QC statistics for lane 6


Date Flowcell Lane Platform Unit Readgroup Sample Library Type Project Genome Centre
2016-10-27 HF5KTBBXX 6 161021_K00198_0118_AHF5KTBBXX_6 WTCHG_323579 30 samples 443/16_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
6.1 75 88 4252388 100.0 374.21 28065.77 27159.45 93.0 7.6 0.00 2.0 5.93 ± 0.11 .0115 11.14 13.12 54.58 13.13 back
6.2 75 88 4264901 100.0 375.31 28148.35 26631.77 92.5 7.7 0.00 2.0 6.53 ± 0.21 .0118 10.91 13.02 49.94 12.84

  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
6.1 47.8 ± 10.0 46.8 ± 9.5 4.62 214 ± 255 19.0 76.7 0.0 0.9 0.0 0.0 33.9
6.2 47.6 ± 10.6 46.6 ± 10.0 2.67 213 ± 225 20.3 80.0 0.0 1.1 0.0 0.0 31.4

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
209 TGTTGGTC WTCHG_323579_209 07A_DARK_TEL_LEFT PAR3810A69 Our indexes RNA-Seq PolyA galGal4 P160354
210 TCGCCACA WTCHG_323579_210 07B_DARK_TEL_RIGHT PAR3810A70 Our indexes RNA-Seq PolyA galGal4 P160354
221 GAGTGTCA WTCHG_323579_221 22A_6HLIGHT_TEL_LEFT PAR3810A81 Our indexes RNA-Seq PolyA galGal4 P160354
222 CTTGGCCA WTCHG_323579_222 22B_6HLIGHT_TEL_RIGHT PAR3810A82 Our indexes RNA-Seq PolyA galGal4 P160354
223 CTATGCGT WTCHG_323579_223 22C_6HLIGHT_RET_LEFT PAR3810A83 Our indexes RNA-Seq PolyA galGal4 P160354
224 CAGGTTCT WTCHG_323579_224 22D_6HLIGHT_RET_RIGHT PAR3810A84 Our indexes RNA-Seq PolyA galGal4 P160354
241 TGAACCTC WTCHG_323579_241 42A_24HLIGHT_TEL_LEFT PAR3810A101 Our indexes RNA-Seq PolyA galGal4 P160354
242 TCCACAAC WTCHG_323579_242 42B_24HLIGHT_TEL_RIGHT PAR3810A102 Our indexes RNA-Seq PolyA galGal4 P160354
243 TAAGGAAG WTCHG_323579_243 42C_24HLIGHT_RET_LEFT PAR3810A103 Our indexes RNA-Seq PolyA galGal4 P160354
244 GCCTCTTC WTCHG_323579_244 42D_24HLIGHT_RET_RIGHT PAR3810A104 Our indexes RNA-Seq PolyA galGal4 P160354
245 GACGTACA WTCHG_323579_245 44A_24HLIGHT_TEL_LEFT PAR3810A105 Our indexes RNA-Seq PolyA galGal4 P160354
246 CTGCTGCA WTCHG_323579_246 44B_24HLIGHT_TEL_RIGHT PAR3810A106 Our indexes RNA-Seq PolyA galGal4 P160354
247 CGTCCTAG WTCHG_323579_247 44C_24HLIGHT_RET_LEFT PAR3810A107 Our indexes RNA-Seq PolyA galGal4 P160354
248 CACCGGTC WTCHG_323579_248 44D_24HLIGHT_RET_RIGHT PAR3810A108 Our indexes RNA-Seq PolyA galGal4 P160354
249 TCTGATCA WTCHG_323579_249 49A_24HLIGHT_TEL_LEFT PAR3810A109 Our indexes RNA-Seq PolyA galGal4 P160354
250 TCATATGT WTCHG_323579_250 49B_24HLIGHT_TEL_RIGHT PAR3810A110 Our indexes RNA-Seq PolyA galGal4 P160354
273 TCTGCAGT WTCHG_323579_273 02A_DARK_TEL_LEFT PAR3810A61 Our indexes RNA-Seq PolyA galGal4 P160354
274 TCATCATG WTCHG_323579_274 02B_DARK_TEL_RIGHT PAR3810A62 Our indexes RNA-Seq PolyA galGal4 P160354
