00 |
0.00 |
0.00 |
1.2 |
27 |
0.583 |
1.26 |
97.61 |
36.78 |
0.00 |
0.00 |
0.00 |
1.2 |
28 |
0.579 |
1.30 |
97.62 |
36.50 |
0.00 |
0.00 |
0.00 |
1.2 |
29 |
0.592 |
1.27 |
97.62 |
36.69 |
0.00 |
0.00 |
0.00 |
1.2 |
30 |
0.603 |
1.31 |
97.61 |
36.58 |
0.00 |
0.00 |
0.00 |
1.2 |
31 |
0.600 |
1.26 |
97.61 |
36.67 |
0.00 |
0.00 |
0.00 |
1.2 |
32 |
0.618 |
1.27 |
97.61 |
36.65 |
0.00 |
0.00 |
0.00 |
1.2 |
33 |
0.618 |
1.21 |
97.66 |
36.85 |
0.00 |
0.00 |
0.00 |
1.2 |
34 |
0.619 |
1.29 |
97.64 |
36.53 |
0.00 |
0.00 |
0.00 |
|
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 |