QC statistics for lane 8


Date Flowcell Lane Platform Unit Readgroup Sample Library Type Project Genome Centre
2016-10-13 HF3WCBBXX 8 161011_K00198_0114_AHF3WCBBXX_8 WTCHG_320658 30 samples 395/16_MPX_10nM_1 Our indexes RNA-Seq PolyA P160354 galGal4 WTCHG

Lane Length Tiles Clusters % PF Yield (Mrd) Yield (Mb) Yield (Mb Q20) % Mapped % Coverage % Primer % Broken % Variants Hets Mean cov.* % high cov. % dups % pair dups Link
8.1 75 88 3962715 100.0 348.72 26153.92 25839.69 80.6 7.9 0.00 1.2 2.18 ± 0.11 .0036 8.87 11.44 45.40 10.78 back
8.2 75 88 3962715 100.0 348.72 26153.92 24990.46 79.3 8.0 0.00 1.2 4.20 ± 0.50 .0034 8.60 11.30 39.30 9.83

  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      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
8.1 47.6 ± 10.1 46.3 ± 9.7 4.59 191 ± 56 15.5 71.3 0.0 0.8 0.0 0.0 33.9
8.2 47.4 ± 10.7 45.8 ± 10.2 2.63 192 ± 57 16.7 74.1 0.0 0.1 0.0 0.0 30.8

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
211 TAGAGAGA WTCHG_320658_211 07C_DARK_RET_LEFT PAR3810A71 Our indexes RNA-Seq PolyA galGal4 P160354
212 GCTCCTCT WTCHG_320658_212 07D_DARK_RET_RIGHT PAR3810A72 Our indexes RNA-Seq PolyA galGal4 P160354
213 GAGTTAGT WTCHG_320658_213 10A_DARK_TEL_LEFT PAR3810A73 Our indexes RNA-Seq PolyA galGal4 P160354
214 CTTGTGGT WTCHG_320658_214 10B_DARK_TEL_RIGHT PAR3810A74 Our indexes RNA-Seq PolyA galGal4 P160354
215 CTATTGTG WTCHG_320658_215 10C_DARK_RET_LEFT PAR3810A75 Our indexes RNA-Seq PolyA galGal4 P160354
216 CATTGGCT WTCHG_320658_216 10D_DARK_RET_RIGHT PAR3810A76 Our indexes RNA-Seq PolyA galGal4 P160354
217 TGCCAATC WTCHG_320658_217 14A_DARK_TEL_LEFT PAR3810A77 Our indexes RNA-Seq PolyA galGal4 P160354
218 TCCAATTG WTCHG_320658_218 14B_DARK_TEL_RIGHT PAR3810A78 Our indexes RNA-Seq PolyA galGal4 P160354
219 TACTTCGA WTCHG_320658_219 14C_DARK_RET_LEFT PAR3810A79 Our indexes RNA-Seq PolyA galGal4 P160354
220 GCGAAGTC WTCHG_320658_220 14D_DARK_RET_RIGHT PAR3810A80 Our indexes RNA-Seq PolyA galGal4 P160354
233 TGAATTCT WTCHG_320658_233 29A_6HLIGHT_TEL_LEFT PAR3810A93 Our indexes RNA-Seq PolyA galGal4 P160354
234 TCCAGCCA WTCHG_320658_234 29B_6HLIGHT_TEL_RIGHT PAR3810A94 Our indexes RNA-Seq PolyA galGal4 P160354
235 TAAGAGGA WTCHG_320658_235 29C_6HLIGHT_RET_LEFT PAR3810A95 Our indexes RNA-Seq PolyA galGal4 P160354
236 GCCTTCCT WTCHG_320658_236 29D_6HLIGHT_RET_RIGHT PAR3810A96 Our indexes RNA-Seq PolyA galGal4 P160354
237 GACGACGT WTCHG_320658_237 31A_6HLIGHT_TEL_LEFT PAR3810A97 Our indexes RNA-Seq PolyA galGal4 P160354
238 CTGCATGT WTCHG_320658_238 31B_6HLIGHT_TEL_RIGHT PAR3810A98 Our indexes RNA-Seq PolyA galGal4 P160354
239 CGTCTCGA WTCHG_320658_239 31C_6HLIGHT_RET_LEFT PAR3810A99 Our indexes RNA-Seq PolyA galGal4 P160354
