QC statistics for 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 |
back |
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.
Multiplex QC statistics
Index |
Tag |
Readgroup |
Sample name |
Sample id |
Library |
Type |
Genome |
Project |
201 |
TGTTAACT |
WTCHG_310912_201 |
HO3 |
CHA3768A1 |
|
Our indexes RNA-Seq PolyA |
GRCh37.EBVB95-8wt.ERCC |
P160524 |
202 |
TCGCGCGT |
WTCHG_310912_202 |
HB3 |
CHA3768A2 |
|
Our indexes RNA-Seq PolyA |
GRCh37.EBVB95-8wt.ERCC |
P160524 |
203 |
TAGAAGAG |
WTCHG_310912_203 |
MOTH |
CHA3768A3 |
|
Our indexes RNA-Seq PolyA |
GRCh37.EBVB95-8wt.ERCC |
P160524 |
204 |
GCTCTCTC |
WTCHG_310912_204 |
CD4COCO |
CHA3768A4 |
|
Our indexes RNA-Seq PolyA |
GRCh37.EBVB95-8wt.ERCC |
P160524 |
205 |
GAGTACTG |
WTCHG_310912_205 |
CDCOCB |
CHA3768A5 |
|
Our indexes RNA-Seq PolyA |
GRCh37.EBVB95-8wt.ERCC |
P160524 |
206 |
CTTGATTG |
WTCHG_310912_206 |
CD4MRO |
CHA3768A6 |
|
Our indexes RNA-Seq PolyA |
GRCh37.EBVB95-8wt.ERCC |
P160524 |
207 |
CTATATAC |
WTCHG_310912_207 |
CD4MRB |
CHA3768A7 |
|
Our indexes RNA-Seq PolyA |
GRCh37.EBVB95-8wt.ERCC |
P160524 |
208 |
CATTAATC |
WTCHG_310912_208 |
CD4THO |
CHA3768A8 |
|
Our indexes RNA-Seq PolyA |
GRCh37.EBVB95-8wt.ERCC |
P160524 |
209 |
TGTTGGTC |
WTCHG_310912_209 |
CD4THB |
CHA3768A9 |
|
Our indexes RNA-Seq PolyA |
GRCh37.EBVB95-8wt.ERCC |
P160524 |
Lane |
Mx |
Sample name |
Sample id |
Mean cvg |
Median cvg |
% > 10X |
% > 20X |
Exonic mean cvg |
Exonic median cvg |
Exonic % > 10X |
Exonic % > 20X |
7 |
201 |
HO3 |
CHA3768A1 |
8.96 |
2 |
1.0 |
0.6 |
32.25 |
14 |
38.8 |
26.8 |
7 |
202 |
HB3 |
CHA3768A2 |
9.85 |
2 |
1.1 |
0.7 |
36.91 |
16 |
41.6 |
29.6 |
7 |
203 |
MOTH |
CHA3768A3 |
8.93 |
2 |
0.9 |
0.6 |
31.54 |
13 |
35.9 |
24.2 |
7 |
204 |
CD4COCO |
CHA3768A4 |
8.90 |
2 |
1.0 |
0.6 |
34.02 |
16 |
38.4 |
27.9 |
7 |
205 |
CDCOCB |
CHA3768A5 |
7.76 |
2 |
1.0 |
0.6 |
30.42 |
14 |
36.9 |
26.1 |
7 |
206 |
CD4MRO |
CHA3768A6 |
7.79 |
2 |
1.1 |
0.7 |
32.45 |
16 |
39.2 |
28.5 |
7 |
207 |
CD4MRB |
CHA3768A7 |
7.74 |
2 |
1.1 |
0.7 |
34.88 |
16 |
40.4 |
29.7 |
7 |
208 |
CD4THO |
CHA3768A8 |
