Flowcell QC summary (lane 7)

Date	Flowcell	Lane	Platform Unit	Readgroup	Sample	Library	Type	Project	Genome	Centre
2011-02-23	62WW0AAXX	7	110223_GAII06_00033_FC_7	WTCHG_11764_12	samples	111/11_MPX	DSN Indexed PE		Rat3.4	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
7.1	51	120	367164	89.6	3.67	186.93	184.33	92.4	3.7	0.00	0.47 ± 0.00	1.63	9.72	4.49	0.79	lane
7.2	51	120	367164	89.6	3.67	186.93	183.76	92.3	3.7	0.00	0.49 ± 0.00	1.63	9.75	4.51	0.79

^⊥ 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	% GC_mapped	σ_pos(%GC)	insert ± MAD	% exonic	% exon cov'ge	%N	max_pos %N	%lowQ	%lowQ_end	avgQ
7.1	46.6 ± 9.0	46.3 ± 8.9	3.41	200 ± 40	12.3	29.3	0.0	0.6	0.7	2.6	36.6
7.2	46.6 ± 9.0	46.4 ± 9.0	3.48	199 ± 40	12.2	29.2	0.1	0.0	1.0	2.9	36.1

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