QC statistics for lane 2


Date Flowcell Lane Platform Unit Readgroup Sample Library Type Project Genome Centre
2016-11-13 HFW7MBBXX 2 161111_K00198_0128_BHFW7MBBXX_2 WTCHG_328670 30 samples 395/16_MPX_10nM_2 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
2.1 75 88 3713823 100.0 326.82 24511.24 24184.32 92.9 8.1 0.00 1.4 5.97 ± 0.00 .0110 9.38 10.87 48.81 11.13 back
2.2 75 88 3713823 100.0 326.82 24511.24 23167.62 92.2 8.2 0.00 1.4 6.77 ± 0.11 .0114 9.16 10.79 43.45 10.80

  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
2.1 47.4 ± 10.0 46.4 ± 9.4 4.69 200 ± 193 18.7 79.0 0.0 0.2 0.0 0.0 32.4
2.2 47.1 ± 10.7 46.0 ± 10.0 2.69 199 ± 171 19.9 82.5 0.1 0.6 0.1 0.1 30.4

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_328670_211 07C_DARK_RET_LEFT PAR3810A71 Our indexes RNA-Seq PolyA galGal4 P160354
212 GCTCCTCT WTCHG_328670_212 07D_DARK_RET_RIGHT PAR3810A72 Our indexes RNA-Seq PolyA galGal4 P160354
213 GAGTTAGT WTCHG_328670_213 10A_DARK_TEL_LEFT PAR3810A73 Our indexes RNA-Seq PolyA galGal4 P160354
214 CTTGTGGT WTCHG_328670_214 10B_DARK_TEL_RIGHT PAR3810A74 Our indexes RNA-Seq PolyA galGal4 P160354
215 CTATTGTG WTCHG_328670_215 10C_DARK_RET_LEFT PAR3810A75 Our indexes RNA-Seq PolyA galGal4 P160354
216 CATTGGCT WTCHG_328670_216 10D_DARK_RET_RIGHT PAR3810A76 Our indexes RNA-Seq PolyA galGal4 P160354
217 TGCCAATC WTCHG_328670_217 14A_DARK_TEL_LEFT PAR3810A77 Our indexes RNA-Seq PolyA galGal4 P160354
218 TCCAATTG WTCHG_328670_218 14B_DARK_TEL_RIGHT PAR3810A78 Our indexes RNA-Seq PolyA galGal4 P160354
219 TACTTCGA WTCHG_328670_219 14C_DARK_RET_LEFT PAR3810A79 Our indexes RNA-Seq PolyA galGal4 P160354
220 GCGAAGTC WTCHG_328670_220 14D_DARK_RET_RIGHT PAR3810A80 Our indexes RNA-Seq PolyA galGal4 P160354
233 TGAATTCT WTCHG_328670_233 29A_6HLIGHT_TEL_LEFT PAR3810A93 Our indexes RNA-Seq PolyA galGal4 P160354
234 TCCAGCCA WTCHG_328670_234 29B_6HLIGHT_TEL_RIGHT PAR3810A94 Our indexes RNA-Seq PolyA galGal4 P160354
235 TAAGAGGA WTCHG_328670_235 29C_6HLIGHT_RET_LEFT PAR3810A95 Our indexes RNA-Seq PolyA galGal4 P160354
236 GCCTTCCT WTCHG_328670_236 29D_6HLIGHT_RET_RIGHT PAR3810A96 Our indexes RNA-Seq PolyA galGal4 P160354
237 GACGACGT WTCHG_328670_237 31A_6HLIGHT_TEL_LEFT PAR3810A97 Our indexes RNA-Seq PolyA galGal4 P160354
238 CTGCATGT WTCHG_328670_238 31B_6HLIGHT_TEL_RIGHT PAR3810A98 Our indexes RNA-Seq PolyA galGal4 P160354
239 CGTCTCGA WTCHG_328670_239 31C_6HLIGHT_RET_LEFT PAR3810A99 Our indexes RNA-Seq PolyA galGal4 P160354
240 CACCAACT WTCHG_328670_240 31D_6HLIGHT_RET_RIGHT PAR3810A100 Our indexes RNA-Seq PolyA galGal4 P160354
251 GTGGTTGA WTCHG_328670_251 49C_24HLIGHT_RET_LEFT PAR3810A111 Our indexes RNA-Seq PolyA galGal4 P160354