8.62 |
2 |
1.0 |
0.7 |
35.96 |
17 |
39.8 |
29.4 |
7 |
209 |
CD4THB |
CHA3768A9 |
7.41 |
2 |
1.0 |
0.6 |
30.19 |
14 |
37.2 |
26.1 |
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 |
7.1 |
All |
364.89 |
27118.11 |
88.8 |
2.36 |
.0023 |
37.6 |
61.1 |
22.28 |
N/A |
0.00 |
48.9 ± 10.2 |
48.7 ± 10.4 |
4.70 |
171 ± 50 |
0.0 |
33.9 |
7.1 |
201 |
41.30 |
3068.81 |
88.3 |
2.42 |
.0021 |
39.5 |
61.7 |
23.94 |
CACACACACA |
0.03 |
49.1 ± 10.4 |
48.8 ± 10.6 |
4.67 |
177 ± 54 |
0.0 |
33.9 |
7.1 |
202 |
47.43 |
3523.99 |
87.8 |
2.60 |
.0023 |
41.5 |
63.4 |
27.65 |
GGCCAATTGA |
0.03 |
49.9 ± 10.4 |
49.7 ± 10.6 |
4.63 |
170 ± 50 |
0.0 |
33.9 |
7.1 |
203 |
42.72 |
3175.09 |
88.0 |
2.39 |
.0021 |
39.5 |
59.9 |
23.63 |
GTCATTTTTG |
0.07 |
50.1 ± 10.2 |
50.0 ± 10.4 |
4.62 |
169 ± 49 |
0.0 |
33.9 |
7.1 |
204 |
38.95 |
2896.06 |
89.0 |
2.38 |
.0023 |
37.1 |
60.1 |
21.97 |
TTTTTTTTTT |
0.04 |
48.6 ± 10.1 |
48.5 ± 10.2 |
4.76 |
170 ± 49 |
0.0 |
34.0 |
7.1 |
205 |
36.20 |
2690.29 |
89.4 |
2.22 |
.0023 |
34.9 |
59.5 |
20.24 |
TTTTTTTTTT |
0.05 |
47.8 ± 10.1 |
47.6 ± 10.2 |
4.78 |
174 ± 51 |
0.0 |
33.9 |
7.1 |
206 |
37.45 |
2782.92 |
89.3 |
2.22 |
.0023 |
36.1 |
61.4 |
18.61 |
TTTTTTTTTT |
0.04 |
48.3 ± 10.2 |
48.1 ± 10.4 |
4.72 |
171 ± 48 |
0.0 |
33.9 |
7.1 |
207 |
43.33 |
3219.92 |
89.5 |
2.30 |
.0025 |
35.8 |
62.8 |
20.96 |
GGCCAATTGA |
0.04 |
48.7 ± 10.2 |
48.6 ± 10.3 |
4.73 |
170 ± 47 |
0.0 |
33.9 |
7.1 |
208 |
40.29 |
2994.24 |
88.9 |
2.43 |
.0021 |
38.7 |
61.0 |
21.83 |
TTTTTTTTTT |
0.06 |
48.9 ± 10.1 |
48.8 ± 10.2 |
4.70 |
167 ± 47 |
0.0 |
33.9 |
7.1 |
209 |
37.23 |
2766.79 |
89.8 |
2.21 |
.0023 |
34.4 |
60.1 |
19.98 |
TTTTTTTTTT |
0.04 |
47.9 ± 10.2 |
47.8 ± 10.4 |
4.76 |
175 ± 52 |
0.0 |
33.9 |
7.2 |
All |
364.89 |
26681.84 |
88.0 |
3.49 |
.0020 |
39.4 |
62.4 |
21.21 |
N/A |
0.00 |
48.8 ± 10.6 |
48.7 ± 10.9 |
2.72 |
172 ± 47 |
0.1 |
31.6 |
7.2 |
201 |
41.30 |
3016.43 |
87.4 |
3.56 |
.0019 |
41.4 |
63.2 |
22.85 |
GCCAGAACAC |
0.02 |
49.0 ± 11.0 |
48.7 ± 11.2 |
2.65 |
177 ± 51 |
0.1 |
31.5 |
7.2 |
202 |
47.43 |
3466.71 |
87.1 |
3.70 |
.0020 |
43.3 |