275 GTCCGGAG WTCHG_323579_275 02C_DARK_RET_LEFT PAR3810A63 Our indexes RNA-Seq PolyA galGal4 P160354
276 GATATATG WTCHG_323579_276 02D_DARK_RET_RIGHT PAR3810A64 Our indexes RNA-Seq PolyA galGal4 P160354
277 GAACTAAC WTCHG_323579_277 03A_DARK_TEL_LEFT PAR3810A65 Our indexes RNA-Seq PolyA galGal4 P160354
278 CTCATGAC WTCHG_323579_278 03B_DARK_TEL_RIGHT PAR3810A66 Our indexes RNA-Seq PolyA galGal4 P160354
279 CGCTCTGA WTCHG_323579_279 03C_DARK_RET_LEFT PAR3810A67 Our indexes RNA-Seq PolyA galGal4 P160354
280 ATGAGATC WTCHG_323579_280 03D_DARK_RET_RIGHT PAR3810A68 Our indexes RNA-Seq PolyA galGal4 P160354
289 TCGCTGTG WTCHG_323579_289 24A_6HLIGHT_TEL_LEFT PAR3810A85 Our indexes RNA-Seq PolyA galGal4 P160354
290 TATCCTGA WTCHG_323579_290 24B_6HLIGHT_TEL_RIGHT PAR3810A86 Our indexes RNA-Seq PolyA galGal4 P160354
291 GTAACCGA WTCHG_323579_291 24C_6HLIGHT_RET_LEFT PAR3810A87 Our indexes RNA-Seq PolyA galGal4 P160354
292 GATACGCA WTCHG_323579_292 24D_6HLIGHT_RET_RIGHT PAR3810A88 Our indexes RNA-Seq PolyA galGal4 P160354
293 GAACCGGT WTCHG_323579_293 25A_6HLIGHT_TEL_LEFT PAR3810A89 Our indexes RNA-Seq PolyA galGal4 P160354
294 CTCACAGT WTCHG_323579_294 25B_6HLIGHT_TEL_RIGHT PAR3810A90 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
6 209 07A_DARK_TEL_LEFT PAR3810A69 7.57 2 1.8 0.9 19.82 10 44.4 25.6
6 210 07B_DARK_TEL_RIGHT PAR3810A70 12.95 2 3.3 2.2 46.77 21 69.5 52.2
6 221 22A_6HLIGHT_TEL_LEFT PAR3810A81 11.99 2 3.2 2.1 45.37 21 68.6 51.0
6 222 22B_6HLIGHT_TEL_RIGHT PAR3810A82 5.25 2 1.1 0.4 12.61 6 29.3 14.4
6 223 22C_6HLIGHT_RET_LEFT PAR3810A83 4.52 2 0.9 0.3 10.65 6 26.2 11.2
6 224 22D_6HLIGHT_RET_RIGHT PAR3810A84 4.01 2 0.7 0.2 8.95 5 20.1 8.1
6 241 42A_24HLIGHT_TEL_LEFT PAR3810A101 3.53 2 0.4 0.1 7.00 4 13.1 5.4
6 242 42B_24HLIGHT_TEL_RIGHT PAR3810A102 3.07 2 0.3 0.1 5.79 3 9.1 3.6
6 243 42C_24HLIGHT_RET_LEFT PAR3810A103 4.95 2 1.1 0.4 12.18 7 30.5 13.7
6 244 42D_24HLIGHT_RET_RIGHT PAR3810A104 5.24 2 1.4 0.5 13.89 8 35.8 17.1
6 245 44A_24HLIGHT_TEL_LEFT PAR3810A105 5.00 2 1.0 0.4 11.58 6 26.9 12.8
6 246 44B_24HLIGHT_TEL_RIGHT PAR3810A106 10.29 2 3.0 1.8 40.17 17 64.2 45.6
6 247 44C_24HLIGHT_RET_LEFT PAR3810A107 7.14 2 2.3 1.2 22.59 12 52.5 31.2
6 248 44D_24HLIGHT_RET_RIGHT PAR3810A108 4.40 2 1.0 0.3 10.76 6 26.6 11.3
6 249 49A_24HLIGHT_TEL_LEFT PAR3810A109 7.35 2 1.7 0.9 19.07 9 42.9 24.5
6 250 49B_24HLIGHT_TEL_RIGHT PAR3810A110 4.16 2 0.6 0.2 8.77 5 18.7 8.1
6 273 02A_DARK_TEL_LEFT PAR3810A61 3.56 2 0.4 0.1 6.85 4 12.2 5.1
6 274 02B_DARK_TEL_RIGHT PAR3810A62 12.57 2 3.2 2.1 45.77 21 69.2 51.5
6 275 02C_DARK_RET_LEFT PAR3810A63 4.93 2 1.1 0.4 11.93 7 30.0 13.3
6 276 02D_DARK_RET_RIGHT PAR3810A64 3.36 2 0.4 0.1 7.09 4 14.2 5.4