240 CACCAACT WTCHG_320658_240 31D_6HLIGHT_RET_RIGHT PAR3810A100 Our indexes RNA-Seq PolyA galGal4 P160354
251 GTGGTTGA WTCHG_320658_251 49C_24HLIGHT_RET_LEFT PAR3810A111 Our indexes RNA-Seq PolyA galGal4 P160354
252 GCAGAGCT WTCHG_320658_252 49D_24HLIGHT_RET_RIGHT PAR3810A112 Our indexes RNA-Seq PolyA galGal4 P160354
253 GACGGTAC WTCHG_320658_253 50A_24HLIGHT_TEL_LEFT PAR3810A113 Our indexes RNA-Seq PolyA galGal4 P160354
254 CTGCGCAC WTCHG_320658_254 50B_24HLIGHT_TEL_RIGHT PAR3810A114 Our indexes RNA-Seq PolyA galGal4 P160354
255 CGGAAGGA WTCHG_320658_255 50C_24HLIGHT_RET_LEFT PAR3810A115 Our indexes RNA-Seq PolyA galGal4 P160354
256 ATTCTCCT WTCHG_320658_256 50D_24HLIGHT_RET_RIGHT PAR3810A116 Our indexes RNA-Seq PolyA galGal4 P160354
257 TCTGTGAC WTCHG_320658_257 54A_24HLIGHT_TEL_LEFT PAR3810A117 Our indexes RNA-Seq PolyA galGal4 P160354
258 TCATTGCA WTCHG_320658_258 54B_24HLIGHT_TEL_RIGHT PAR3810A118 Our indexes RNA-Seq PolyA galGal4 P160354
259 GTGGCCAG WTCHG_320658_259 54C_24HLIGHT_RET_LEFT PAR3810A119 Our indexes RNA-Seq PolyA galGal4 P160354
295 CGAGGAGA WTCHG_320658_295 25C_6HLIGHT_RET_LEFT PAR3810A91 Our indexes RNA-Seq PolyA galGal4 P160354
296 ATCTCTCT WTCHG_320658_296 25D_6HLIGHT_RET_RIGHT PAR3810A92 Our indexes RNA-Seq PolyA galGal4 P160354
301 ATAGAGTC WTCHG_320658_301 54D_24HLIGHT_RET_RIGHT PAR3810A120 Our indexes RNA-Seq PolyA galGal4 P160354

Lane Mx Sample name Sample id Mean cvg Median cvg % > 10X % > 20X Exonic mean cvg Exonic median cvg Exonic % > 10X Exonic % > 20X
8 211 07C_DARK_RET_LEFT PAR3810A71 3.75 2 0.6 0.2 7.52 4 14.8 5.8
8 212 07D_DARK_RET_RIGHT PAR3810A72 3.71 2 0.6 0.2 7.41 4 14.0 5.5
8 213 10A_DARK_TEL_LEFT PAR3810A73 6.63 2 1.4 0.7 14.59 7 30.7 16.1
8 214 10B_DARK_TEL_RIGHT PAR3810A74 4.45 2 0.7 0.3 8.47 4 15.8 7.0
8 215 10C_DARK_RET_LEFT PAR3810A75 6.69 2 2.0 1.0 17.70 9 39.1 21.5
8 216 10D_DARK_RET_RIGHT PAR3810A76 7.41 2 2.3 1.2 20.85 11 43.9 25.9
8 217 14A_DARK_TEL_LEFT PAR3810A77 8.89 2 2.2 1.3 23.74 10 44.9 27.9
8 218 14B_DARK_TEL_RIGHT PAR3810A78 7.54 2 1.8 1.0 18.72 8 37.9 21.9
8 219 14C_DARK_RET_LEFT PAR3810A79 3.69 2 0.6 0.2 7.61 4 14.7 5.8
8 220 14D_DARK_RET_RIGHT PAR3810A80 3.90 2 0.7 0.2 8.24 5 16.7 6.8
8 233 29A_6HLIGHT_TEL_LEFT PAR3810A93 5.35 2 1.1 0.5 11.39 6 24.3 11.6
8 234 29B_6HLIGHT_TEL_RIGHT PAR3810A94 8.51 2 2.2 1.3 22.90 10 45.0 27.6
8 235 29C_6HLIGHT_RET_LEFT PAR3810A95 7.87 2 2.4 1.3 21.56 11 45.1 27.2
8 236 29D_6HLIGHT_RET_RIGHT PAR3810A96 5.43 2 1.4 0.6 13.18 7 30.4 14.6
8 237 31A_6HLIGHT_TEL_LEFT PAR3810A97 6.47 2 1.6 0.8 16.79 8 34.7 19.1
8 238 31B_6HLIGHT_TEL_RIGHT PAR3810A98 7.05 2 1.7 0.9 17.30 8 36.0 20.2
8 239 31C_6HLIGHT_RET_LEFT PAR3810A99 4.68 2 1.0 0.4 10.40 6 23.2 10.2