64.9 |
26.54 |
GCCAGAACAC |
0.02 |
49.9 ± 10.8 |
49.6 ± 11.0 |
2.73 |
171 ± 47 |
0.1 |
31.6 |
7.2 |
203 |
42.72 |
3130.21 |
87.1 |
3.65 |
.0019 |
41.6 |
61.5 |
22.61 |
CGCGGGTCTG |
0.10 |
50.2 ± 10.6 |
49.9 ± 10.9 |
2.75 |
171 ± 48 |
0.1 |
31.7 |
7.2 |
204 |
38.95 |
2857.56 |
88.2 |
3.42 |
.0021 |
39.0 |
61.4 |
20.88 |
CACATGCCTA |
0.02 |
48.5 ± 10.5 |
48.4 ± 10.7 |
2.75 |
171 ± 46 |
0.1 |
31.9 |
7.2 |
205 |
36.20 |
2651.48 |
88.5 |
3.27 |
.0021 |
36.6 |
60.9 |
19.13 |
GTTGACTATT |
0.02 |
47.6 ± 10.5 |
47.3 ± 10.6 |
2.70 |
175 ± 48 |
0.1 |
31.8 |
7.2 |
206 |
37.45 |
2733.52 |
88.5 |
3.39 |
.0021 |
37.6 |
62.5 |
17.60 |
TTTTTTTTTT |
0.04 |
48.2 ± 10.6 |
47.9 ± 10.8 |
2.70 |
172 ± 46 |
0.1 |
31.5 |
7.2 |
207 |
43.33 |
3162.46 |
88.7 |
3.47 |
.0023 |
37.3 |
64.0 |
20.01 |
TTTTTTTTTT |
0.05 |
48.6 ± 10.6 |
48.5 ± 10.8 |
2.72 |
171 ± 45 |
0.1 |
31.4 |
7.2 |
208 |
40.29 |
2945.92 |
88.0 |
3.54 |
.0019 |
40.4 |
62.3 |
20.67 |
TTTTTTTTTT |
0.05 |
49.0 ± 10.4 |
48.9 ± 10.7 |
2.78 |
167 ± 45 |
0.1 |
31.6 |
7.2 |
209 |
37.23 |
2717.56 |
88.9 |
3.34 |
.0021 |
35.9 |
61.2 |
18.92 |
GTTGACTATT |
0.02 |
47.8 ± 10.7 |
47.6 ± 10.9 |
2.67 |
176 ± 50 |
0.1 |
31.5 |
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 (%) |
7.1 |
1 |
3.373 |
2.11 |
88.89 |
39.58 |
0.01 |
0.01 |
0.02 |
7.1 |
2 |
3.404 |
2.11 |
88.94 |
39.64 |
0.01 |
0.01 |
0.02 |
7.1 |
3 |
3.444 |
2.12 |
88.93 |
39.65 |
0.01 |
0.01 |
0.02 |
7.1 |
4 |
3.391 |
2.11 |
88.92 |
39.64 |
0.01 |
0.01 |
0.02 |
7.1 |
5 |
3.388 |
2.10 |
88.96 |
39.64 |
0.01 |
0.01 |
0.02 |
7.1 |
6 |
3.339 |
2.11 |
88.94 |
39.57 |
0.01 |
0.01 |
0.02 |
7.1 |
7 |
3.358 |
2.10 |
88.93 |
39.59 |
0.01 |
0.01 |
0.02 |
7.1 |
8 |
3.330 |
2.11 |
88.94 |
39.59 |
0.01 |
0.01 |
0.02 |
7.1 |
9 |
3.356 |
2.11 |
88.92 |
39.62 |
0.01 |
0.01 |
0.02 |
7.1 |
10 |
3.380 |
2.11 |
88.94 |
39.60 |
0.01 |
0.01 |
0.02 |
7.1 |
11 |
3.356 |
2.11 |
88.89 |
39.57 |
0.01 |
0.01 |
0.02 |
7.1 |
12 |
3.373 |
2.10 |
88.93 |
39.60 |
0.01 |
0.01 |
0.02 |
7.1 |
13 |
3.320 |
2.11 |
88.90 |
39.56 |
0.01 |
0.01 |
0.02 |
7.1 |
14 |
3.377 |
2.10 |
88.90 |
39.62 |
0.01 |