6 277 03A_DARK_TEL_LEFT PAR3810A65 14.00 3 3.2 2.2 48.58 22 69.8 52.7
6 278 03B_DARK_TEL_RIGHT PAR3810A66 5.15 2 0.9 0.4 11.19 6 25.4 12.0
6 279 03C_DARK_RET_LEFT PAR3810A67 11.67 3 3.7 2.4 47.12 25 70.9 55.5
6 280 03D_DARK_RET_RIGHT PAR3810A68 3.70 2 0.5 0.2 8.01 5 17.2 6.7
6 289 24A_6HLIGHT_TEL_LEFT PAR3810A85 8.46 2 2.2 1.2 24.00 11 50.9 31.4
6 290 24B_6HLIGHT_TEL_RIGHT PAR3810A86 4.01 2 0.6 0.2 8.31 4 17.2 7.4
6 291 24C_6HLIGHT_RET_LEFT PAR3810A87 11.26 3 3.6 2.4 45.29 24 69.8 54.2
6 292 24D_6HLIGHT_RET_RIGHT PAR3810A88 3.38 2 0.5 0.1 7.25 4 14.8 5.6
6 293 25A_6HLIGHT_TEL_LEFT PAR3810A89 5.30 2 1.0 0.4 11.82 6 27.2 13.1
6 294 25B_6HLIGHT_TEL_RIGHT PAR3810A90 6.16 2 1.3 0.6 14.72 7 34.4 17.8

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
6.1 All 374.21 27159.45 93.0 5.78 .0115 19.0 76.7 13.13 N/A 0.00 47.8 ± 10.0 46.8 ± 9.5 4.62 214 ± 255 0.0 33.9
6.1 209 12.05 874.91 92.9 5.82 .0107 19.2 83.7 10.71 TTTTTTTTTT 0.05 47.8 ± 10.1 46.8 ± 9.5 4.58 219 ± 267 0.0 33.9
6.1 210 32.33 2345.36 92.8 5.89 .0142 19.5 95.1 16.42 TTTTTTTTTT 0.05 48.0 ± 10.1 47.0 ± 9.5 4.60 216 ± 264 0.0 33.9
6.1 221 31.81 2309.65 92.9 5.78 .0144 19.2 95.0 15.78 TTTTTTTTTT 0.05 47.9 ± 10.0 46.9 ± 9.4 4.64 211 ± 255 0.0 33.9
6.1 222 6.89 500.36 92.2 5.90 .0092 19.2 75.3 8.94 TTTTTTTTTT 0.04 48.4 ± 10.0 47.4 ± 9.6 4.62 207 ± 245 0.0 33.9
6.1 223 5.77 418.84 92.6 5.78 .0097 18.4 72.7 8.90 TTTTTTTTTT 0.06 47.7 ± 10.1 46.7 ± 9.6 4.61 211 ± 236 0.0 33.9
6.1 224 4.50 326.61 92.4 5.79 .0091 18.6 67.7 8.19 TTTTTTTTTT 0.04 47.9 ± 10.2 46.9 ± 9.7 4.59 211 ± 236 0.0 33.9
6.1 241 3.04 220.70 92.5 5.78 .0069 18.3 59.0 7.17 TTTTTTTTTT 0.05 48.1 ± 10.3 47.1 ± 9.7 4.59 213 ± 253 0.0 33.9
6.1 242 2.16 156.69 93.0 5.85 .0059 18.3 51.6 6.77 TTTTTTTTTT 0.05 47.8 ± 10.2 46.9 ± 9.6 4.61 213 ± 257 0.0 33.9
6.1 243 6.81 494.00 93.2 5.71 .0100 18.5 75.0 8.38 TTTTTTTTTT 0.04 47.5 ± 10.1 46.5 ± 9.5 4.68 212 ± 239 0.0 33.9
6.1 244 8.26 599.63 92.8 5.70 .0110 18.3 78.3 8.37 TTTTTTTTTT 0.04 47.8 ± 10.1 46.8 ± 9.6 4.68 211 ± 232 0.0 33.9
6.1 245 6.26 454.05 92.8 5.79 .0087 18.8 73.7 8.60 TTTTTTTTTT 0.04 48.0 ± 10.1 47.1 ± 9.6 4.66 207 ± 243 0.0 33.9
6.1 246 30.14 2189.28 94.3 5.54 .0136 18.7 93.3 17.43 TTTTTTTTTT 0.06 47.2 ± 9.4 46.5 ± 9.0 4.67 212 ± 268 0.0 34.0
6.1 247 14.61 1060.79 92.9 5.70 .0127 18.3 85.0 10.44 TTTTTTTTTT 0.05 47.6 ± 10.1 46.7 ± 9.5 4.66 208 ± 228 0.0 33.9
6.1 248 6.03 438.13 92.7 5.64 .0102 17.9 73.1 7.80 TTTTTTTTTT 0.04 47.6 ± 10.1 46.6 ± 9.6 4.62 212 ± 232 0.0 33.9
6.1 249 11.54 837.37 92.8 5.87 .0106 19.3 83.4 11.21 TTTTTTTTTT 0.03 47.8 ± 10.1 46.8 ± 9.5 4.57 212 ± 256 0.0 33.9
6.1 250 4.28 310.95 92.6 5.77 .0075 18.4 66.0 8.53 TTTTTTTTTT 0.03 47.9 ± 10.1 46.9 ± 9.6 4.60 215 ± 256 0.0 33.9