8 240 31D_6HLIGHT_RET_RIGHT PAR3810A100 4.56 2 1.0 0.4 10.25 6 22.4 9.8
8 251 49C_24HLIGHT_RET_LEFT PAR3810A111 3.77 2 0.6 0.2 7.76 4 15.1 6.0
8 252 49D_24HLIGHT_RET_RIGHT PAR3810A112 3.87 2 0.7 0.2 8.22 5 16.6 6.7
8 253 50A_24HLIGHT_TEL_LEFT PAR3810A113 9.06 2 2.5 1.4 25.96 12 48.5 31.0
8 254 50B_24HLIGHT_TEL_RIGHT PAR3810A114 7.84 2 2.1 1.2 21.46 10 43.6 26.1
8 255 50C_24HLIGHT_RET_LEFT PAR3810A115 3.82 2 0.7 0.2 8.00 5 16.1 6.4
8 256 50D_24HLIGHT_RET_RIGHT PAR3810A116 4.26 2 0.9 0.3 9.27 5 19.9 8.4
8 257 54A_24HLIGHT_TEL_LEFT PAR3810A117 9.19 2 2.5 1.5 26.30 12 48.2 31.0
8 258 54B_24HLIGHT_TEL_RIGHT PAR3810A118 4.08 2 0.6 0.2 7.93 4 14.7 6.4
8 259 54C_24HLIGHT_RET_LEFT PAR3810A119 5.61 2 1.6 0.7 13.85 7 31.7 15.6
8 295 25C_6HLIGHT_RET_LEFT PAR3810A91 8.05 2 2.6 1.4 24.47 12 48.7 30.8
8 296 25D_6HLIGHT_RET_RIGHT PAR3810A92 5.56 2 1.6 0.7 14.15 7 33.4 16.6
8 301 54D_24HLIGHT_RET_RIGHT PAR3810A120 5.85 2 1.7 0.8 14.95 8 34.2 17.5

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
8.1 All 348.72 25839.69 80.6 2.18 .0036 15.5 71.3 10.78 N/A 0.00 47.6 ± 10.1 46.3 ± 9.7 4.59 191 ± 56 0.0 33.9
8.1 211 4.73 350.62 80.8 2.15 .0032 15.2 60.8 6.99 TTTTTTTTTT 0.04 47.4 ± 10.1 45.9 ± 9.7 4.63 198 ± 58 0.0 33.9
8.1 212 4.54 336.43 80.8 2.22 .0032 15.2 59.2 7.42 TTTTTTTTTT 0.03 47.4 ± 10.0 46.1 ± 9.6 4.63 192 ± 56 0.0 33.9
8.1 213 10.83 802.58 80.2 2.22 .0037 16.3 72.7 10.43 TTTTTTTTTT 0.03 48.0 ± 10.0 46.7 ± 9.7 4.57 189 ± 55 0.0 33.9
8.1 214 5.19 384.36 80.7 2.18 .0033 15.6 59.3 8.49 TTTTTTTTTT 0.03 47.5 ± 10.0 46.2 ± 9.7 4.60 191 ± 57 0.0 33.9
8.1 215 14.18 1050.41 81.2 2.17 .0038 15.3 76.0 9.93 TTTTTTTTTT 0.04 47.1 ± 9.9 45.8 ± 9.7 4.62 194 ± 57 0.0 33.9
8.1 216 17.28 1280.12 80.9 2.18 .0039 15.5 78.5 11.54 TTTTTTTTTT 0.04 47.3 ± 10.0 46.0 ± 9.7 4.59 193 ± 57 0.0 33.9
8.1 217 20.47 1516.87 80.2 2.19 .0040 15.9 81.7 12.61 TTTTTTTTTT 0.04 47.8 ± 10.2 46.3 ± 9.8 4.55 190 ± 57 0.0 33.9
8.1 218 15.28 1132.41 80.3 2.16 .0038 15.7 77.5 11.05 TTTTTTTTTT 0.03 47.7 ± 10.1 46.4 ± 9.7 4.59 194 ± 58 0.0 33.9
8.1 219 4.77 353.52 81.0 2.23 .0033 15.2 60.3 6.63 TTTTTTTTTT 0.03 47.4 ± 10.1 46.0 ± 9.7 4.62 191 ± 57 0.0 33.9
8.1 220 5.42 401.80 80.8 2.23 .0034 15.2 62.8 6.67 TTTTTTTTTT 0.02 47.6 ± 10.1 46.3 ± 9.8 4.61 191 ± 55 0.0 33.9
8.1 233 8.23 609.86 80.3 2.14 .0033 15.4 68.6 9.56 TTTTTTTTTT 0.05 47.7 ± 10.1 46.3 ± 9.8 4.52 192 ± 58 0.0 33.9
8.1 234 19.76 1463.93 80.3 2.15 .0039 15.8 81.8 12.48 TTTTTTTTTT 0.04 47.8 ± 10.1 46.5 ± 9.7 4.60 195 ± 58 0.0 33.9
8.1 235 18.63 1380.73 80.9 2.19 .0040 15.4 80.5 11.69 TTTTTTTTTT 0.04 47.5 ± 10.2 46.1 ± 9.9 4.62 193 ± 57 0.0 33.9
8.1 236 9.95 737.37 80.5 2.21 .0035 15.5 72.1 8.91 TTTTTTTTTT 0.04 47.7 ± 10.1 46.4 ± 9.8 4.64 193 ± 56 0.0 33.9
