QC statistics for lane 1


Date Flowcell Lane Platform Unit Readgroup Sample Library Type Project Genome Centre
2016-11-13 HFW7MBBXX 1 161111_K00198_0128_BHFW7MBBXX_1 WTCHG_328669 30 samples 394/16_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
1.1 75 88 3669324 100.0 322.90 24217.54 23882.57 92.9 7.8 0.00 1.4 6.01 ± 0.11 .0108 9.53 10.10 48.78 10.96 back
1.2 75 88 3669324 100.0 322.90 24217.54 22697.07 92.1 8.0 0.00 1.4 6.99 ± 0.11 .0112 9.29 10.03 43.36 10.62

  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
1.1 47.4 ± 10.1 46.5 ± 9.5 4.69 200 ± 192 18.8 78.6 0.0 1.1 0.0 0.0 32.4
1.2 47.1 ± 10.7 46.1 ± 10.1 2.74 199 ± 173 20.0 82.1 0.1 0.7 0.1 0.1 30.0

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_328669_209 07A_DARK_TEL_LEFT PAR3810A69 Our indexes RNA-Seq PolyA galGal4 P160354
210 TCGCCACA WTCHG_328669_210 07B_DARK_TEL_RIGHT PAR3810A70 Our indexes RNA-Seq PolyA galGal4 P160354
221 GAGTGTCA WTCHG_328669_221 22A_6HLIGHT_TEL_LEFT PAR3810A81 Our indexes RNA-Seq PolyA galGal4 P160354
222 CTTGGCCA WTCHG_328669_222 22B_6HLIGHT_TEL_RIGHT PAR3810A82 Our indexes RNA-Seq PolyA galGal4 P160354
223 CTATGCGT WTCHG_328669_223 22C_6HLIGHT_RET_LEFT PAR3810A83 Our indexes RNA-Seq PolyA galGal4 P160354
224 CAGGTTCT WTCHG_328669_224 22D_6HLIGHT_RET_RIGHT PAR3810A84 Our indexes RNA-Seq PolyA galGal4 P160354
241 TGAACCTC WTCHG_328669_241 42A_24HLIGHT_TEL_LEFT PAR3810A101 Our indexes RNA-Seq PolyA galGal4 P160354
242 TCCACAAC WTCHG_328669_242 42B_24HLIGHT_TEL_RIGHT PAR3810A102 Our indexes RNA-Seq PolyA galGal4 P160354
243 TAAGGAAG WTCHG_328669_243 42C_24HLIGHT_RET_LEFT PAR3810A103 Our indexes RNA-Seq PolyA galGal4 P160354
244 GCCTCTTC WTCHG_328669_244 42D_24HLIGHT_RET_RIGHT PAR3810A104 Our indexes RNA-Seq PolyA galGal4 P160354
245 GACGTACA WTCHG_328669_245 44A_24HLIGHT_TEL_LEFT PAR3810A105 Our indexes RNA-Seq PolyA galGal4 P160354
246 CTGCTGCA WTCHG_328669_246 44B_24HLIGHT_TEL_RIGHT PAR3810A106 Our indexes RNA-Seq PolyA galGal4 P160354
247 CGTCCTAG WTCHG_328669_247 44C_24HLIGHT_RET_LEFT PAR3810A107 Our indexes RNA-Seq PolyA galGal4 P160354
248 CACCGGTC WTCHG_328669_248 44D_24HLIGHT_RET_RIGHT PAR3810A108 Our indexes RNA-Seq PolyA galGal4 P160354
249 TCTGATCA WTCHG_328669_249 49A_24HLIGHT_TEL_LEFT PAR3810A109 Our indexes RNA-Seq PolyA galGal4 P160354
250 TCATATGT WTCHG_328669_250 49B_24HLIGHT_TEL_RIGHT PAR3810A110 Our indexes RNA-Seq PolyA galGal4 P160354