6.1 273 2.82 204.87 92.6 5.84 .0063 18.6 57.0 8.05 TTTTTTTTTT 0.03 48.1 ± 10.2 47.1 ± 9.7 4.55 219 ± 268 0.0 33.9
6.1 274 31.86 2311.83 92.9 5.81 .0144 19.3 94.9 15.46 TTTTTTTTTT 0.04 47.9 ± 10.1 46.9 ± 9.5 4.58 221 ± 272 0.0 33.9
6.1 275 6.61 479.94 93.1 5.71 .0100 18.6 74.8 8.14 TTTTTTTTTT 0.05 47.5 ± 9.9 46.6 ± 9.5 4.64 219 ± 256 0.0 33.9
6.1 276 3.36 244.00 92.9 5.68 .0083 18.0 62.7 6.32 TTTTTTTTTT 0.04 47.6 ± 10.1 46.6 ± 9.5 4.66 213 ± 240 0.0 33.9
6.1 277 32.60 2363.97 93.2 5.96 .0142 20.1 94.9 17.28 TTTTTTTTTT 0.05 47.9 ± 10.0 46.9 ± 9.5 4.59 219 ± 278 0.0 33.9
6.1 278 5.71 414.34 93.1 5.88 .0080 19.4 71.8 8.85 TTTTTTTTTT 0.05 47.7 ± 10.0 46.8 ± 9.5 4.60 217 ± 270 0.0 33.9
6.1 279 32.62 2367.29 93.0 5.74 .0155 18.8 93.0 14.64 TTTTTTTTTT 0.05 47.6 ± 10.1 46.7 ± 9.5 4.63 216 ± 248 0.0 33.9
6.1 280 3.83 277.97 92.8 5.81 .0085 18.7 65.5 7.20 TTTTTTTTTT 0.04 47.8 ± 10.1 46.9 ± 9.5 4.60 215 ± 255 0.0 33.9
6.1 289 15.28 1109.02 92.7 5.79 .0116 19.0 86.9 11.92 TTTTTTTTTT 0.06 47.8 ± 10.1 46.9 ± 9.7 4.63 211 ± 248 0.0 33.9
6.1 290 3.94 286.05 92.8 5.74 .0076 18.2 64.0 7.49 TTTTTTTTTT 0.04 47.8 ± 10.1 46.8 ± 9.5 4.65 216 ± 256 0.0 33.9
6.1 291 31.09 2256.84 92.6 5.76 .0152 18.7 92.0 14.19 TTTTTTTTTT 0.04 47.9 ± 10.1 46.9 ± 9.6 4.66 212 ± 240 0.0 33.9
6.1 292 3.47 251.63 92.5 5.69 .0087 17.9 63.4 6.65 TTTTTTTTTT 0.03 47.9 ± 10.1 47.0 ± 9.6 4.67 210 ± 231 0.0 33.9
6.1 293 6.25 453.71 92.4 5.88 .0083 19.2 73.6 9.51 TTTTTTTTTT 0.04 48.2 ± 10.3 47.2 ± 9.7 4.63 212 ± 253 0.0 33.9
6.1 294 8.28 600.66 92.3 5.90 .0094 19.5 78.4 10.35 TTTTTTTTTT 0.05 48.4 ± 10.2 47.3 ± 9.7 4.61 214 ± 261 0.0 33.9
6.2 All 375.31 26631.77 92.5 6.36 .0118 20.3 80.0 12.84 N/A 0.00 47.6 ± 10.6 46.6 ± 10.0 2.67 213 ± 225 0.0 31.4
6.2 209 12.09 855.94 92.5 6.44 .0108 20.6 87.4 10.38 TTTTTTTTTT 0.07 47.6 ± 10.6 46.4 ± 10.1 2.69 218 ± 240 0.0 31.3
6.2 210 32.42 2297.43 92.3 6.47 .0143 20.9 97.8 16.04 TTTTTTTTTT 0.06 47.8 ± 10.6 46.7 ± 10.0 2.63 215 ± 235 0.0 31.3
6.2 221 31.91 2268.41 92.5 6.32 .0146 20.4 97.4 15.40 TTTTTTTTTT 0.06 47.7 ± 10.6 46.6 ± 10.0 2.74 208 ± 211 0.0 31.4
6.2 222 6.91 491.29 91.8 6.40 .0095 20.3 79.0 8.70 TTTTTTTTTT 0.06 48.4 ± 10.7 47.2 ± 10.2 2.73 206 ± 213 0.0 31.5
6.2 223 5.79 410.60 92.2 6.32 .0099 19.6 76.3 8.76 TTTTTTTTTT 0.08 47.5 ± 10.6 46.5 ± 10.1 2.66 212 ± 223 0.0 31.4
6.2 224 4.51 320.12 92.0 6.34 .0095 19.8 71.4 8.08 TTTTTTTTTT 0.06 47.7 ± 10.7 46.7 ± 10.2 2.71 211 ± 225 0.0 31.4
6.2 241 3.05 216.50 92.0 6.31 .0070 19.6 62.4 6.94 TTTTTTTTTT 0.07 47.9 ± 10.8 46.8 ± 10.2 2.75 211 ± 221 0.0 31.5
6.2 242 2.17 153.51 92.4 6.41 .0061 19.7 55.0 6.58 TTTTTTTTTT 0.08 47.5 ± 10.6 46.5 ± 10.1 2.62 211 ± 227 0.0 31.3