8.1 237 14.34 1062.71 81.9 2.07 .0036 15.0 76.5 12.01 TTTTTTTTTT 0.05 47.1 ± 9.7 45.9 ± 9.3 4.65 189 ± 56 0.0 33.9
8.1 238 14.31 1060.41 80.7 2.12 .0037 15.3 76.5 11.93 TTTTTTTTTT 0.05 47.7 ± 10.0 46.3 ± 9.5 4.62 191 ± 56 0.0 33.9
8.1 239 7.28 539.40 80.6 2.26 .0034 15.6 68.1 7.75 TTTTTTTTTT 0.04 47.6 ± 10.1 46.2 ± 9.9 4.63 189 ± 55 0.0 33.9
8.1 240 7.10 525.74 80.4 2.23 .0034 15.5 66.7 8.17 TTTTTTTTTT 0.03 47.6 ± 10.1 46.2 ± 9.9 4.58 192 ± 57 0.0 33.9
8.1 251 4.85 359.13 81.1 2.22 .0032 15.3 60.5 6.89 TTTTTTTTTT 0.03 47.4 ± 10.1 46.0 ± 9.6 4.64 190 ± 56 0.0 33.9
8.1 252 5.33 395.27 80.8 2.22 .0032 15.1 61.9 7.88 TTTTTTTTTT 0.04 47.5 ± 10.1 46.0 ± 9.7 4.64 190 ± 55 0.0 33.9
8.1 253 23.10 1711.78 80.5 2.20 .0040 15.8 83.7 13.70 TTTTTTTTTT 0.03 47.8 ± 10.1 46.5 ± 9.7 4.61 188 ± 55 0.0 33.9
8.1 254 18.47 1368.52 80.3 2.19 .0038 16.0 81.4 12.57 TTTTTTTTTT 0.04 47.8 ± 10.1 46.4 ± 9.6 4.59 190 ± 56 0.0 33.9
8.1 255 5.13 380.00 80.8 2.21 .0032 14.9 61.2 6.96 TTTTTTTTTT 0.04 47.2 ± 10.1 45.8 ± 9.7 4.65 190 ± 56 0.0 33.9
8.1 256 6.24 462.48 80.5 2.22 .0033 15.0 64.5 8.20 TTTTTTTTTT 0.03 47.4 ± 10.1 45.9 ± 9.7 4.59 191 ± 56 0.0 33.9
8.1 257 24.01 1779.66 80.4 2.11 .0037 15.1 83.2 13.89 TTTTTTTTTT 0.05 47.7 ± 10.2 46.2 ± 9.7 4.60 192 ± 55 0.0 33.9
8.1 258 4.92 364.27 80.5 2.13 .0029 15.2 58.7 7.72 TTTTTTTTTT 0.04 47.7 ± 10.1 46.3 ± 9.6 4.60 193 ± 57 0.0 33.9
8.1 259 10.84 803.15 81.0 2.19 .0033 15.0 72.9 8.59 TTTTTTTTTT 0.03 47.4 ± 10.1 46.1 ± 9.7 4.66 192 ± 56 0.0 33.9
8.1 295 20.66 1531.24 80.2 2.25 .0041 15.9 81.6 11.47 CACACACACA 0.01 47.9 ± 10.1 46.6 ± 9.8 4.56 189 ± 53 0.0 33.9
8.1 296 10.94 811.13 79.0 2.28 .0036 16.1 75.3 9.23 TTTTTTTTTT 0.06 48.4 ± 10.3 46.9 ± 9.9 4.20 196 ± 64 0.0 33.9
8.1 301 11.92 883.80 80.8 2.22 .0034 15.1 74.4 9.51 TTTTTTTTTT 0.04 47.6 ± 10.1 46.3 ± 9.7 4.67 189 ± 54 0.0 33.9
8.2 All 348.72 24990.46 79.3 4.20 .0034 16.7 74.1 9.83 N/A 0.00 47.4 ± 10.7 45.8 ± 10.2 2.63 192 ± 57 0.0 30.8
8.2 211 4.73 338.39 79.5 4.22 .0031 16.5 64.0 6.38 TTTTTTTTTT 0.08 47.1 ± 10.6 45.6 ± 10.2 2.66 199 ± 58 0.0 30.7
8.2 212 4.54 326.18 79.7 4.13 .0030 16.4 62.2 6.88 TTTTTTTTTT 0.05 47.2 ± 10.6 45.6 ± 10.2 2.67 192 ± 57 0.0 30.9
8.2 213 10.83 778.86 79.0 4.17 .0034 17.7 75.7 9.49 TTTTTTTTTT 0.05 47.7 ± 10.6 46.2 ± 10.1 2.71 190 ± 55 0.0 31.0
8.2 214 5.19 371.79 79.4 4.21 .0031 16.9 62.5 7.75 TTTTTTTTTT 0.06 47.4 ± 10.6 45.9 ± 10.2 2.61 192 ± 57 0.0 30.8
8.2 215 14.18 1014.67 80.0 4.22 .0036 16.5 78.6 9.03 TTTTTTTTTT 0.08 46.8 ± 10.5 45.4 ± 10.1 2.57 195 ± 58 0.0 30.8
8.2 216 17.28 1237.98 79.7 4.19 .0037 16.7 80.9 10.58 TTTTTTTTTT 0.07 47.0 ± 10.6 45.5 ± 10.1 2.64 194 ± 58 0.0 30.8
8.2 217 20.47 1467.83 78.9 4.20 .0037 17.2 84.0 11.49 TTTTTTTTTT 0.07 47.7 ± 10.8 46.0 ± 10.3 2.71 191 ± 57 0.0 30.9