273 TCTGCAGT WTCHG_328669_273 02A_DARK_TEL_LEFT PAR3810A61 Our indexes RNA-Seq PolyA galGal4 P160354
274 TCATCATG WTCHG_328669_274 02B_DARK_TEL_RIGHT PAR3810A62 Our indexes RNA-Seq PolyA galGal4 P160354
275 GTCCGGAG WTCHG_328669_275 02C_DARK_RET_LEFT PAR3810A63 Our indexes RNA-Seq PolyA galGal4 P160354
276 GATATATG WTCHG_328669_276 02D_DARK_RET_RIGHT PAR3810A64 Our indexes RNA-Seq PolyA galGal4 P160354
277 GAACTAAC WTCHG_328669_277 03A_DARK_TEL_LEFT PAR3810A65 Our indexes RNA-Seq PolyA galGal4 P160354
278 CTCATGAC WTCHG_328669_278 03B_DARK_TEL_RIGHT PAR3810A66 Our indexes RNA-Seq PolyA galGal4 P160354
279 CGCTCTGA WTCHG_328669_279 03C_DARK_RET_LEFT PAR3810A67 Our indexes RNA-Seq PolyA galGal4 P160354
280 ATGAGATC WTCHG_328669_280 03D_DARK_RET_RIGHT PAR3810A68 Our indexes RNA-Seq PolyA galGal4 P160354
289 TCGCTGTG WTCHG_328669_289 24A_6HLIGHT_TEL_LEFT PAR3810A85 Our indexes RNA-Seq PolyA galGal4 P160354
290 TATCCTGA WTCHG_328669_290 24B_6HLIGHT_TEL_RIGHT PAR3810A86 Our indexes RNA-Seq PolyA galGal4 P160354
291 GTAACCGA WTCHG_328669_291 24C_6HLIGHT_RET_LEFT PAR3810A87 Our indexes RNA-Seq PolyA galGal4 P160354
292 GATACGCA WTCHG_328669_292 24D_6HLIGHT_RET_RIGHT PAR3810A88 Our indexes RNA-Seq PolyA galGal4 P160354
293 GAACCGGT WTCHG_328669_293 25A_6HLIGHT_TEL_LEFT PAR3810A89 Our indexes RNA-Seq PolyA galGal4 P160354
294 CTCACAGT WTCHG_328669_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
1 209 07A_DARK_TEL_LEFT PAR3810A69 5.64 2 1.1 0.5 12.63 6 29.2 14.3
1 210 07B_DARK_TEL_RIGHT PAR3810A70 4.25 2 0.6 0.2 8.59 4 17.7 7.8
1 221 22A_6HLIGHT_TEL_LEFT PAR3810A81 4.04 2 0.6 0.2 8.48 4 17.3 7.6
1 222 22B_6HLIGHT_TEL_RIGHT PAR3810A82 7.25 2 1.9 1.0 20.43 10 45.4 26.4
1 223 22C_6HLIGHT_RET_LEFT PAR3810A83 7.32 2 2.3 1.1 22.05 12 51.2 30.3
1 224 22D_6HLIGHT_RET_RIGHT PAR3810A84 7.92 2 2.4 1.3 24.63 13 53.8 33.3
1 241 42A_24HLIGHT_TEL_LEFT PAR3810A101 8.85 2 2.3 1.3 26.21 12 53.4 33.8
1 242 42B_24HLIGHT_TEL_RIGHT PAR3810A102 9.70 2 2.5 1.5 29.28 14 56.9 37.2
1 243 42C_24HLIGHT_RET_LEFT PAR3810A103 6.56 2 1.9 0.9 18.46 10 44.8 24.4
1 244 42D_24HLIGHT_RET_RIGHT PAR3810A104 5.86 2 1.7 0.7 16.23 9 41.1 21.0
1 245 44A_24HLIGHT_TEL_LEFT PAR3810A105 6.88 2 1.7 0.9 18.58 9 42.4 23.8
1 246 44B_24HLIGHT_TEL_RIGHT PAR3810A106 3.77 2 0.5 0.2 8.50 4 16.4 7.5
1 247 44C_24HLIGHT_RET_LEFT PAR3810A107 4.64 2 1.1 0.4 11.35 6 28.0 12.2