252 GCAGAGCT WTCHG_328670_252 49D_24HLIGHT_RET_RIGHT PAR3810A112 Our indexes RNA-Seq PolyA galGal4 P160354
253 GACGGTAC WTCHG_328670_253 50A_24HLIGHT_TEL_LEFT PAR3810A113 Our indexes RNA-Seq PolyA galGal4 P160354
254 CTGCGCAC WTCHG_328670_254 50B_24HLIGHT_TEL_RIGHT PAR3810A114 Our indexes RNA-Seq PolyA galGal4 P160354
255 CGGAAGGA WTCHG_328670_255 50C_24HLIGHT_RET_LEFT PAR3810A115 Our indexes RNA-Seq PolyA galGal4 P160354
256 ATTCTCCT WTCHG_328670_256 50D_24HLIGHT_RET_RIGHT PAR3810A116 Our indexes RNA-Seq PolyA galGal4 P160354
257 TCTGTGAC WTCHG_328670_257 54A_24HLIGHT_TEL_LEFT PAR3810A117 Our indexes RNA-Seq PolyA galGal4 P160354
258 TCATTGCA WTCHG_328670_258 54B_24HLIGHT_TEL_RIGHT PAR3810A118 Our indexes RNA-Seq PolyA galGal4 P160354
259 GTGGCCAG WTCHG_328670_259 54C_24HLIGHT_RET_LEFT PAR3810A119 Our indexes RNA-Seq PolyA galGal4 P160354
295 CGAGGAGA WTCHG_328670_295 25C_6HLIGHT_RET_LEFT PAR3810A91 Our indexes RNA-Seq PolyA galGal4 P160354
296 ATCTCTCT WTCHG_328670_296 25D_6HLIGHT_RET_RIGHT PAR3810A92 Our indexes RNA-Seq PolyA galGal4 P160354
301 ATAGAGTC WTCHG_328670_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
2 211 07C_DARK_RET_LEFT PAR3810A71 3.91 2 0.7 0.2 8.53 5 19.7 7.7
2 212 07D_DARK_RET_RIGHT PAR3810A72 3.93 2 0.7 0.2 8.60 5 19.4 7.6
2 213 10A_DARK_TEL_LEFT PAR3810A73 7.16 2 1.6 0.8 17.65 9 40.0 22.0
2 214 10B_DARK_TEL_RIGHT PAR3810A74 4.72 2 0.8 0.3 9.95 5 21.6 9.8
2 215 10C_DARK_RET_LEFT PAR3810A75 7.16 2 2.2 1.1 21.29 12 49.6 28.7
2 216 10D_DARK_RET_RIGHT PAR3810A76 8.02 2 2.5 1.4 25.57 14 55.2 34.7
2 217 14A_DARK_TEL_LEFT PAR3810A77 9.63 2 2.5 1.4 29.05 13 55.9 36.4
2 218 14B_DARK_TEL_RIGHT PAR3810A78 8.16 2 2.1 1.1 22.85 11 48.4 29.2
2 219 14C_DARK_RET_LEFT PAR3810A79 3.91 2 0.7 0.2 8.71 5 19.7 7.8
2 220 14D_DARK_RET_RIGHT PAR3810A80 4.12 2 0.8 0.3 9.51 5 22.5 9.0
2 233 29A_6HLIGHT_TEL_LEFT PAR3810A93 5.74 2 1.3 0.5 13.68 7 32.3 16.2
2 234 29B_6HLIGHT_TEL_RIGHT PAR3810A94 9.21 2 2.5 1.4 28.07 13 56.1 36.1
2 235 29C_6HLIGHT_RET_LEFT PAR3810A95 8.40 2 2.6 1.4 26.06 14 56.2 35.8
2 236 29D_6HLIGHT_RET_RIGHT PAR3810A96 5.81 2 1.6 0.7 15.74 9 39.8 20.0
2 237 31A_6HLIGHT_TEL_LEFT PAR3810A97 6.97 2 1.8 0.9 20.50 9 44.2 25.7
2 238 31B_6HLIGHT_TEL_RIGHT PAR3810A98 7.63 2 1.9 1.0 21.16 10 46.2 27.2
2 239 31C_6HLIGHT_RET_LEFT PAR3810A99 4.95 2 1.2 0.4 12.09 7 30.4 13.7
2 240 31D_6HLIGHT_RET_RIGHT PAR3810A100 4.87 2 1.1 0.4 12.10 7 29.9 13.5
2 251 49C_24HLIGHT_RET_LEFT PAR3810A111 4.00 2 0.7 0.2 9.05 5 20.5 8.3
2 252 49D_24HLIGHT_RET_RIGHT PAR3810A112 4.12 2 0.8 0.3 9.57 5 22.4 9.1
2 253 50A_24HLIGHT_TEL_LEFT PAR3810A113 9.84 2 2.7 1.6 32.07 15 60.0 40.3