8.2 218 15.28 1092.98 79.0 4.25 .0036 17.0 80.3 10.00 TTTTTTTTTT 0.07 47.6 ± 10.7 46.0 ± 10.2 2.63 195 ± 58 0.0 30.8
8.2 219 4.77 342.03 79.8 4.23 .0031 16.4 63.3 6.08 TTTTTTTTTT 0.08 47.2 ± 10.6 45.6 ± 10.2 2.64 192 ± 57 0.0 30.8
8.2 220 5.42 389.46 79.6 4.19 .0032 16.3 65.7 6.11 TTTTTTTTTT 0.05 47.4 ± 10.7 45.9 ± 10.3 2.71 192 ± 56 0.0 31.0
8.2 233 8.23 588.95 78.9 4.19 .0031 16.8 71.8 8.62 TTTTTTTTTT 0.10 47.6 ± 10.9 46.0 ± 10.3 2.51 194 ± 57 0.0 30.7
8.2 234 19.76 1415.23 79.0 4.19 .0036 17.1 84.5 11.32 TTTTTTTTTT 0.08 47.7 ± 10.8 46.0 ± 10.3 2.69 196 ± 58 0.0 30.8
8.2 235 18.63 1333.62 79.6 4.26 .0037 16.6 82.8 10.71 TTTTTTTTTT 0.10 47.2 ± 10.8 45.6 ± 10.3 2.62 194 ± 58 0.0 30.7
8.2 236 9.95 714.33 79.2 4.24 .0034 16.6 75.0 8.16 CGTATGCCGT 0.26 47.5 ± 10.6 45.9 ± 10.2 2.84 194 ± 57 0.0 30.9
8.2 237 14.34 1030.31 80.6 3.93 .0035 16.3 79.0 10.97 TTTTTTTTTT 0.06 46.9 ± 10.3 45.5 ± 9.8 2.69 191 ± 54 0.0 30.9
8.2 238 14.31 1024.93 79.3 4.14 .0034 16.7 79.5 10.85 TTTTTTTTTT 0.07 47.5 ± 10.6 45.9 ± 10.1 2.60 192 ± 56 0.0 30.8
8.2 239 7.28 521.66 79.4 4.29 .0032 16.8 71.0 7.05 TTTTTTTTTT 0.07 47.3 ± 10.7 45.8 ± 10.4 2.66 190 ± 56 0.0 30.8
8.2 240 7.10 508.28 79.1 4.28 .0032 16.7 69.6 7.46 TTTTTTTTTT 0.08 47.5 ± 10.7 45.9 ± 10.3 2.67 192 ± 58 0.0 30.8
8.2 251 4.85 347.09 79.8 4.26 .0031 16.4 63.3 6.34 TTTTTTTTTT 0.06 47.0 ± 10.7 45.4 ± 10.2 2.67 190 ± 57 0.0 30.8
8.2 252 5.33 382.70 79.6 4.17 .0031 16.3 65.0 7.27 TTTTTTTTTT 0.06 47.2 ± 10.7 45.6 ± 10.2 2.60 191 ± 56 0.0 30.9
8.2 253 23.10 1656.22 79.3 4.18 .0037 17.0 86.0 12.59 TTTTTTTTTT 0.06 47.5 ± 10.7 45.9 ± 10.2 2.71 190 ± 55 0.0 30.8
8.2 254 18.47 1323.92 79.1 4.19 .0036 17.3 83.9 11.49 TTTTTTTTTT 0.06 47.6 ± 10.7 46.0 ± 10.2 2.68 191 ± 56 0.0 30.9
8.2 255 5.13 367.34 79.6 4.17 .0031 16.0 64.4 6.33 TTTTTTTTTT 0.08 46.9 ± 10.7 45.4 ± 10.2 2.68 191 ± 56 0.0 30.8
8.2 256 6.24 447.97 79.3 4.16 .0031 16.2 67.7 7.54 TTTTTTTTTT 0.07 47.1 ± 10.7 45.6 ± 10.2 2.61 192 ± 57 0.0 30.9
8.2 257 24.01 1716.05 79.1 4.18 .0034 16.3 85.7 12.65 TTTTTTTTTT 0.08 47.3 ± 10.8 45.7 ± 10.3 2.69 193 ± 55 0.0 30.7
8.2 258 4.92 352.13 79.2 4.12 .0027 16.6 61.7 6.97 TTTTTTTTTT 0.08 47.5 ± 10.7 45.8 ± 10.1 2.63 194 ± 57 0.0 30.8
8.2 259 10.84 776.64 79.8 4.18 .0031 16.0 75.6 7.84 TTTTTTTTTT 0.07 46.9 ± 10.8 45.4 ± 10.3 2.73 192 ± 56 0.0 30.8
8.2 295 20.66 1482.48 79.0 4.29 .0038 17.0 83.5 10.51 TTTTTTTTTT 0.06 47.7 ± 10.7 46.3 ± 10.3 2.74 190 ± 54 0.0 30.9
8.2 296 10.94 784.68 77.8 4.56 .0034 17.2 78.0 8.36 TTTTTTTTTT 0.09 48.6 ± 11.0 47.0 ± 10.5 1.60 197 ± 64 0.0 30.8
8.2 301 11.92 855.79 79.6 4.16 .0031 16.2 77.1 8.71 TTTTTTTTTT 0.08 47.3 ± 10.7 45.6 ± 10.2 2.74 189 ± 55 0.0 30.9