1 248 44D_24HLIGHT_RET_RIGHT PAR3810A108 6.76 2 2.2 1.1 20.49 11 49.1 27.9
1 249 49A_24HLIGHT_TEL_LEFT PAR3810A109 6.00 2 1.2 0.6 13.88 7 32.2 16.4
1 250 49B_24HLIGHT_TEL_RIGHT PAR3810A110 7.99 2 2.1 1.1 22.74 11 48.8 29.5
1 273 02A_DARK_TEL_LEFT PAR3810A61 9.97 3 2.4 1.4 28.66 13 55.7 36.1
1 274 02B_DARK_TEL_RIGHT PAR3810A62 3.81 2 0.5 0.2 7.55 4 14.5 6.2
1 275 02C_DARK_RET_LEFT PAR3810A63 6.61 2 1.9 0.9 18.33 10 44.9 24.4
1 276 02D_DARK_RET_RIGHT PAR3810A64 7.40 2 2.4 1.2 23.00 12 52.5 31.6
1 277 03A_DARK_TEL_LEFT PAR3810A65 4.01 2 0.5 0.2 7.82 4 15.0 6.5
1 278 03B_DARK_TEL_RIGHT PAR3810A66 7.87 2 1.8 0.9 20.30 10 44.8 26.0
1 279 03C_DARK_RET_LEFT PAR3810A67 3.64 2 0.5 0.2 7.75 4 16.2 6.3
1 280 03D_DARK_RET_RIGHT PAR3810A68 8.18 2 2.6 1.4 26.22 14 56.5 36.0
1 289 24A_6HLIGHT_TEL_LEFT PAR3810A85 5.51 2 1.1 0.5 12.30 6 28.6 13.8
1 290 24B_6HLIGHT_TEL_RIGHT PAR3810A86 7.90 2 2.1 1.1 22.39 11 48.4 29.0
1 291 24C_6HLIGHT_RET_LEFT PAR3810A87 3.81 2 0.6 0.2 8.35 5 18.4 7.2
1 292 24D_6HLIGHT_RET_RIGHT PAR3810A88 7.56 2 2.5 1.3 24.27 13 54.1 33.5
1 293 25A_6HLIGHT_TEL_LEFT PAR3810A89 7.77 2 1.9 1.0 20.40 10 45.1 26.2
1 294 25B_6HLIGHT_TEL_RIGHT PAR3810A90 7.33 2 1.7 0.9 18.82 9 42.3 23.9

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
1.1 All 322.90 23882.57 92.9 6.01 .0108 18.8 78.6 10.96 N/A 0.00 47.4 ± 10.1 46.5 ± 9.5 4.69 200 ± 192 0.0 32.4
1.1 209 6.92 512.06 93.1 6.06 .0086 18.9 74.8 8.95 TTTTTTTTTT 0.05 47.4 ± 10.1 46.3 ± 9.5 4.65 204 ± 206 0.0 32.4
1.1 210 4.02 297.25 92.9 6.14 .0070 19.0 64.8 8.15 TTTTTTTTTT 0.04 47.6 ± 10.0 46.6 ± 9.5 4.67 200 ± 199 0.0 32.4
1.1 221 4.00 296.29 93.0 6.02 .0074 18.6 64.5 7.81 TTTTTTTTTT 0.04 47.5 ± 10.0 46.5 ± 9.4 4.70 197 ± 195 0.0 32.4
1.1 222 12.73 941.54 92.4 6.13 .0109 19.2 84.6 11.13 TTTTTTTTTT 0.03 47.9 ± 10.1 46.9 ± 9.5 4.69 195 ± 191 0.0 32.4
1.1 223 14.06 1040.20 92.7 5.98 .0122 18.6 84.8 11.67 TTTTTTTTTT 0.05 47.3 ± 10.1 46.3 ± 9.5 4.68 198 ± 182 0.0 32.4
1.1 224 15.84 1172.35 92.5 6.00 .0126 18.8 85.4 11.99 TTTTTTTTTT 0.03 47.5 ± 10.1 46.5 ± 9.5 4.65 198 ± 182 0.0 32.4
1.1 241 17.38 1286.20 92.7 6.01 .0118 18.9 88.5 12.63 TTTTTTTTTT 0.04 47.6 ± 10.1 46.7 ± 9.6 4.66 200 ± 196 0.0 32.4
1.1 242 19.24 1423.20 93.2 6.06 .0119 19.2 89.6 13.52 TTTTTTTTTT 0.04 47.3 ± 10.0 46.4 ± 9.4 4.70 199 ± 198 0.0 32.4
1.1 243 11.35 839.77 93.4 5.96 .0115 18.5 81.8 10.00 TTTTTTTTTT 0.03 47.0 ± 9.9 46.2 ± 9.4 4.74 199 ± 184 0.0 32.4