2 254 50B_24HLIGHT_TEL_RIGHT PAR3810A114 8.36 2 2.3 1.3 25.70 12 53.9 33.6
2 255 50C_24HLIGHT_RET_LEFT PAR3810A115 4.04 2 0.8 0.2 9.21 5 21.5 8.7
2 256 50D_24HLIGHT_RET_RIGHT PAR3810A116 4.54 2 1.0 0.4 10.94 6 27.0 11.7
2 257 54A_24HLIGHT_TEL_LEFT PAR3810A117 9.88 2 2.7 1.6 31.83 15 59.0 39.7
2 258 54B_24HLIGHT_TEL_RIGHT PAR3810A118 4.32 2 0.7 0.3 9.21 5 19.8 8.8
2 259 54C_24HLIGHT_RET_LEFT PAR3810A119 5.93 2 1.7 0.7 16.20 9 40.5 20.7
2 295 25C_6HLIGHT_RET_LEFT PAR3810A91 8.68 2 2.8 1.6 29.64 16 60.0 40.0
2 296 25D_6HLIGHT_RET_RIGHT PAR3810A92 6.00 2 1.8 0.8 17.08 10 43.6 22.9
2 301 54D_24HLIGHT_RET_RIGHT PAR3810A120 6.25 2 1.9 0.9 17.84 10 44.0 23.6

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
2.1 All 326.82 24184.32 92.9 5.97 .0110 18.7 79.0 11.13 N/A 0.00 47.4 ± 10.0 46.4 ± 9.4 4.69 200 ± 193 0.0 32.4
2.1 211 4.35 322.19 93.1 5.93 .0087 18.2 68.7 7.38 TTTTTTTTTT 0.04 47.1 ± 9.9 46.2 ± 9.4 4.73 206 ± 198 0.0 32.4
2.1 212 4.33 320.24 93.0 5.97 .0084 18.2 67.4 7.92 TTTTTTTTTT 0.03 47.1 ± 9.9 46.3 ± 9.4 4.73 200 ± 190 0.0 32.5
2.1 213 10.32 763.78 93.0 6.17 .0097 19.6 81.5 10.80 TTTTTTTTTT 0.03 47.7 ± 10.0 46.7 ± 9.4 4.68 199 ± 207 0.0 32.5
2.1 214 4.95 366.42 93.2 6.03 .0075 18.8 68.1 9.01 TTTTTTTTTT 0.03 47.3 ± 9.9 46.4 ± 9.4 4.70 200 ± 201 0.0 32.4
2.1 215 13.24 979.50 93.5 5.93 .0122 18.5 83.0 10.25 TTTTTTTTTT 0.04 46.8 ± 9.7 45.9 ± 9.4 4.72 202 ± 193 0.0 32.4
2.1 216 16.35 1210.22 93.2 5.94 .0127 18.6 85.3 11.92 TTTTTTTTTT 0.04 47.1 ± 9.9 46.0 ± 9.4 4.69 201 ± 191 0.0 32.4
2.1 217 19.19 1419.76 92.9 6.06 .0122 19.2 89.6 12.84 TTTTTTTTTT 0.04 47.5 ± 10.1 46.6 ± 9.6 4.66 199 ± 201 0.0 32.4
2.1 218 14.40 1065.48 92.9 6.04 .0112 19.1 85.6 11.37 TTTTTTTTTT 0.04 47.5 ± 10.0 46.5 ± 9.4 4.69 204 ± 209 0.0 32.4
2.1 219 4.47 330.96 93.1 5.95 .0088 18.2 68.3 7.05 TTTTTTTTTT 0.03 47.1 ± 9.9 46.2 ± 9.4 4.72 199 ± 186 0.0 32.4
2.1 220 5.08 375.80 92.8 5.92 .0094 18.2 70.5 7.20 TTTTTTTTTT 0.02 47.4 ± 10.1 46.3 ± 9.5 4.71 198 ± 183 0.0 32.4
2.1 233 7.83 579.79 92.9 6.00 .0092 18.7 77.4 10.01 TTTTTTTTTT 0.05 47.5 ± 10.1 46.4 ± 9.5 4.62 201 ± 199 0.0 32.4
2.1 234 18.45 1365.20 93.0 6.02 .0121 19.1 89.5 12.78 TTTTTTTTTT 0.04 47.5 ± 10.0 46.5 ± 9.4 4.70 204 ± 208 0.0 32.4
2.1 235 17.38 1285.94 92.9 5.87 .0129 18.5 87.4 11.99 TTTTTTTTTT 0.04 47.3 ± 10.1 46.2 ± 9.6 4.71 200 ± 179 0.0 32.4
2.1 236 9.39 694.45 92.8 5.97 .0112 18.6 79.7 9.31 TTTTTTTTTT 0.04 47.4 ± 10.0 46.4 ± 9.5 4.74 202 ± 194 0.0 32.4
2.1 237 13.40 991.63 94.0 5.77 .0110 18.4 84.2 12.34 TTTTTTTTTT 0.05 46.9 ± 9.6 46.0 ± 9.0 4.74 198 ± 200 0.0 32.5
2.1 238 13.52 1000.11 93.0 5.91 .0111 18.7 84.8 12.25 TTTTTTTTTT 0.05 47.3 ± 9.9 46.5 ± 9.4 4.72 200 ± 199 0.0 32.4