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 (%)
8.1 1 2.943 1.73 80.51 39.36 0.00 0.00 0.00
8.1 2 3.072 1.72 80.59 39.45 0.01 0.01 0.00
8.1 3 3.091 1.72 80.58 39.44 0.01 0.01 0.00
8.1 4 3.107 1.72 80.55 39.45 0.01 0.01 0.00
8.1 5 3.123 1.72 80.58 39.45 0.01 0.01 0.01
8.1 6 3.137 1.73 80.56 39.44 0.01 0.01 0.01
8.1 7 3.178 1.73 80.56 39.48 0.01 0.01 0.02
8.1 8 3.174 1.73 80.53 39.48 0.01 0.01 0.01
8.1 9 3.187 1.73 80.52 39.47 0.01 0.01 0.02
8.1 10 3.198 1.74 80.55 39.49 0.01 0.01 0.02
8.1 11 3.218 1.74 80.54 39.50 0.02 0.02 0.02
8.1 12 3.199 1.73 80.49 39.47 0.01 0.01 0.02
8.1 13 3.164 1.74 80.60 39.42 0.01 0.01 0.02
8.1 14 3.153 1.74 80.60 39.40 0.01 0.01 0.02
8.1 15 3.178 1.74 80.60 39.41 0.01 0.01 0.02
8.1 16 3.204 1.74 80.61 39.42 0.02 0.02 0.03
8.1 17 3.213 1.76 80.62 39.44 0.02 0.02 0.02
8.1 18 3.209 1.76 80.59 39.43 0.02 0.02 0.02
8.1 19 3.222 1.75 80.58 39.43 0.02 0.02 0.03
8.1 20 3.229 1.75 80.61 39.42 0.02 0.02 0.02
8.1 21 6.220 1.75 80.59 39.33 0.02 0.02 0.02
8.1 22 6.243 1.75 80.59 39.35 0.02 0.02 0.02
8.1 23 6.246 1.75 80.59 39.33 0.02 0.02 0.02
8.1 24 6.248 1.76 80.60 39.34 0.02 0.02 0.02
8.1 25 6.235 1.77 80.57 39.24 0.02 0.02 0.02
8.1 26 6.200 1.75 80.59 39.33 0.02 0.02 0.02
8.1 27 6.199 1.76 80.60 39.30 0.02 0.02 0.02
8.1 28 6.225 1.74 80.59 39.35 0.02 0.02 0.02
8.1 29 3.040 1.74 80.62 39.30 0.02 0.02 0.02
8.1 30 3.060 1.75 80.62 39.32 0.02 0.02 0.02
8.1 31 3.083 1.75 80.58 39.36 0.02 0.02 0.03
8.1 32 3.057 1.74 80.60 39.31 0.02 0.02 0.02
8.1 33 3.039 1.74 80.61 39.28 0.02 0.02 0.02
8.1 34 3.040 1.74 80.58 39.29 0.02 0.02 0.02
8.1 35 3.063 1.74 80.63 39.33 0.02 0.02 0.02
8.1 36 3.077 1.75 80.58 39.34 0.02 0.02 0.02
8.1 37 3.076 1.74 80.60 39.33 0.02 0.02 0.02
8.1 38 3.053 1.74 80.55 39.30 0.02 0.02 0.02
8.1 39 3.069 1.74 80.55 39.31 0.02 0.02 0.02
8.1 40 3.075 1.74 80.60 39.31 0.02 0.02 0.02
8.1 41 6.153 1.74 80.57 39.35 0.01 0.01 0.02
8.1 42 6.181 1.74 80.62 39.36 0.01 0.01 0.01
8.1 43 6.217 1.74 80.60 39.37 0.01 0.01 0.02
8.1 44 6.241 1.74 80.59 39.38 0.02 0.02 0.02
8.1 45 6.236 1.78 80.56 39.24 0.01 0.01 0.02
8.1 46 6.193 1.75 80.59 39.37 0.01 0.01 0.02
8.1 47 6.238 1.77 80.55 39.30 0.01 0.01 0.02
8.1 48 6.266 1.75 80.55 39.37 0.01 0.01 0.02
8.1 49 3.207 1.74 80.64 39.46 0.01 0.01 0.02
8.1 50 3.213 1.74 80.60 39.48 0.01 0.01 0.02
8.1 51 3.226 1.76 80.57 39.48 0.01 0.01 0.02
8.1 52 3.203 1.75 80.57 39.46 0.01 0.01 0.02
8.1 53 3.178 1.75 80.62 39.42 0.01 0.01 0.02
8.1 54 3.179 1.75 80.57 39.39 0.01 0.01 0.02
8.1 55 3.179 1.75 80.61 39.37 0.01 0.01 0.02
8.1 56 3.201 1.75 80.60 39.37 0.01 0.01 0.02
8.1 57 3.197 1.75 80.60 39.39 0.01 0.01 0.02
8.1 58 3.192 1.76 80.61 39.36 0.01 0.01 0.02
8.1 59 3.188 1.76 80.56 39.34 0.01 0.01 0.02