1.1 244 10.02 741.12 92.9 5.90 .0112 18.2 80.6 8.93 TTTTTTTTTT 0.04 47.4 ± 10.0 46.4 ± 9.5 4.75 199 ± 181 0.0 32.4
1.1 245 11.49 849.19 92.8 6.03 .0104 18.8 83.1 10.52 TTTTTTTTTT 0.03 47.6 ± 10.0 46.6 ± 9.4 4.72 194 ± 187 0.0 32.4
1.1 246 4.25 314.18 94.4 5.74 .0076 18.1 63.1 9.29 TTTTTTTTTT 0.05 46.8 ± 9.4 46.0 ± 8.9 4.73 197 ± 207 0.0 32.4
1.1 247 6.42 474.39 93.0 5.92 .0096 18.0 73.7 7.90 TTTTTTTTTT 0.04 47.1 ± 9.9 46.3 ± 9.4 4.72 197 ± 176 0.0 32.4
1.1 248 13.31 984.71 92.9 5.85 .0122 17.9 83.6 10.03 TTTTTTTTTT 0.03 47.1 ± 10.0 46.2 ± 9.6 4.69 199 ± 178 0.0 32.4
1.1 249 7.82 578.94 92.9 6.10 .0089 19.1 77.1 10.08 TTTTTTTTTT 0.02 47.4 ± 10.1 46.3 ± 9.5 4.63 200 ± 199 0.0 32.4
1.1 250 14.71 1087.99 92.7 6.00 .0111 18.8 86.2 12.41 TTTTTTTTTT 0.02 47.5 ± 10.1 46.5 ± 9.4 4.66 201 ± 196 0.0 32.4
1.1 273 18.77 1388.52 92.8 6.08 .0119 19.3 89.0 14.06 TTTTTTTTTT 0.03 47.7 ± 10.1 46.6 ± 9.5 4.61 203 ± 205 0.0 32.4
1.1 274 3.35 248.01 93.1 6.06 .0068 18.6 60.8 7.17 TTTTTTTTTT 0.03 47.5 ± 10.0 46.5 ± 9.4 4.65 205 ± 209 0.0 32.4
1.1 275 11.27 833.22 93.3 5.95 .0115 18.6 82.1 9.60 TTTTTTTTTT 0.04 47.1 ± 9.9 46.2 ± 9.5 4.70 205 ± 196 0.0 32.4
1.1 276 14.88 1096.00 93.1 5.93 .0126 18.4 85.3 10.15 TTTTTTTTTT 0.03 47.1 ± 9.9 46.2 ± 9.4 4.71 200 ± 186 0.0 32.1
1.1 277 3.34 246.97 93.3 6.20 .0065 19.5 60.8 7.68 TTTTTTTTTT 0.05 47.4 ± 9.9 46.5 ± 9.4 4.66 204 ± 216 0.0 32.4
1.1 278 12.29 909.13 93.2 6.14 .0102 19.5 84.0 11.42 TTTTTTTTTT 0.04 47.3 ± 9.9 46.4 ± 9.5 4.66 202 ± 207 0.0 32.4
1.1 279 3.75 277.57 93.1 5.97 .0084 18.2 64.6 6.84 TTTTTTTTTT 0.04 47.1 ± 9.9 46.2 ± 9.5 4.69 201 ± 190 0.0 32.4
1.1 280 16.74 1238.76 92.9 6.06 .0130 19.0 86.5 11.58 TTTTTTTTTT 0.03 47.4 ± 9.9 46.5 ± 9.5 4.66 202 ± 197 0.0 32.4
1.1 289 6.73 497.96 92.8 6.02 .0085 18.7 74.3 9.05 TTTTTTTTTT 0.05 47.5 ± 10.1 46.4 ± 9.6 4.69 198 ± 191 0.0 32.4
1.1 290 14.39 1064.23 92.9 5.96 .0112 18.5 85.5 11.40 TTTTTTTTTT 0.04 47.4 ± 10.0 46.4 ± 9.5 4.72 202 ± 196 0.0 32.4
1.1 291 4.17 308.60 92.8 5.96 .0087 18.2 66.8 7.31 TTTTTTTTTT 0.03 47.4 ± 10.1 46.4 ± 9.5 4.73 199 ± 184 0.0 32.4
1.1 292 15.83 1170.22 92.6 5.91 .0128 18.2 85.3 10.61 CACACACACA 0.01 47.5 ± 10.1 46.5 ± 9.5 4.72 198 ± 177 0.0 32.4
1.1 293 12.53 926.93 92.6 6.11 .0104 19.3 84.2 11.86 TTTTTTTTTT 0.04 47.8 ± 10.2 46.8 ± 9.6 4.70 199 ± 197 0.0 32.4