2.1 239 6.77 501.07 93.0 6.00 .0099 18.7 75.8 7.97 TTTTTTTTTT 0.04 47.3 ± 10.1 46.3 ± 9.5 4.73 197 ± 184 0.0 32.4
2.1 240 6.72 497.41 92.7 6.01 .0101 18.6 74.5 8.59 TTTTTTTTTT 0.03 47.4 ± 10.1 46.4 ± 9.5 4.69 200 ± 190 0.0 32.4
2.1 251 4.59 339.76 93.2 5.96 .0090 18.3 68.4 7.38 TTTTTTTTTT 0.03 47.1 ± 9.9 46.2 ± 9.4 4.75 197 ± 183 0.0 32.4
2.1 252 5.05 373.77 92.9 5.92 .0093 18.1 69.7 8.42 TTTTTTTTTT 0.04 47.3 ± 10.0 46.3 ± 9.5 4.75 197 ± 181 0.0 32.5
2.1 253 21.78 1611.83 92.9 5.96 .0125 19.0 91.2 14.05 TTTTTTTTTT 0.03 47.6 ± 10.1 46.6 ± 9.5 4.71 196 ± 188 0.0 32.4
2.1 254 16.92 1251.95 92.9 6.04 .0118 19.3 89.0 12.73 TTTTTTTTTT 0.04 47.6 ± 10.1 46.6 ± 9.5 4.70 198 ± 194 0.0 32.4
2.1 255 4.79 354.54 93.0 5.89 .0091 17.8 68.8 7.36 TTTTTTTTTT 0.04 46.8 ± 10.0 46.0 ± 9.5 4.76 198 ± 184 0.0 32.4
2.1 256 5.95 440.29 92.7 5.96 .0098 18.0 72.5 8.69 TTTTTTTTTT 0.03 47.1 ± 10.0 46.1 ± 9.5 4.68 199 ± 188 0.0 32.4
2.1 257 22.09 1634.63 92.7 5.87 .0123 18.3 90.5 14.14 TTTTTTTTTT 0.05 47.4 ± 10.1 46.3 ± 9.6 4.70 199 ± 188 0.0 32.4
2.1 258 4.62 341.91 92.9 5.90 .0075 18.3 67.0 8.19 TTTTTTTTTT 0.04 47.4 ± 10.0 46.4 ± 9.4 4.70 202 ± 200 0.0 32.4
2.1 259 9.97 737.24 93.0 5.84 .0108 18.0 80.0 8.79 TTTTTTTTTT 0.03 47.2 ± 10.0 46.2 ± 9.5 4.77 199 ± 180 0.0 32.4
2.1 295 19.30 1428.86 92.6 6.05 .0135 19.0 88.0 11.79 TTTTTTTTTT 0.02 47.7 ± 10.1 46.7 ± 9.6 4.67 198 ± 189 0.0 32.5
2.1 296 10.41 770.57 91.6 6.16 .0119 19.3 83.0 9.88 TTTTTTTTTT 0.06 48.2 ± 10.3 47.1 ± 9.7 4.29 203 ± 197 0.0 33.8
2.1 301 11.20 829.02 92.7 5.87 .0112 18.1 81.6 10.12 TTTTTTTTTT 0.04 47.3 ± 10.1 46.3 ± 9.5 4.77 195 ± 175 0.0 33.8
2.2 All 326.82 23167.62 92.2 6.77 .0114 19.9 82.5 10.80 N/A 0.00 47.1 ± 10.7 46.0 ± 10.0 2.69 199 ± 171 0.1 30.4
2.2 211 4.35 307.97 92.4 6.80 .0094 19.5 72.6 7.23 TTTTTTTTTT 0.06 46.7 ± 10.5 45.8 ± 10.0 2.72 206 ± 186 0.1 30.3
2.2 212 4.33 307.96 92.5 6.69 .0091 19.3 71.1 7.78 AAAAAAAAAA 0.03 46.9 ± 10.5 45.9 ± 10.0 2.74 200 ± 179 0.1 30.6
2.2 213 10.32 736.12 92.4 6.88 .0099 20.9 85.1 10.48 AAAAAAAAAA 0.03 47.4 ± 10.6 46.4 ± 9.9 2.78 198 ± 182 0.1 30.6
2.2 214 4.95 351.40 92.5 6.85 .0077 20.1 72.0 8.77 AAAAAAAAAA 0.04 47.0 ± 10.5 46.1 ± 10.0 2.67 199 ± 177 0.1 30.4
2.2 215 13.24 935.92 92.8 6.77 .0127 19.7 86.5 9.97 TTTTTTTTTT 0.05 46.5 ± 10.4 45.7 ± 9.9 2.62 202 ± 181 0.1 30.4
2.2 216 16.35 1160.51 92.6 6.74 .0132 19.8 88.5 11.61 TTTTTTTTTT 0.05 46.7 ± 10.5 45.7 ± 9.9 2.70 201 ± 179 0.1 30.5
2.2 217 19.19 1360.22 92.1 6.84 .0121 20.4 92.5 12.40 TTTTTTTTTT 0.05 47.3 ± 10.8 46.2 ± 10.2 2.77 198 ± 174 0.1 30.5
2.2 218 14.40 1016.71 92.2 6.89 .0116 20.3 89.2 10.98 TTTTTTTTTT 0.05 47.2 ± 10.7 46.1 ± 10.0 2.70 202 ± 180 0.1 30.3