0.01 |
0.02 |
7.1 |
15 |
3.362 |
2.12 |
88.90 |
39.56 |
0.01 |
0.01 |
0.02 |
7.1 |
16 |
3.366 |
2.12 |
88.92 |
39.62 |
0.01 |
0.01 |
0.02 |
7.1 |
17 |
3.390 |
2.11 |
88.95 |
39.62 |
0.01 |
0.01 |
0.02 |
7.1 |
18 |
3.410 |
2.11 |
88.94 |
39.64 |
0.01 |
0.01 |
0.02 |
7.1 |
19 |
3.399 |
2.11 |
88.95 |
39.64 |
0.01 |
0.01 |
0.02 |
7.1 |
20 |
3.351 |
2.11 |
88.94 |
39.62 |
0.01 |
0.01 |
0.02 |
7.1 |
21 |
6.503 |
2.09 |
88.87 |
39.57 |
0.02 |
0.02 |
0.04 |
7.1 |
22 |
6.559 |
2.09 |
88.88 |
39.60 |
0.03 |
0.03 |
0.04 |
7.1 |
23 |
6.536 |
2.10 |
88.87 |
39.59 |
0.03 |
0.03 |
0.04 |
7.1 |
24 |
6.563 |
2.10 |
88.86 |
39.60 |
0.03 |
0.03 |
0.04 |
7.1 |
25 |
6.556 |
2.09 |
88.87 |
39.60 |
0.03 |
0.03 |
0.04 |
7.1 |
26 |
6.505 |
2.10 |
88.87 |
39.57 |
0.03 |
0.03 |
0.04 |
7.1 |
27 |
6.499 |
2.27 |
88.66 |
39.55 |
0.03 |
0.03 |
0.04 |
7.1 |
28 |
6.558 |
2.09 |
88.78 |
39.60 |
0.03 |
0.03 |
0.04 |
7.1 |
29 |
3.152 |
2.09 |
88.74 |
39.50 |
0.05 |
0.05 |
0.07 |
7.1 |
30 |
3.175 |
2.08 |
88.70 |
39.53 |
0.05 |
0.05 |
0.07 |
7.1 |
31 |
3.192 |
2.08 |
88.74 |
39.54 |
0.05 |
0.05 |
0.07 |
7.1 |
32 |
3.181 |
2.08 |
88.71 |
39.53 |
0.05 |
0.05 |
0.07 |
7.1 |
33 |
3.193 |
2.08 |
88.73 |
39.56 |
0.05 |
0.05 |
0.07 |
7.1 |
34 |
3.184 |
2.08 |
88.69 |
39.55 |
0.05 |
0.05 |
0.07 |
7.1 |
35 |
3.185 |
2.09 |
88.72 |
39.55 |
0.05 |
0.05 |
0.07 |
7.1 |
36 |
3.198 |
2.08 |
88.74 |
39.55 |
0.05 |
0.05 |
0.07 |
7.1 |
37 |
3.182 |
2.07 |
88.72 |
39.52 |
0.05 |
0.05 |
0.07 |
7.1 |
38 |
3.208 |
2.08 |
88.74 |
39.55 |
0.05 |
0.05 |
0.07 |
7.1 |
39 |
3.186 |
2.08 |
88.73 |
39.53 |
0.05 |
0.05 |
0.07 |
7.1 |
40 |
3.134 |
2.09 |
88.74 |
39.49 |
0.05 |
0.05 |
0.07 |
7.1 |
41 |
6.475 |
2.09 |
88.82 |
39.52 |
0.02 |
0.02 |
0.04 |
7.1 |
42 |
6.493 |
2.10 |
88.85 |
39.56 |
0.02 |
0.02 |
0.04 |
7.1 |
43 |
6.506 |
2.10 |
88.82 |
39.54 |
0.02 |
0.02 |
0.03 |
7.1 |
44 |
6.489 |
2.09 |
88.84 |
39.54 |
0.02 |
0.02 |
0.03 |
7.1 |
45 |
6.491 |
2.09 |
88.84 |
39.56 |
0.03 |
0.03 |
0.04 |
7.1 |
46 |
6.476 |
2.09 |
88.83 |
39.54 |
0.03 |
0.03 |
0.04 |
7.1 |
47 |
6.487 |
2.10 |
88.87 |
39.56 |
0.03 |