6.2 243 6.82 484.09 92.8 6.28 .0109 19.7 78.6 8.26 TTTTTTTTTT 0.08 47.2 ± 10.6 46.1 ± 10.1 2.65 212 ± 226 0.0 31.3
6.2 244 8.28 588.95 92.4 6.19 .0115 19.4 81.9 8.22 TTTTTTTTTT 0.06 47.4 ± 10.6 46.4 ± 10.0 2.75 211 ± 218 0.0 31.5
6.2 245 6.27 446.22 92.3 6.27 .0091 20.0 77.5 8.37 TTTTTTTTTT 0.05 47.7 ± 10.6 46.7 ± 10.0 2.75 205 ± 209 0.0 31.5
6.2 246 30.25 2151.22 93.9 6.18 .0140 20.1 95.8 17.11 TTTTTTTTTT 0.06 47.1 ± 10.2 46.3 ± 9.6 2.58 204 ± 178 0.0 31.5
6.2 247 14.65 1040.31 92.5 6.21 .0130 19.4 88.0 10.24 TTTTTTTTTT 0.07 47.4 ± 10.6 46.3 ± 10.0 2.67 209 ± 216 0.0 31.4
6.2 248 6.05 429.52 92.3 6.17 .0106 19.0 76.6 7.66 TTTTTTTTTT 0.07 47.4 ± 10.7 46.3 ± 10.2 2.72 213 ± 219 0.0 31.4
6.2 249 11.57 821.70 92.3 6.43 .0108 20.5 86.8 10.93 TTTTTTTTTT 0.07 47.6 ± 10.7 46.5 ± 10.3 2.57 211 ± 227 0.0 31.4
6.2 250 4.29 304.68 92.1 6.33 .0080 19.7 69.6 8.33 TTTTTTTTTT 0.07 47.6 ± 10.7 46.6 ± 10.2 2.57 214 ± 224 0.0 31.3
6.2 273 2.83 200.78 92.1 6.44 .0064 20.0 60.3 7.89 TTTTTTTTTT 0.07 48.0 ± 10.8 46.9 ± 10.2 2.74 217 ± 234 0.0 31.3
6.2 274 31.95 2264.69 92.5 6.41 .0146 20.6 97.7 15.09 TTTTTTTTTT 0.07 47.7 ± 10.6 46.8 ± 10.1 2.65 219 ± 240 0.0 31.3
6.2 275 6.63 469.96 92.7 6.33 .0105 19.8 78.7 8.02 TTTTTTTTTT 0.07 47.2 ± 10.5 46.2 ± 10.1 2.70 220 ± 242 0.0 31.3
6.2 276 3.37 239.81 92.6 6.21 .0089 19.2 66.6 6.25 TTTTTTTTTT 0.05 47.3 ± 10.6 46.3 ± 10.0 2.70 214 ± 227 0.0 31.4
6.2 277 32.71 2319.72 92.8 6.57 .0143 21.5 97.6 16.87 TTTTTTTTTT 0.07 47.7 ± 10.6 46.7 ± 10.0 2.60 218 ± 247 0.0 31.4
6.2 278 5.73 405.53 92.6 6.51 .0082 20.8 75.8 8.63 TTTTTTTTTT 0.07 47.6 ± 10.6 46.5 ± 10.1 2.62 216 ± 239 0.0 31.3
6.2 279 32.71 2316.05 92.6 6.36 .0157 20.0 95.3 14.32 TTTTTTTTTT 0.08 47.4 ± 10.6 46.3 ± 10.1 2.72 216 ± 235 0.0 31.2
6.2 280 3.84 273.05 92.4 6.37 .0091 19.9 69.2 7.11 TTTTTTTTTT 0.06 47.6 ± 10.6 46.6 ± 10.0 2.76 215 ± 239 0.0 31.5
6.2 289 15.32 1087.11 92.3 6.34 .0116 20.2 90.2 11.58 TTTTTTTTTT 0.07 47.5 ± 10.7 46.4 ± 10.1 2.67 210 ± 221 0.0 31.4
6.2 290 3.95 280.32 92.3 6.30 .0079 19.5 67.8 7.30 TTTTTTTTTT 0.07 47.6 ± 10.6 46.5 ± 10.0 2.69 214 ± 225 0.0 31.3
6.2 291 31.17 2212.85 92.2 6.30 .0156 19.7 94.2 13.92 TTTTTTTTTT 0.06 47.6 ± 10.7 46.6 ± 10.1 2.72 213 ± 227 0.0 31.4
6.2 292 3.48 247.17 92.1 6.21 .0092 19.0 66.9 6.58 TTTTTTTTTT 0.05 47.6 ± 10.7 46.6 ± 10.1 2.74 211 ± 218 0.0 31.5
6.2 293 6.27 445.25 92.0 6.42 .0087 20.5 77.3 9.28 TTTTTTTTTT 0.06 48.0 ± 10.8 46.9 ± 10.2 2.68 211 ± 228 0.0 31.4
6.2 294 8.30 588.96 91.9 6.46 .0096 20.8 82.1 10.05 TTTTTTTTTT 0.07 48.1 ± 10.8 47.0 ± 10.2 2.70 213 ± 232 0.0 31.4

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 (%)
6.1 1 3.341 5.55 93.00 39.32 0.02 0.02 0.00