2.2 219 4.47 317.29 92.5 6.73 .0094 19.4 71.9 6.91 TTTTTTTTTT 0.05 46.7 ± 10.5 45.8 ± 10.0 2.70 199 ± 175 0.1 30.4
2.2 220 5.08 360.43 92.2 6.65 .0101 19.3 74.1 7.05 AAAAAAAAAA 0.03 47.1 ± 10.7 46.0 ± 10.1 2.78 199 ± 173 0.1 30.6
2.2 233 7.83 554.95 92.1 6.82 .0093 19.9 81.1 9.66 TTTTTTTTTT 0.06 47.2 ± 10.7 46.2 ± 10.1 2.55 200 ± 172 0.1 30.3
2.2 234 18.45 1309.10 92.2 6.81 .0123 20.4 92.8 12.34 TTTTTTTTTT 0.07 47.2 ± 10.7 46.1 ± 10.0 2.75 203 ± 181 0.1 30.4
2.2 235 17.38 1231.63 92.2 6.70 .0136 19.8 90.5 11.69 TTTTTTTTTT 0.07 46.9 ± 10.7 45.8 ± 10.1 2.68 200 ± 168 0.1 30.4
2.2 236 9.39 667.44 92.2 6.77 .0117 19.7 83.3 9.08 CGTATGCCGT 0.21 47.2 ± 10.6 46.1 ± 9.9 2.91 201 ± 181 0.1 30.5
2.2 237 13.40 954.26 93.3 6.56 .0117 19.8 87.5 11.98 CCCAAACCCA 0.04 46.7 ± 10.3 45.8 ± 9.6 2.75 194 ± 144 0.1 30.6
2.2 238 13.52 958.54 92.3 6.72 .0112 20.0 88.3 11.86 TTTTTTTTTT 0.05 47.2 ± 10.5 46.1 ± 9.9 2.67 198 ± 159 0.1 30.4
2.2 239 6.77 479.54 92.3 6.79 .0104 19.8 79.4 7.77 TTTTTTTTTT 0.06 47.0 ± 10.7 45.9 ± 10.1 2.72 197 ± 174 0.1 30.4
2.2 240 6.72 476.94 92.1 6.74 .0106 19.7 78.3 8.39 TTTTTTTTTT 0.05 47.1 ± 10.7 46.1 ± 10.1 2.74 200 ± 178 0.1 30.4
2.2 251 4.59 324.32 92.5 6.84 .0094 19.5 71.9 7.22 AAAAAAAAAA 0.04 46.7 ± 10.7 45.7 ± 10.1 2.72 197 ± 174 0.1 30.2
2.2 252 5.05 358.60 92.3 6.67 .0098 19.3 73.5 8.26 TTTTTTTTTT 0.04 47.0 ± 10.6 45.9 ± 10.0 2.66 197 ± 169 0.1 30.5
2.2 253 21.78 1543.69 92.2 6.74 .0126 20.2 94.3 13.65 TTTTTTTTTT 0.04 47.2 ± 10.6 46.1 ± 10.1 2.78 195 ± 160 0.1 30.4
2.2 254 16.92 1199.17 92.2 6.80 .0122 20.5 92.2 12.32 TTTTTTTTTT 0.05 47.4 ± 10.7 46.2 ± 10.1 2.75 196 ± 167 0.1 30.5
2.2 255 4.79 339.61 92.3 6.69 .0098 18.9 72.8 7.17 TTTTTTTTTT 0.07 46.6 ± 10.6 45.6 ± 10.0 2.74 198 ± 169 0.1 30.4
2.2 256 5.95 422.95 92.1 6.70 .0101 19.1 76.1 8.50 TTTTTTTTTT 0.04 46.9 ± 10.7 45.8 ± 10.0 2.66 199 ± 174 0.1 30.5
2.2 257 22.09 1557.97 91.9 6.74 .0123 19.5 93.6 13.66 TTTTTTTTTT 0.05 47.0 ± 10.8 45.9 ± 10.1 2.74 198 ± 160 0.1 30.2
2.2 258 4.62 327.69 92.2 6.72 .0077 19.6 70.9 7.95 TTTTTTTTTT 0.06 47.1 ± 10.6 46.0 ± 10.0 2.69 200 ± 167 0.1 30.4
2.2 259 9.97 705.08 92.3 6.64 .0113 19.0 83.3 8.57 TTTTTTTTTT 0.05 46.7 ± 10.7 45.6 ± 10.1 2.78 199 ± 171 0.1 30.4
2.2 295 19.30 1367.54 91.9 6.87 .0142 20.0 90.8 11.47 TTTTTTTTTT 0.04 47.4 ± 10.7 46.3 ± 10.0 2.80 198 ± 178 0.1 30.3
2.2 296 10.41 739.21 90.9 7.05 .0126 20.2 86.4 9.59 TTTTTTTTTT 0.05 48.3 ± 10.9 47.1 ± 10.3 1.63 203 ± 186 0.1 30.5
2.2 301 11.20 794.88 92.2 6.59 .0118 19.1 84.9 9.87 TTTTTTTTTT 0.05 47.0 ± 10.6 45.8 ± 10.0 2.80 195 ± 164 0.1 30.6

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 (%)
2.1 1 2.787 5.57 92.95 39.01 0.00 0.00 0.00
2.1 2 2.883 5.55 92.98 39.08 0.00 0.00 0.00