0.03 |
0.04 |
7.1 |
48 |
6.508 |
2.09 |
88.86 |
39.58 |
0.03 |
0.03 |
0.04 |
7.1 |
49 |
3.379 |
2.10 |
88.96 |
39.64 |
0.01 |
0.01 |
0.01 |
7.1 |
50 |
3.391 |
2.10 |
88.95 |
39.66 |
0.01 |
0.01 |
0.01 |
7.1 |
51 |
3.395 |
2.10 |
88.95 |
39.64 |
0.01 |
0.01 |
0.01 |
7.1 |
52 |
3.371 |
2.10 |
88.95 |
39.58 |
0.01 |
0.01 |
0.01 |
7.1 |
53 |
3.387 |
2.10 |
88.95 |
39.63 |
0.01 |
0.01 |
0.01 |
7.1 |
54 |
3.384 |
2.10 |
88.93 |
39.63 |
0.01 |
0.01 |
0.01 |
7.1 |
55 |
3.364 |
2.10 |
88.97 |
39.62 |
0.01 |
0.01 |
0.01 |
7.1 |
56 |
3.406 |
2.11 |
88.96 |
39.64 |
0.01 |
0.01 |
0.01 |
7.1 |
57 |
3.410 |
2.10 |
88.99 |
39.65 |
0.01 |
0.01 |
0.01 |
7.1 |
58 |
3.396 |
2.10 |
88.96 |
39.63 |
0.01 |
0.01 |
0.01 |
7.1 |
59 |
3.394 |
2.10 |
88.96 |
39.62 |
0.01 |
0.01 |
0.01 |
7.1 |
60 |
3.360 |
2.11 |
88.97 |
39.57 |
0.01 |
0.01 |
0.01 |
7.1 |
61 |
6.413 |
2.09 |
88.87 |
39.51 |
0.02 |
0.02 |
0.03 |
7.1 |
62 |
6.457 |
2.09 |
88.91 |
39.54 |
0.02 |
0.02 |
0.03 |
7.1 |
63 |
6.470 |
2.10 |
88.85 |
39.53 |
0.02 |
0.02 |
0.03 |
7.1 |
64 |
6.481 |
2.09 |
88.88 |
39.54 |
0.02 |
0.02 |
0.03 |
7.1 |
65 |
6.461 |
2.09 |
88.86 |
39.54 |
0.02 |
0.02 |
0.03 |
7.1 |
66 |
6.456 |
2.10 |
88.89 |
39.52 |
0.02 |
0.02 |
0.03 |
7.1 |
67 |
6.482 |
2.10 |
88.87 |
39.55 |
0.02 |
0.02 |
0.03 |
7.1 |
68 |
6.524 |
2.09 |
88.87 |
39.56 |
0.02 |
0.02 |
0.03 |
7.1 |
69 |
3.120 |
2.08 |
88.73 |
39.46 |
0.04 |
0.04 |
0.06 |
7.1 |
70 |
3.115 |
2.08 |
88.73 |
39.47 |
0.04 |
0.04 |
0.06 |
7.1 |
71 |
3.139 |
2.09 |
88.71 |
39.48 |
0.04 |
0.04 |
0.06 |
7.1 |
72 |
3.148 |
2.08 |
88.78 |
39.50 |
0.04 |
0.04 |
0.06 |
7.1 |
73 |
3.167 |
2.08 |
88.74 |
39.53 |
0.04 |
0.04 |
0.06 |
7.1 |
74 |
3.176 |
2.08 |
88.71 |
39.53 |
0.05 |
0.05 |
0.06 |
7.1 |
75 |
3.162 |
2.08 |
88.73 |
39.50 |
0.05 |
0.05 |
0.06 |
7.1 |
76 |
3.172 |
2.08 |
88.72 |
39.53 |
0.05 |
0.05 |
0.06 |
7.1 |
77 |
3.166 |
2.08 |
88.71 |
39.51 |
0.05 |
0.05 |
0.05 |
7.1 |
78 |
3.158 |
2.08 |
88.73 |
39.49 |
0.04 |
0.04 |
0.05 |
7.1 |
79 |
3.146 |
2.08 |
88.70 |
39.47 |
0.04 |
0.04 |
0.05 |
7.1 |
80 |
3.139 |
2.08 |
88.71 |
39.47 |
0.04 |