8.1 60 3.194 1.77 80.58 39.32 0.01 0.01 0.02
8.1 61 6.216 1.88 80.55 39.19 0.01 0.01 0.02
8.1 62 6.211 1.81 80.59 39.27 0.01 0.01 0.01
8.1 63 6.233 1.74 80.57 39.29 0.01 0.01 0.01
8.1 64 6.233 1.75 80.61 39.30 0.01 0.01 0.01
8.1 65 6.244 1.76 80.59 39.22 0.01 0.01 0.01
8.1 66 6.174 1.75 80.59 39.31 0.01 0.01 0.01
8.1 67 6.184 1.85 80.52 39.18 0.01 0.01 0.01
8.1 68 6.221 1.74 80.58 39.35 0.01 0.01 0.01
8.1 69 3.030 1.75 80.60 39.28 0.01 0.01 0.01
8.1 70 3.023 2.02 80.53 39.14 0.01 0.01 0.01
8.1 71 3.061 2.27 80.37 38.88 0.01 0.01 0.01
8.1 72 3.038 1.74 80.65 39.27 0.01 0.01 0.01
8.1 73 3.040 1.73 80.60 39.28 0.01 0.01 0.01
8.1 74 3.066 1.72 80.58 39.31 0.01 0.01 0.01
8.1 75 3.065 2.04 80.25 39.00 0.01 0.01 0.01
8.1 76 3.079 1.64 80.19 39.34 0.01 0.01 0.01
8.1 77 3.070 1.74 80.58 39.32 0.01 0.01 0.01
8.1 78 3.069 1.69 80.35 39.33 0.01 0.01 0.01
8.1 79 3.082 1.74 80.48 39.31 0.01 0.01 0.01
8.1 80 3.070 1.79 80.44 39.24 0.01 0.01 0.01
8.1 81 3.085 1.74 80.60 39.33 0.01 0.01 0.01
8.1 82 3.070 1.72 80.54 39.30 0.01 0.01 0.01
8.1 83 3.078 1.72 80.52 39.33 0.01 0.01 0.01
8.1 84 3.076 1.72 80.54 39.31 0.01 0.01 0.01
8.1 85 3.033 1.77 80.43 39.04 0.01 0.01 0.01
8.1 86 2.999 1.70 80.32 39.27 0.01 0.01 0.01
8.1 87 3.052 1.75 80.49 39.18 0.01 0.01 0.01
8.1 88 3.086 1.74 80.51 39.31 0.01 0.01 0.01

Lane Tile Yield (pf, Mrd) Variant rate (%) Mapped (%) Average Q N bases (%) LowQ (%) Last base lowQ (%)
8.2 1 2.943 3.95 79.02 36.58 0.00 0.00 0.00
8.2 2 3.072 3.75 79.15 36.76 0.00 0.00 0.00
8.2 3 3.091 3.64 79.17 36.87 0.00 0.00 0.00
8.2 4 3.107 3.60 79.14 36.90 0.00 0.00 0.00
8.2 5 3.123 3.47 79.25 37.12 0.00 0.00 0.00
8.2 6 3.137 3.38 79.27 37.32 0.00 0.00 0.00
8.2 7 3.178 3.33 79.31 37.32 0.00 0.00 0.00
8.2 8 3.174 3.27 79.31 37.41 0.00 0.00 0.00
8.2 9 3.187 3.25 79.34 37.44 0.00 0.00 0.00
8.2 10 3.198 3.22 79.36 37.56 0.00 0.00 0.00
8.2 11 3.218 3.23 79.31 37.49 0.00 0.00 0.00
8.2 12 3.199 3.23 79.30 37.51 0.00 0.00 0.00
8.2 13 3.164 3.21 79.40 37.51 0.00 0.00 0.00
8.2 14 3.153 3.18 79.38 37.56 0.00 0.00 0.00
8.2 15 3.178 3.14 79.43 37.71 0.00 0.00 0.00
8.2 16 3.204 3.03 79.49 37.86 0.00 0.00 0.00
8.2 17 3.213 3.01 79.51 37.94 0.00 0.00 0.00
8.2 18 3.209 2.99 79.47 37.96 0.00 0.00 0.00
8.2 19 3.222 2.98 79.48 37.98 0.00 0.00 0.00
8.2 20 3.229 2.97 79.50 38.06 0.00 0.00 0.00
8.2 21 6.220 3.44 79.35 37.32 0.02 0.02 0.00
8.2 22 6.243 3.32 79.38 37.49 0.02 0.02 0.00
8.2 23 6.246 3.35 79.36 37.45 0.02 0.02 0.00
8.2 24 6.248 3.31 79.38 37.51 0.02 0.02 0.00
8.2 25 6.235 3.38 79.33 37.38 0.01 0.01 0.00
8.2 26 6.200 3.28 79.37 37.50 0.01 0.01 0.00
8.2 27 6.199 3.17 79.47 37.67 0.01 0.01 0.00
8.2 28 6.225 3.16 79.40 37.69 0.01 0.01 0.00
8.2 29 3.040 3.32 79.47 37.47 0.02 0.02 0.01