2.1 3 2.895 5.55 92.95 39.11 0.00 0.00 0.00
2.1 4 2.903 5.56 92.95 39.12 0.00 0.00 0.00
2.1 5 2.907 5.56 92.95 39.11 0.00 0.00 0.00
2.1 6 2.913 5.54 92.92 39.11 0.00 0.00 0.00
2.1 7 2.944 5.55 92.91 39.15 0.00 0.00 0.00
2.1 8 2.955 5.55 92.92 39.18 0.00 0.00 0.00
2.1 9 2.962 5.55 92.89 39.17 0.00 0.00 0.00
2.1 10 2.973 5.55 92.90 39.19 0.00 0.00 0.00
2.1 11 2.980 5.56 92.90 39.20 0.00 0.00 0.00
2.1 12 2.983 5.53 92.88 39.20 0.00 0.00 0.00
2.1 13 2.989 5.52 92.88 39.21 0.00 0.00 0.00
2.1 14 2.995 5.55 92.91 39.19 0.00 0.00 0.00
2.1 15 3.020 5.55 92.85 39.21 0.00 0.00 0.00
2.1 16 3.032 5.54 92.86 39.26 0.00 0.00 0.00
2.1 17 3.033 5.53 92.85 39.25 0.00 0.00 0.00
2.1 18 3.021 5.53 92.87 39.25 0.00 0.00 0.00
2.1 19 3.047 5.52 92.86 39.25 0.00 0.00 0.00
2.1 20 3.063 5.53 92.81 39.28 0.00 0.00 0.00
2.1 21 5.745 5.56 92.92 39.12 0.00 0.00 0.00
2.1 22 5.798 5.55 92.93 39.16 0.00 0.00 0.00
2.1 23 5.811 5.53 92.92 39.16 0.00 0.00 0.00
2.1 24 5.821 5.54 92.90 39.16 0.00 0.00 0.00
2.1 25 5.838 5.54 92.91 39.13 0.00 0.00 0.00
2.1 26 5.837 5.53 92.91 39.18 0.00 0.00 0.00
2.1 27 5.791 5.55 92.93 39.17 0.00 0.00 0.00
2.1 28 5.869 5.53 92.91 39.17 0.00 0.00 0.00
2.1 29 2.783 5.54 93.02 39.05 0.00 0.00 0.00
2.1 30 2.798 5.54 93.00 39.07 0.00 0.00 0.00
2.1 31 2.793 5.52 93.01 39.07 0.00 0.00 0.00
2.1 32 2.819 5.55 92.98 39.09 0.00 0.00 0.00
2.1 33 2.829 5.53 92.97 39.10 0.00 0.00 0.00
2.1 34 2.840 5.52 92.97 39.12 0.00 0.00 0.00
2.1 35 2.856 5.52 92.96 39.13 0.00 0.00 0.00
2.1 36 2.869 5.53 92.98 39.16 0.00 0.00 0.00
2.1 37 2.865 5.52 92.95 39.15 0.00 0.00 0.00
2.1 38 2.836 5.52 92.95 39.12 0.00 0.00 0.00
2.1 39 2.866 5.52 92.91 39.13 0.00 0.00 0.00
2.1 40 2.878 5.51 92.95 39.15 0.00 0.00 0.00
2.1 41 5.676 5.55 92.96 39.05 0.00 0.00 0.00
2.1 42 5.798 5.55 92.96 39.13 0.00 0.00 0.00
2.1 43 5.799 5.54 92.95 39.15 0.00 0.00 0.00
2.1 44 5.829 5.53 92.94 39.15 0.00 0.00 0.00
2.1 45 5.829 5.57 92.93 39.10 0.00 0.00 0.00
2.1 46 5.827 5.60 92.92 39.15 0.00 0.00 0.00
2.1 47 5.815 5.53 92.93 39.20 0.00 0.00 0.00
2.1 48 5.896 5.53 92.93 39.21 0.00 0.00 0.00
2.1 49 2.969 5.53 92.92 39.19 0.00 0.00 0.00
2.1 50 2.990 5.54 92.89 39.23 0.00 0.00 0.00
2.1 51 3.004 5.54 92.87 39.25 0.00 0.00 0.00
2.1 52 3.028 5.53 92.84 39.26 0.00 0.00 0.00
2.1 53 3.030 5.52 92.86 39.28 0.00 0.00 0.00
2.1 54 3.036 5.51 92.83 39.27 0.00 0.00 0.00
2.1 55 3.032 5.53 92.86 39.24 0.00 0.00 0.00
2.1 56 3.060 5.52 92.84 39.29 0.00 0.00 0.00
2.1 57 3.059 5.54 92.86 39.28 0.00 0.00 0.00
2.1 58 3.056 5.52 92.80 39.28 0.00 0.00 0.00
2.1 59 3.069 5.53 92.84 39.29 0.00 0.00 0.00
2.1 60 3.090 5.54 92.85 39.32 0.00 0.00 0.00
2.1 61 5.818 5.59 92.93 39.13 0.01 0.01 0.00
