Flowcell QC summary (lanes 1,2,3,4)


Date Flowcell Lane Platform Unit Readgroup Sample Library Type Project Genome Centre
B04D1ABXX 1 110311_SN228_0126_BB04D1ABXX_1 WTCHG_13405 samples 4619/10 gDNA PE P100244 Mouse37 WTCHG
B04D1ABXX 2 110311_SN228_0126_BB04D1ABXX_2 WTCHG_13406 samples 4620/10 gDNA PE P100244 Mouse37 WTCHG
B04D1ABXX 3 110311_SN228_0126_BB04D1ABXX_3 WTCHG_13407 samples 4623/10 gDNA PE P100244 Mouse37 WTCHG
B04D1ABXX 4 110311_SN228_0126_BB04D1ABXX_4 WTCHG_13408 samples 4624/10 gDNA PE P100244 Mouse37 WTCHG

Lane Length Tiles Clusters PF % PF Yield (Mrd) Yield (Mb) Yield (Mb Q20) % Mapped % Coverage⊥ % Primer % Variants Mean cov.* % high cov.ℵ % dups % pair dups Link
1.1 101 32 3182781 95.6 97.37 9834.80 9428.55 98.4 84.7 0.00 0.93 ± 0.24 4.19 14.33 2.00 0.68 lane
1.2 101 32 3182781 95.6 97.37 9834.80 9193.70 98.0 84.7 0.00 1.00 ± 0.24 4.18 14.32 2.00 0.69
2.1 101 32 2964184 95.8 90.83 9174.14 8821.11 98.4 87.0 0.00 0.93 ± 0.00 3.81 14.35 1.57 0.50 lane
2.2 101 32 2964184 95.8 90.83 9174.14 8583.59 98.1 87.0 0.00 0.98 ± 0.00 3.80 14.34 1.56 0.49
3.1 101 32 3380301 94.9 102.64 10366.82 9935.00 98.5 88.4 0.00 0.94 ± 0.00 4.24 15.11 1.57 0.47 lane
3.2 101 32 3380301 94.9 102.64 10366.82 9651.66 98.3 88.4 0.00 0.99 ± 0.00 4.23 15.10 1.56 0.47
4.1 101 32 3326660 95.0 101.17 10218.49 9803.45 98.5 88.2 0.00 0.93 ± 0.24 4.19 14.46 1.67 0.53 lane
4.2 101 32 3326660 95.0 101.17 10218.49 9559.25 98.3 88.2 0.00 0.99 ± 0.33 4.17 14.48 1.66 0.53

⊥   Fraction of reference that is covered at least once   *   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 42.0 ± 7.9 42.0 ± 8.0 0.39 362 ± 53 1.4 94.2 0.1 0.1 3.0 15.2 32.4
1.2 41.0 ± 9.8 41.2 ± 9.5 0.36 362 ± 53 1.4 94.1 0.1 0.4 5.0 21.3 30.7
2.1 41.4 ± 8.1 41.3 ± 8.1 0.34 402 ± 53 1.3 94.0 0.0 0.2 2.8 14.7 32.6
2.2 40.6 ± 9.8 40.6 ± 9.6 0.32 402 ± 53 1.3 94.1 0.1 0.6 5.0 21.9 30.7
3.1 40.8 ± 7.9 40.8 ± 7.9 0.38 379 ± 43 1.1 93.3 0.1 0.2 3.0 15.4 32.5
3.2 39.6 ± 9.8 39.7 ± 9.5 0.34 379 ± 43 1.1 93.2 0.1 0.7 5.3 22.2 30.5
4.1 41.0 ± 7.9 41.0 ± 7.9 0.34 356 ± 39 1.1 93.7 0.1 0.2 2.9 14.8 32.5
4.2 39.9 ± 9.6 40.0 ± 9.4 0.32 356 ± 39 1.1 93.4 0.1 0.7 4.9 20.8 30.7

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
Log coverage histogram
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.   





QC version: 2.1