8.2 30 3.060 3.27 79.45 37.54 0.01 0.01 0.01
8.2 31 3.083 3.24 79.42 37.57 0.02 0.02 0.01
8.2 32 3.057 3.28 79.40 37.51 0.01 0.01 0.01
8.2 33 3.039 3.25 79.44 37.46 0.01 0.01 0.02
8.2 34 3.040 3.27 79.41 37.50 0.01 0.01 0.02
8.2 35 3.063 3.23 79.44 37.63 0.01 0.01 0.02
8.2 36 3.077 3.18 79.43 37.65 0.01 0.01 0.03
8.2 37 3.076 3.24 79.42 37.56 0.01 0.01 0.03
8.2 38 3.053 3.33 79.31 37.35 0.01 0.01 0.03
8.2 39 3.069 3.30 79.33 37.37 0.01 0.01 0.04
8.2 40 3.075 3.22 79.44 37.49 0.02 0.02 0.03
8.2 41 6.153 3.42 79.36 37.36 0.01 0.01 0.02
8.2 42 6.181 3.37 79.41 37.40 0.01 0.01 0.02
8.2 43 6.217 3.29 79.42 37.55 0.01 0.01 0.01
8.2 44 6.241 3.24 79.43 37.62 0.01 0.01 0.02
8.2 45 6.236 3.44 79.36 37.50 0.01 0.01 0.02
8.2 46 6.193 3.26 79.40 37.61 0.01 0.01 0.01
8.2 47 6.238 3.18 79.40 37.70 0.01 0.01 0.02
8.2 48 6.266 3.18 79.39 37.70 0.01 0.01 0.02
8.2 49 3.207 3.04 79.51 38.04 0.00 0.00 0.00
8.2 50 3.213 3.04 79.49 38.07 0.00 0.00 0.00
8.2 51 3.226 3.04 79.46 38.04 0.00 0.00 0.00
8.2 52 3.203 3.03 79.47 38.02 0.00 0.00 0.00
8.2 53 3.178 3.05 79.54 37.96 0.00 0.00 0.00
8.2 54 3.179 3.05 79.49 38.01 0.00 0.00 0.00
8.2 55 3.179 3.01 79.54 38.10 0.00 0.00 0.00
8.2 56 3.201 2.96 79.51 38.17 0.00 0.00 0.00
8.2 57 3.197 2.96 79.50 38.22 0.00 0.00 0.00
8.2 58 3.192 2.96 79.53 38.19 0.00 0.00 0.00
8.2 59 3.188 2.91 79.49 38.20 0.00 0.00 0.00
8.2 60 3.194 2.87 79.57 38.32 0.00 0.00 0.00
8.2 61 6.216 3.37 79.38 37.47 0.01 0.01 0.00
8.2 62 6.211 3.31 79.42 37.61 0.01 0.01 0.00
8.2 63 6.233 3.45 79.26 37.42 0.01 0.01 0.00
8.2 64 6.233 3.28 79.41 37.62 0.01 0.01 0.00
8.2 65 6.244 3.38 79.31 37.47 0.01 0.01 0.00
8.2 66 6.174 3.19 79.40 37.67 0.01 0.01 0.00
8.2 67 6.184 3.41 79.24 37.51 0.00 0.00 0.00
8.2 68 6.221 3.20 79.35 37.73 0.00 0.00 0.00
8.2 69 3.030 3.46 79.35 37.29 0.00 0.00 0.00
8.2 70 3.023 3.52 79.29 37.26 0.00 0.00 0.00
8.2 71 3.061 3.45 79.19 37.34 0.00 0.00 0.00
8.2 72 3.038 3.35 79.44 37.43 0.00 0.00 0.00
8.2 73 3.040 3.40 79.31 37.37 0.00 0.00 0.00
8.2 74 3.066 3.56 79.22 37.30 0.00 0.00 0.00
8.2 75 3.065 3.66 78.66 37.30 0.00 0.00 0.00
8.2 76 3.079 5.32 77.96 36.91 0.00 0.00 0.00
8.2 77 3.070 3.20 79.38 37.57 0.00 0.00 0.00
8.2 78 3.069 4.20 78.49 35.93 0.00 0.00 0.00
8.2 79 3.082 4.16 78.77 35.63 0.00 0.00 0.00
8.2 80 3.070 3.62 79.04 37.00 0.00 0.00 0.00
8.2 81 3.085 3.26 79.31 37.44 0.00 0.00 0.00
8.2 82 3.070 3.69 79.04 36.98 0.00 0.00 0.00
8.2 83 3.078 3.68 79.04 36.94 0.01 0.01 0.00
8.2 84 3.076 4.09 79.04 36.87 0.01 0.01 0.00
8.2 85 3.033 4.17 78.82 36.49 0.01 0.01 0.00
8.2 86 2.999 3.52 78.19 37.10 1.34 1.34 0.00
8.2 87 3.052 3.59 79.08 37.16 0.01 0.01 0.00
8.2 88 3.086 3.33 79.24 37.40 0.01 0.01 0.01


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