6.1 2 3.402 5.47 93.02 39.55 0.02 0.02 0.00
6.1 3 3.445 5.47 92.97 39.57 0.03 0.03 0.00
6.1 4 3.458 5.46 92.99 39.58 0.03 0.03 0.00
6.1 5 3.476 5.47 92.99 39.59 0.03 0.03 0.00
6.1 6 3.478 5.47 92.95 39.60 0.03 0.03 0.00
6.1 7 3.505 5.48 92.95 39.63 0.04 0.04 0.01
6.1 8 3.518 5.46 92.96 39.65 0.04 0.04 0.01
6.1 9 3.513 5.44 92.93 39.64 0.04 0.04 0.00
6.1 10 3.512 5.47 92.94 39.65 0.03 0.03 0.00
6.1 11 3.500 5.48 92.99 39.64 0.04 0.04 0.00
6.1 12 3.477 5.45 92.97 39.61 0.04 0.04 0.01
6.1 13 3.460 5.48 93.01 39.58 0.03 0.03 0.00
6.1 14 3.454 5.45 92.99 39.56 0.04 0.04 0.00
6.1 15 3.453 5.44 92.96 39.56 0.03 0.03 0.00
6.1 16 3.480 5.45 92.96 39.59 0.03 0.03 0.00
6.1 17 3.483 5.46 92.96 39.60 0.03 0.03 0.00
6.1 18 3.484 5.45 92.94 39.60 0.04 0.04 0.00
6.1 19 3.522 5.45 92.91 39.66 0.04 0.04 0.01
6.1 20 3.484 5.46 92.95 39.60 0.04 0.04 0.00
6.1 21 6.698 5.46 93.02 39.45 0.02 0.02 0.00
6.1 22 6.703 5.46 93.03 39.49 0.02 0.02 0.00
6.1 23 6.705 5.46 93.02 39.50 0.02 0.02 0.00
6.1 24 6.763 5.45 93.00 39.54 0.02 0.02 0.00
6.1 25 6.752 5.47 93.02 39.49 0.02 0.02 0.00
6.1 26 6.713 5.45 93.02 39.52 0.02 0.02 0.00
6.1 27 6.723 5.45 92.99 39.51 0.01 0.01 0.00
6.1 28 6.735 5.44 92.98 39.53 0.01 0.01 0.00
6.1 29 3.324 5.43 93.04 39.50 0.01 0.01 0.00
6.1 30 3.339 5.44 93.03 39.52 0.01 0.01 0.00
6.1 31 3.341 5.62 92.97 39.38 0.01 0.01 0.00
6.1 32 3.349 5.63 92.99 39.39 0.01 0.01 0.00
6.1 33 3.358 5.57 92.96 39.29 0.01 0.01 0.00
6.1 34 3.365 5.44 93.01 39.53 0.01 0.01 0.00
6.1 35 3.377 5.43 93.02 39.55 0.01 0.01 0.00
6.1 36 3.375 5.44 92.99 39.56 0.01 0.01 0.00
6.1 37 3.367 5.43 93.02 39.56 0.01 0.01 0.00
6.1 38 3.351 5.46 93.06 39.51 0.01 0.01 0.00
6.1 39 3.353 5.78 92.89 39.24 0.01 0.01 0.00
6.1 40 3.367 5.44 92.99 39.56 0.01 0.01 0.00
6.1 41 6.323 5.45 93.00 39.49 0.01 0.01 0.00
6.1 42 3.829 6.22 92.27 39.34 0.00 0.00 0.00
6.1 43 6.828 5.45 93.00 39.57 0.01 0.01 0.00
6.1 44 6.828 5.58 92.95 39.43 0.02 0.02 0.02
6.1 45 6.837 5.47 93.02 39.53 0.02 0.02 0.02
6.1 46 6.809 5.44 93.00 39.57 0.01 0.01 0.02
6.1 47 6.830 5.46 92.99 39.57 0.02 0.02 0.02
6.1 48 6.825 5.44 92.99 39.57 0.02 0.02 0.02
6.1 49 3.471 5.45 92.97 39.59 0.02 0.02 0.04
6.1 50 3.487 5.45 92.96 39.61 0.03 0.03 0.04
6.1 51 3.479 5.45 92.97 39.61 0.03 0.03 0.04
6.1 52 3.500 5.44 92.96 39.62 0.03 0.03 0.04
6.1 53 3.489 5.44 92.96 39.59 0.03 0.03 0.04
6.1 54 3.471 5.45 92.98 39.58 0.03 0.03 0.04
6.1 55 3.484 5.46 92.97 39.60 0.03 0.03 0.03
6.1 56 3.501 5.44 92.96 39.61 0.03 0.03 0.04
6.1 57 3.509 5.46 92.96 39.63 0.03 0.03 0.04
6.1 58 3.501 5.44 92.97 39.61 0.03 0.03 0.03
6.1 59 3.539 5.44 92.94 39.67 0.03 0.03 0.04
6.1 60 3.525 5.45 92.96 39.64 0.03 0.03 0.04
6.1 61 6.329 5.48 93.03 39.45 0.02 0.02 0.02