0.04 |
0.05 |
7.1 |
81 |
3.112 |
2.09 |
88.75 |
39.45 |
0.03 |
0.03 |
0.05 |
7.1 |
82 |
3.144 |
2.09 |
88.78 |
39.49 |
0.03 |
0.03 |
0.04 |
7.1 |
83 |
3.137 |
2.08 |
88.77 |
39.49 |
0.03 |
0.03 |
0.04 |
7.1 |
84 |
3.127 |
2.08 |
88.81 |
39.46 |
0.03 |
0.03 |
0.04 |
7.1 |
85 |
3.102 |
2.08 |
88.78 |
39.46 |
0.04 |
0.04 |
0.05 |
7.1 |
86 |
3.088 |
2.08 |
88.77 |
39.44 |
0.04 |
0.04 |
0.05 |
7.1 |
87 |
3.074 |
2.09 |
88.78 |
39.44 |
0.04 |
0.04 |
0.05 |
7.1 |
88 |
3.081 |
2.08 |
88.79 |
39.43 |
0.04 |
0.04 |
0.05 |
|
Lane |
Tile |
Yield (pf, Mrd) |
Variant rate (%) |
Mapped (%) |
Average Q |
N bases (%) |
LowQ (%) |
Last base lowQ (%) |
7.2 |
1 |
3.373 |
3.00 |
88.25 |
39.03 |
0.03 |
0.03 |
0.05 |
7.2 |
2 |
3.404 |
2.94 |
88.31 |
39.15 |
0.03 |
0.03 |
0.05 |
7.2 |
3 |
3.444 |
2.97 |
88.24 |
39.14 |
0.03 |
0.03 |
0.06 |
7.2 |
4 |
3.391 |
2.92 |
88.29 |
39.15 |
0.03 |
0.03 |
0.06 |
7.2 |
5 |
3.388 |
2.88 |
88.29 |
39.18 |
0.04 |
0.04 |
0.07 |
7.2 |
6 |
3.339 |
2.92 |
88.27 |
39.07 |
0.03 |
0.03 |
0.06 |
7.2 |
7 |
3.358 |
2.90 |
88.27 |
39.08 |
0.05 |
0.05 |
0.10 |
7.2 |
8 |
3.330 |
2.84 |
88.31 |
39.17 |
0.03 |
0.03 |
0.06 |
7.2 |
9 |
3.356 |
2.83 |
88.32 |
39.21 |
0.04 |
0.04 |
0.08 |
7.2 |
10 |
3.380 |
2.88 |
88.28 |
39.13 |
0.04 |
0.04 |
0.10 |
7.2 |
11 |
3.356 |
2.95 |
88.19 |
38.96 |
0.03 |
0.03 |
0.07 |
7.2 |
12 |
3.373 |
2.85 |
88.26 |
39.16 |
0.04 |
0.04 |
0.08 |
7.2 |
13 |
3.320 |
2.88 |
88.25 |
39.13 |
0.03 |
0.03 |
0.06 |
7.2 |
14 |
3.377 |
2.85 |
88.21 |
39.16 |
0.04 |
0.04 |
0.08 |
7.2 |
15 |
3.362 |
2.85 |
88.25 |
39.14 |
0.04 |
0.04 |
0.08 |
7.2 |
16 |
3.366 |
2.82 |
88.24 |
39.22 |
0.03 |
0.03 |
0.07 |
7.2 |
17 |
3.390 |
2.78 |
88.27 |
39.25 |
0.04 |
0.04 |
0.08 |
7.2 |
18 |
3.410 |
2.80 |
88.27 |
39.30 |
0.05 |
0.05 |
0.09 |
7.2 |
19 |
3.399 |
2.83 |
88.27 |
39.22 |
0.04 |
0.04 |
0.08 |
7.2 |
20 |
3.351 |
2.83 |
88.27 |
39.21 |
0.04 |
0.04 |
0.06 |
7.2 |
21 |
6.503 |
3.12 |
88.06 |
38.63 |
0.05 |
0.05 |
0.11 |
7.2 |
22 |
6.559 |
3.14 |
88.04 |
38.64 |
0.05 |
0.05 |
0.11 |
7.2 |
23 |
6.536 |
3.13 |
88.05 |
38.65 |
0.05 |
0.05 |