2.1 62 5.858 5.58 92.90 39.15 0.01 0.01 0.00
2.1 63 5.838 5.53 92.93 39.19 0.01 0.01 0.00
2.1 64 5.894 5.52 92.88 39.22 0.01 0.01 0.00
2.1 65 5.869 5.54 92.89 39.15 0.01 0.01 0.00
2.1 66 5.861 5.54 92.91 39.22 0.01 0.01 0.00
2.1 67 5.828 5.64 92.88 39.05 0.01 0.01 0.00
2.1 68 5.880 5.52 92.91 39.20 0.01 0.01 0.00
2.1 69 2.788 5.54 93.00 39.06 0.01 0.01 0.00
2.1 70 2.800 5.62 92.99 39.02 0.01 0.01 0.00
2.1 71 2.798 5.67 93.02 38.96 0.01 0.01 0.00
2.1 72 2.814 5.54 93.03 39.10 0.01 0.01 0.00
2.1 73 2.830 5.53 92.98 39.13 0.01 0.01 0.00
2.1 74 2.835 5.53 92.97 39.12 0.01 0.01 0.00
2.1 75 2.846 5.54 92.97 39.14 0.01 0.01 0.00
2.1 76 2.869 5.52 92.97 39.16 0.01 0.01 0.00
2.1 77 2.870 5.53 92.92 39.15 0.01 0.01 0.00
2.1 78 2.861 5.53 92.95 39.15 0.01 0.01 0.00
2.1 79 2.870 5.53 92.96 39.14 0.01 0.01 0.00
2.1 80 2.873 5.52 92.97 39.15 0.01 0.01 0.00
2.1 81 2.893 5.50 92.95 39.19 0.01 0.01 0.00
2.1 82 2.901 5.52 92.95 39.19 0.01 0.01 0.00
2.1 83 2.894 5.54 92.95 39.17 0.01 0.01 0.00
2.1 84 2.933 5.54 92.91 39.25 0.01 0.01 0.00
2.1 85 2.920 5.57 92.91 39.05 0.01 0.01 0.00
2.1 86 2.897 5.53 92.95 39.23 0.01 0.01 0.00
2.1 87 2.842 5.65 92.93 39.07 0.01 0.01 0.00
2.1 88 2.918 5.55 92.92 39.18 0.01 0.01 0.00

Lane Tile Yield (pf, Mrd) Variant rate (%) Mapped (%) Average Q N bases (%) LowQ (%) Last base lowQ (%)
2.2 1 2.787 6.36 92.33 36.44 0.03 0.03 0.00
2.2 2 2.883 6.25 92.37 36.74 0.03 0.03 0.00
2.2 3 2.895 6.24 92.34 36.84 0.03 0.03 0.00
2.2 4 2.903 6.25 92.34 36.85 0.03 0.03 0.00
2.2 5 2.907 6.25 92.32 36.79 0.03 0.03 0.00
2.2 6 2.913 6.26 92.27 36.76 0.03 0.03 0.00
2.2 7 2.944 6.22 92.28 36.87 0.04 0.04 0.00
2.2 8 2.955 6.20 92.30 36.95 0.04 0.04 0.00
2.2 9 2.962 6.23 92.26 36.90 0.04 0.04 0.00
2.2 10 2.973 6.22 92.26 36.95 0.04 0.04 0.00
2.2 11 2.980 6.21 92.28 36.96 0.04 0.04 0.00
2.2 12 2.983 6.19 92.26 37.07 0.04 0.04 0.00
2.2 13 2.989 6.24 92.22 36.92 0.04 0.04 0.00
2.2 14 2.995 6.24 92.25 36.92 0.04 0.04 0.00
2.2 15 3.020 6.26 92.19 36.88 0.04 0.04 0.00
2.2 16 3.032 6.20 92.22 37.07 0.04 0.04 0.00
2.2 17 3.033 6.20 92.21 36.98 0.04 0.04 0.00
2.2 18 3.021 6.20 92.23 37.01 0.04 0.04 0.00
2.2 19 3.047 6.21 92.22 36.97 0.04 0.04 0.00
2.2 20 3.063 6.18 92.18 37.10 0.04 0.04 0.00
2.2 21 5.745 6.25 92.26 36.71 0.06 0.06 0.04
2.2 22 5.798 6.24 92.25 36.76 0.06 0.06 0.03
2.2 23 5.811 6.25 92.23 36.76 0.06 0.06 0.04
2.2 24 5.821 6.27 92.19 36.71 0.06 0.06 0.03
2.2 25 5.838 6.25 92.23 36.79 0.06 0.06 0.04
2.2 26 5.837 6.25 92.24 36.78 0.06 0.06 0.04
2.2 27 5.791 6.24 92.24 36.78 0.06 0.06 0.03
2.2 28 5.869 6.24 92.22 36.80 0.06 0.06 0.03
2.2 29 2.783 6.25 92.29 36.55 0.08 0.08 0.06
2.2 30 2.798 6.27 92.27 36.51 0.08 0.08 0.08