6.1 62 4.415 6.60 90.71 38.25 0.02 0.02 0.04
6.1 63 6.724 5.46 93.01 39.51 0.02 0.02 0.02
6.1 64 6.749 5.45 93.01 39.54 0.01 0.01 0.03
6.1 65 6.744 5.44 93.01 39.49 0.01 0.01 0.02
6.1 66 6.690 5.57 92.97 39.37 0.01 0.01 0.02
6.1 67 6.742 5.45 93.01 39.52 0.01 0.01 0.02
6.1 68 6.746 5.45 93.01 39.53 0.01 0.01 0.02
6.1 69 3.295 5.48 93.04 39.46 0.00 0.00 0.00
6.1 70 3.273 6.09 93.01 39.15 0.00 0.00 0.00
6.1 71 3.338 5.45 93.02 39.51 0.00 0.00 0.00
6.1 72 3.348 5.46 93.03 39.51 0.00 0.00 0.00
6.1 73 3.351 5.47 93.04 39.49 0.00 0.00 0.02
6.1 74 3.353 5.46 93.02 39.52 0.00 0.00 0.00
6.1 75 3.367 5.47 93.01 39.53 0.00 0.00 0.00
6.1 76 3.370 5.84 92.97 39.00 0.00 0.00 0.00
6.1 77 3.366 5.44 93.02 39.55 0.00 0.00 0.02
6.1 78 3.317 5.54 93.01 39.40 0.00 0.00 0.00
6.1 79 3.358 5.45 93.03 39.54 0.00 0.00 0.00
6.1 80 3.353 5.46 93.01 39.53 0.00 0.00 0.00
6.1 81 3.360 5.43 93.03 39.54 0.00 0.00 0.00
6.1 82 3.359 5.43 93.01 39.54 0.00 0.00 0.01
6.1 83 3.357 5.43 93.02 39.55 0.00 0.00 0.00
6.1 84 3.338 5.43 93.03 39.53 0.00 0.00 0.00
6.1 85 3.293 5.47 93.00 39.39 0.00 0.00 0.01
6.1 86 3.129 5.50 93.01 39.36 0.00 0.00 0.00
6.1 87 3.270 5.47 93.04 39.45 0.00 0.00 0.00
6.1 88 3.308 5.57 93.00 39.36 0.00 0.00 0.01

Lane Tile Yield (pf, Mrd) Variant rate (%) Mapped (%) Average Q N bases (%) LowQ (%) Last base lowQ (%)
6.2 1 3.354 5.97 92.60 38.39 0.03 0.03 0.01
6.2 2 3.413 5.91 92.62 38.64 0.03 0.03 0.01
6.2 3 3.456 5.93 92.59 38.72 0.04 0.04 0.03
6.2 4 3.470 5.92 92.64 38.74 0.04 0.04 0.01
6.2 5 3.488 5.89 92.63 38.87 0.04 0.04 0.02
6.2 6 3.491 5.90 92.61 38.89 0.04 0.04 0.02
6.2 7 3.517 5.89 92.61 38.91 0.05 0.05 0.03
6.2 8 3.530 5.89 92.62 38.93 0.05 0.05 0.04
6.2 9 3.525 5.88 92.60 39.01 0.05 0.05 0.03
6.2 10 3.524 5.89 92.60 38.95 0.04 0.04 0.01
6.2 11 3.511 5.91 92.62 38.87 0.05 0.05 0.03
6.2 12 3.489 5.91 92.62 38.85 0.05 0.05 0.02
6.2 13 3.473 5.92 92.66 38.89 0.05 0.05 0.03
6.2 14 3.466 5.91 92.64 38.82 0.05 0.05 0.03
6.2 15 3.465 5.91 92.60 38.83 0.05 0.05 0.03
6.2 16 3.492 5.90 92.60 38.91 0.05 0.05 0.03
6.2 17 3.495 5.92 92.58 38.80 0.05 0.05 0.03
6.2 18 3.495 5.93 92.56 38.74 0.05 0.05 0.04
6.2 19 3.534 5.95 92.52 38.74 0.06 0.06 0.04
6.2 20 3.496 5.92 92.58 38.80 0.05 0.05 0.04
6.2 21 6.718 6.00 92.58 38.23 0.03 0.03 0.02
6.2 22 6.724 6.00 92.58 38.26 0.03 0.03 0.02
6.2 23 6.726 6.01 92.56 38.23 0.03 0.03 0.03
6.2 24 6.783 5.98 92.57 38.35 0.03 0.03 0.02
6.2 25 6.773 6.01 92.56 38.25 0.03 0.03 0.02
6.2 26 6.733 5.99 92.58 38.34 0.03 0.03 0.03
6.2 27 6.735 6.06 92.52 38.24 0.03 0.03 0.02
6.2 28 6.756 5.99 92.55 38.36 0.03 0.03 0.02
6.2 29 3.334 6.05 92.57 38.00 0.01 0.01 0.00
6.2 30 3.348 6.03 92.55 38.04 0.01 0.01 0.00