0.11 |
7.2 |
24 |
6.563 |
3.09 |
88.07 |
38.73 |
0.05 |
0.05 |
0.12 |
7.2 |
25 |
6.556 |
3.11 |
88.04 |
38.66 |
0.05 |
0.05 |
0.12 |
7.2 |
26 |
6.505 |
3.12 |
88.02 |
38.62 |
0.05 |
0.05 |
0.12 |
7.2 |
27 |
6.499 |
3.16 |
87.98 |
38.74 |
0.06 |
0.06 |
0.12 |
7.2 |
28 |
6.558 |
3.97 |
87.75 |
38.50 |
0.07 |
0.07 |
0.13 |
7.2 |
29 |
3.152 |
3.48 |
87.64 |
37.96 |
0.13 |
0.13 |
0.25 |
7.2 |
30 |
3.175 |
3.60 |
87.53 |
37.96 |
0.13 |
0.13 |
0.25 |
7.2 |
31 |
3.192 |
3.40 |
87.68 |
38.12 |
0.14 |
0.14 |
0.25 |
7.2 |
32 |
3.181 |
3.37 |
87.71 |
38.16 |
0.12 |
0.12 |
0.21 |
7.2 |
33 |
3.193 |
3.38 |
87.69 |
38.18 |
0.12 |
0.12 |
0.18 |
7.2 |
34 |
3.184 |
3.41 |
87.67 |
38.14 |
0.10 |
0.10 |
0.14 |
7.2 |
35 |
3.185 |
3.38 |
87.73 |
38.20 |
0.10 |
0.10 |
0.14 |
7.2 |
36 |
3.198 |
3.34 |
87.70 |
38.24 |
0.12 |
0.12 |
0.21 |
7.2 |
37 |
3.182 |
3.41 |
87.64 |
38.09 |
0.13 |
0.13 |
0.24 |
7.2 |
38 |
3.208 |
3.29 |
87.71 |
38.24 |
0.13 |
0.13 |
0.28 |
7.2 |
39 |
3.186 |
2.60 |
87.65 |
38.15 |
0.11 |
0.11 |
0.19 |
7.2 |
40 |
3.134 |
2.64 |
87.63 |
38.01 |
0.09 |
0.09 |
0.12 |
7.2 |
41 |
6.475 |
3.29 |
87.89 |
38.41 |
0.05 |
0.05 |
0.07 |
7.2 |
42 |
6.493 |
3.17 |
87.99 |
38.59 |
0.05 |
0.05 |
0.07 |
7.2 |
43 |
6.506 |
3.24 |
87.90 |
38.45 |
0.06 |
0.06 |
0.08 |
7.2 |
44 |
6.489 |
3.11 |
87.99 |
38.59 |
0.06 |
0.06 |
0.07 |
7.2 |
45 |
6.491 |
2.80 |
87.95 |
38.59 |
0.06 |
0.06 |
0.08 |
7.2 |
46 |
6.476 |
3.18 |
87.94 |
38.54 |
0.06 |
0.06 |
0.08 |
7.2 |
47 |
6.487 |
3.13 |
87.97 |
38.61 |
0.06 |
0.06 |
0.08 |
7.2 |
48 |
6.508 |
2.75 |
87.96 |
38.65 |
0.06 |
0.06 |
0.08 |
7.2 |
49 |
3.379 |
2.84 |
88.29 |
39.14 |
0.04 |
0.04 |
0.04 |
7.2 |
50 |
3.391 |
2.83 |
88.30 |
39.23 |
0.03 |
0.03 |
0.04 |
7.2 |
51 |
3.395 |
2.89 |
88.25 |
39.10 |
0.04 |
0.04 |
0.04 |
7.2 |
52 |
3.371 |
2.86 |
88.29 |
39.11 |
0.04 |
0.04 |
0.04 |
7.2 |
53 |
3.387 |
2.83 |
88.29 |
39.17 |
0.04 |
0.04 |
0.06 |
7.2 |
54 |
3.384 |
2.82 |
88.28 |
39.23 |
0.03 |
0.03 |
0.05 |
7.2 |
55 |
3.364 |
2.85 |
88.31 |
39.15 |
0.03 |
0.03 |
0.05 |
7.2 |
56 |
3.406 |
2.80 |
88.29 |
39.24 |
0.04 |
0.04 |