2.2 31 2.793 6.27 92.25 36.50 0.08 0.08 0.06
2.2 32 2.819 6.26 92.24 36.61 0.08 0.08 0.06
2.2 33 2.829 6.28 92.23 36.56 0.08 0.08 0.06
2.2 34 2.840 6.26 92.23 36.66 0.08 0.08 0.06
2.2 35 2.856 6.30 92.18 36.54 0.08 0.08 0.06
2.2 36 2.869 6.29 92.20 36.51 0.08 0.08 0.06
2.2 37 2.865 6.24 92.16 36.59 0.08 0.08 0.06
2.2 38 2.836 6.32 92.12 36.43 0.08 0.08 0.06
2.2 39 2.866 6.56 92.08 36.17 0.09 0.09 0.06
2.2 40 2.878 6.26 92.19 36.65 0.09 0.09 0.06
2.2 41 5.676 6.24 92.30 36.72 0.06 0.06 0.03
2.2 42 5.798 6.23 92.29 36.78 0.07 0.07 0.03
2.2 43 5.799 6.26 92.25 36.76 0.06 0.06 0.03
2.2 44 5.829 6.26 92.23 36.71 0.06 0.06 0.02
2.2 45 5.829 6.26 92.24 36.80 0.07 0.07 0.04
2.2 46 5.827 6.21 92.25 36.94 0.06 0.06 0.03
2.2 47 5.815 6.21 92.27 36.95 0.07 0.07 0.03
2.2 48 5.896 6.23 92.24 36.93 0.07 0.07 0.03
2.2 49 2.969 6.19 92.32 37.11 0.05 0.05 0.03
2.2 50 2.990 6.19 92.30 37.17 0.05 0.05 0.03
2.2 51 3.004 6.16 92.26 37.21 0.05 0.05 0.04
2.2 52 3.028 6.15 92.25 37.31 0.05 0.05 0.04
2.2 53 3.030 6.18 92.29 37.29 0.05 0.05 0.03
2.2 54 3.036 6.18 92.24 37.30 0.05 0.05 0.05
2.2 55 3.032 6.24 92.22 37.03 0.05 0.05 0.04
2.2 56 3.060 6.18 92.23 37.25 0.05 0.05 0.06
2.2 57 3.059 6.20 92.21 37.15 0.05 0.05 0.05
2.2 58 3.056 6.23 92.18 37.12 0.05 0.05 0.07
2.2 59 3.069 6.21 92.22 37.14 0.05 0.05 0.06
2.2 60 3.090 6.18 92.22 37.22 0.05 0.05 0.07
2.2 61 5.818 6.25 92.28 36.72 0.06 0.06 0.08
2.2 62 5.858 6.21 92.26 36.86 0.07 0.07 0.08
2.2 63 5.838 6.24 92.26 36.86 0.07 0.07 0.08
2.2 64 5.894 6.35 92.19 36.82 0.07 0.07 0.08
2.2 65 5.869 6.24 92.22 36.87 0.07 0.07 0.09
2.2 66 5.861 6.23 92.25 36.90 0.07 0.07 0.09
2.2 67 5.828 6.39 92.19 36.65 0.07 0.07 0.09
2.2 68 5.880 6.20 92.24 36.93 0.07 0.07 0.10
2.2 69 2.788 6.25 92.29 36.59 0.09 0.09 0.09
2.2 70 2.800 6.40 92.27 36.41 0.09 0.09 0.09
2.2 71 2.798 6.25 92.33 36.64 0.09 0.09 0.09
2.2 72 2.814 6.22 92.32 36.66 0.09 0.09 0.09
2.2 73 2.830 6.26 92.27 36.73 0.09 0.09 0.10
2.2 74 2.835 6.24 92.26 36.76 0.09 0.09 0.08
2.2 75 2.846 6.25 92.25 36.71 0.09 0.09 0.09
2.2 76 2.869 6.23 92.24 36.77 0.10 0.10 0.10
2.2 77 2.870 6.26 92.16 36.70 0.10 0.10 0.10
2.2 78 2.861 6.25 92.22 36.72 0.10 0.10 0.10
2.2 79 2.870 6.25 92.22 36.68 0.10 0.10 0.10
2.2 80 2.873 6.24 92.23 36.77 0.10 0.10 0.10
2.2 81 2.893 6.23 92.21 36.77 0.10 0.10 0.10
2.2 82 2.901 6.21 92.22 36.82 0.10 0.10 0.10
2.2 83 2.894 6.22 92.19 36.80 0.10 0.10 0.10
2.2 84 2.933 6.27 92.13 36.76 0.10 0.10 0.09
2.2 85 2.920 6.28 92.12 36.58 0.10 0.10 0.09
2.2 86 2.897 6.23 92.23 36.84 0.10 0.10 0.10
2.2 87 2.842 6.27 92.19 36.72 0.10 0.10 0.08
2.2 88 2.918 6.26 92.16 36.73 0.10 0.10 0.08


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