6.2 31 3.350 6.20 92.48 37.81 0.01 0.01 0.00
6.2 32 3.366 6.04 92.54 38.05 0.01 0.01 0.00
6.2 33 3.349 6.64 92.34 37.19 0.01 0.01 0.00
6.2 34 3.374 6.04 92.53 38.06 0.01 0.01 0.00
6.2 35 3.386 6.06 92.52 37.98 0.01 0.01 0.00
6.2 36 3.385 6.03 92.51 38.08 0.01 0.01 0.00
6.2 37 3.377 6.05 92.51 38.02 0.01 0.01 0.00
6.2 38 3.361 6.06 92.57 37.98 0.01 0.01 0.00
6.2 39 3.368 6.28 92.39 37.82 0.01 0.01 0.00
6.2 40 3.376 6.05 92.49 38.03 0.01 0.01 0.00
6.2 41 6.342 6.01 92.56 38.24 0.01 0.01 0.00
6.2 42 3.825 6.77 90.10 36.70 0.01 0.01 0.00
6.2 43 6.849 5.98 92.59 38.51 0.02 0.02 0.00
6.2 44 6.829 6.28 92.46 38.14 0.02 0.02 0.00
6.2 45 6.851 6.05 92.58 38.40 0.02 0.02 0.00
6.2 46 6.830 5.95 92.59 38.53 0.02 0.02 0.00
6.2 47 6.852 5.97 92.57 38.49 0.02 0.02 0.00
6.2 48 6.848 5.96 92.59 38.55 0.02 0.02 0.00
6.2 49 3.483 5.88 92.65 39.00 0.02 0.02 0.00
6.2 50 3.500 5.87 92.64 39.00 0.02 0.02 0.00
6.2 51 3.490 5.89 92.63 38.94 0.02 0.02 0.01
6.2 52 3.513 5.89 92.65 39.00 0.03 0.03 0.01
6.2 53 3.501 5.89 92.65 38.97 0.02 0.02 0.01
6.2 54 3.484 5.87 92.67 39.02 0.02 0.02 0.00
6.2 55 3.497 5.87 92.67 39.05 0.02 0.02 0.00
6.2 56 3.513 5.87 92.65 39.06 0.02 0.02 0.00
6.2 57 3.522 5.89 92.62 38.99 0.03 0.03 0.01
6.2 58 3.511 5.89 92.61 38.85 0.03 0.03 0.01
6.2 59 3.551 5.92 92.60 38.89 0.04 0.04 0.01
6.2 60 3.538 5.88 92.61 38.96 0.03 0.03 0.01
6.2 61 6.349 6.03 92.59 38.22 0.02 0.02 0.00
6.2 62 4.457 5.97 92.46 37.78 0.03 0.03 0.00
6.2 63 6.745 6.00 92.55 38.29 0.02 0.02 0.00
6.2 64 6.770 5.99 92.56 38.35 0.02 0.02 0.00
6.2 65 6.749 6.38 92.50 38.05 0.02 0.02 0.00
6.2 66 6.705 6.18 92.51 38.12 0.02 0.02 0.00
6.2 67 6.757 6.03 92.55 38.32 0.02 0.02 0.00
6.2 68 6.766 5.97 92.56 38.41 0.02 0.02 0.00
6.2 69 3.304 6.05 92.55 37.98 0.00 0.00 0.00
6.2 70 3.280 6.27 92.48 37.67 0.00 0.00 0.00
6.2 71 3.344 6.16 92.50 37.89 0.00 0.00 0.00
6.2 72 3.356 6.05 92.55 38.01 0.00 0.00 0.00
6.2 73 3.358 6.09 92.55 37.96 0.00 0.00 0.00
6.2 74 3.362 6.04 92.54 38.07 0.00 0.00 0.00
6.2 75 3.377 6.05 92.51 38.01 0.00 0.00 0.00
6.2 76 3.389 6.02 92.50 38.06 0.00 0.00 0.00
6.2 77 3.375 6.08 92.47 37.91 0.00 0.00 0.00
6.2 78 3.328 6.15 92.39 37.77 0.00 0.00 0.00
6.2 79 3.367 6.05 92.51 37.98 0.00 0.00 0.00
6.2 80 3.363 6.05 92.50 38.06 0.00 0.00 0.00
6.2 81 3.369 6.04 92.52 38.05 0.00 0.00 0.00
6.2 82 3.365 6.15 92.47 37.95 0.00 0.00 0.00
6.2 83 3.363 6.08 92.52 38.08 0.00 0.00 0.00
6.2 84 3.347 6.06 92.53 38.06 0.00 0.00 0.00
6.2 85 3.300 6.21 92.19 37.57 0.00 0.00 0.00
6.2 86 3.133 6.44 91.64 37.15 0.00 0.00 0.00
6.2 87 3.277 6.19 92.33 37.61 0.00 0.00 0.00
6.2 88 3.323 6.07 92.47 37.89 0.00 0.00 0.00


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