0.05 |
7.2 |
57 |
3.410 |
2.81 |
88.30 |
39.25 |
0.04 |
0.04 |
0.06 |
7.2 |
58 |
3.396 |
2.85 |
88.24 |
39.18 |
0.04 |
0.04 |
0.06 |
7.2 |
59 |
3.394 |
2.87 |
88.23 |
39.13 |
0.04 |
0.04 |
0.05 |
7.2 |
60 |
3.360 |
2.89 |
88.26 |
39.05 |
0.04 |
0.04 |
0.04 |
7.2 |
61 |
6.413 |
3.20 |
88.07 |
38.51 |
0.04 |
0.04 |
0.08 |
7.2 |
62 |
6.457 |
3.14 |
88.10 |
38.60 |
0.04 |
0.04 |
0.08 |
7.2 |
63 |
6.470 |
3.17 |
88.07 |
38.58 |
0.04 |
0.04 |
0.09 |
7.2 |
64 |
6.481 |
3.14 |
88.08 |
38.60 |
0.04 |
0.04 |
0.09 |
7.2 |
65 |
6.461 |
3.16 |
88.04 |
38.51 |
0.04 |
0.04 |
0.10 |
7.2 |
66 |
6.456 |
3.12 |
88.07 |
38.59 |
0.04 |
0.04 |
0.10 |
7.2 |
67 |
6.482 |
3.09 |
88.06 |
38.66 |
0.05 |
0.05 |
0.11 |
7.2 |
68 |
6.524 |
3.13 |
88.04 |
38.62 |
0.05 |
0.05 |
0.11 |
7.2 |
69 |
3.120 |
3.42 |
87.69 |
38.02 |
0.10 |
0.10 |
0.22 |
7.2 |
70 |
3.115 |
3.34 |
87.75 |
38.17 |
0.11 |
0.11 |
0.22 |
7.2 |
71 |
3.139 |
3.38 |
87.73 |
38.10 |
0.11 |
0.11 |
0.23 |
7.2 |
72 |
3.148 |
3.39 |
87.79 |
38.14 |
0.11 |
0.11 |
0.23 |
7.2 |
73 |
3.167 |
3.36 |
87.79 |
38.22 |
0.12 |
0.12 |
0.24 |
7.2 |
74 |
3.176 |
3.37 |
87.78 |
38.20 |
0.12 |
0.12 |
0.24 |
7.2 |
75 |
3.162 |
3.34 |
87.77 |
38.23 |
0.12 |
0.12 |
0.24 |
7.2 |
76 |
3.172 |
3.30 |
87.80 |
38.29 |
0.12 |
0.12 |
0.26 |
7.2 |
77 |
3.166 |
3.30 |
87.75 |
38.20 |
0.12 |
0.12 |
0.26 |
7.2 |
78 |
3.158 |
3.30 |
87.77 |
38.19 |
0.11 |
0.11 |
0.25 |
7.2 |
79 |
3.146 |
3.37 |
87.66 |
38.02 |
0.11 |
0.11 |
0.25 |
7.2 |
80 |
3.139 |
3.33 |
87.71 |
38.08 |
0.11 |
0.11 |
0.26 |
7.2 |
81 |
3.112 |
3.28 |
87.80 |
38.18 |
0.08 |
0.08 |
0.17 |
7.2 |
82 |
3.144 |
2.58 |
87.74 |
38.11 |
0.06 |
0.06 |
0.10 |
7.2 |
83 |
3.137 |
2.55 |
87.80 |
38.15 |
0.06 |
0.06 |
0.10 |
7.2 |
84 |
3.127 |
2.57 |
87.81 |
38.11 |
0.06 |
0.06 |
0.09 |
7.2 |
85 |
3.102 |
2.56 |
87.81 |
38.14 |
0.07 |
0.07 |
0.10 |
7.2 |
86 |
3.088 |
2.57 |
87.73 |
38.03 |
0.07 |
0.07 |
0.10 |
7.2 |
87 |
3.074 |
2.56 |
87.82 |
38.14 |
0.07 |
0.07 |
0.10 |
7.2 |
88 |
3.081 |
3.37 |
87.76 |
38.05 |
0.07 |
0.07 |
0.10 |
|
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 |