1.1 294 11.32 837.08 92.5 6.12 .0101 19.4 82.8 11.36 TTTTTTTTTT 0.04 47.8 ± 10.1 46.7 ± 9.5 4.69 200 ± 201 0.0 32.4
1.2 All 322.90 22697.07 92.1 6.98 .0112 20.0 82.1 10.62 N/A 0.00 47.1 ± 10.7 46.1 ± 10.1 2.74 199 ± 173 0.1 30.0
1.2 209 6.92 484.17 92.1 7.09 .0085 20.3 78.8 8.61 TTTTTTTTTT 0.05 47.1 ± 10.7 46.1 ± 10.1 2.74 203 ± 184 0.1 30.0
1.2 210 4.02 281.87 91.9 7.14 .0072 20.4 68.2 7.91 TTTTTTTTTT 0.06 47.4 ± 10.6 46.2 ± 10.1 2.67 200 ± 180 0.1 29.9
1.2 221 4.00 282.46 92.2 6.95 .0076 20.0 68.1 7.55 TTTTTTTTTT 0.05 47.3 ± 10.5 46.2 ± 9.9 2.79 195 ± 161 0.1 30.2
1.2 222 12.73 896.11 91.5 7.05 .0112 20.4 88.2 10.75 TTTTTTTTTT 0.05 47.8 ± 10.7 46.7 ± 10.1 2.78 194 ± 165 0.1 30.1
1.2 223 14.06 988.94 92.0 6.94 .0126 19.7 88.1 11.35 TTTTTTTTTT 0.06 47.0 ± 10.7 46.0 ± 10.1 2.71 198 ± 171 0.1 30.1
1.2 224 15.84 1113.46 91.7 6.98 .0130 19.9 88.5 11.66 TTTTTTTTTT 0.04 47.3 ± 10.7 46.1 ± 10.1 2.77 198 ± 173 0.1 30.0
1.2 241 17.38 1222.55 91.9 6.92 .0118 20.1 91.7 12.16 TTTTTTTTTT 0.06 47.4 ± 10.9 46.3 ± 10.2 2.81 199 ± 171 0.1 30.2
1.2 242 19.24 1351.76 92.3 7.03 .0119 20.4 93.0 13.05 TTTTTTTTTT 0.07 47.0 ± 10.7 46.0 ± 10.0 2.68 198 ± 176 0.1 30.1
1.2 243 11.35 795.70 92.5 6.97 .0121 19.7 85.3 9.75 TTTTTTTTTT 0.06 46.6 ± 10.5 45.7 ± 10.0 2.70 199 ± 174 0.1 30.0
1.2 244 10.02 705.39 92.2 6.79 .0117 19.3 84.1 8.69 TTTTTTTTTT 0.05 47.0 ± 10.6 46.0 ± 10.0 2.80 199 ± 169 0.1 30.2
1.2 245 11.49 808.30 92.0 6.93 .0106 20.0 86.7 10.17 TTTTTTTTTT 0.04 47.3 ± 10.6 46.2 ± 9.9 2.79 193 ± 159 0.1 30.0
1.2 246 4.25 299.50 93.6 6.79 .0084 19.6 66.5 9.05 CCCAAACCCA 0.05 46.7 ± 10.0 45.9 ± 9.5 2.62 192 ± 131 0.1 30.1
1.2 247 6.42 449.70 92.2 6.90 .0101 19.1 77.4 7.71 TTTTTTTTTT 0.06 46.8 ± 10.5 45.9 ± 10.0 2.72 197 ± 168 0.1 30.0
1.2 248 13.31 934.51 92.1 6.79 .0125 19.0 86.7 9.75 TTTTTTTTTT 0.06 46.9 ± 10.7 45.8 ± 10.1 2.77 199 ± 167 0.1 30.1
1.2 249 7.82 550.57 92.0 7.09 .0092 20.4 80.8 9.75 TTTTTTTTTT 0.06 47.1 ± 10.8 46.0 ± 10.1 2.61 199 ± 177 0.1 30.0
1.2 250 14.71 1033.88 91.9 6.97 .0115 19.9 89.7 12.03 TTTTTTTTTT 0.05 47.2 ± 10.7 46.1 ± 10.1 2.61 200 ± 171 0.1 30.0
1.2 273 18.77 1319.40 91.9 7.08 .0118 20.6 92.5 13.61 TTTTTTTTTT 0.05 47.4 ± 10.8 46.3 ± 10.1 2.78 202 ± 179 0.1 30.0
1.2 274 3.35 235.02 92.2 7.08 .0070 20.0 64.6 6.95 TTTTTTTTTT 0.06 47.2 ± 10.7 46.2 ± 10.0 2.69 203 ± 183 0.1 30.0
1.2 275 11.27 788.16 92.4 7.03 .0119 19.8 85.7 9.34 TTTTTTTTTT 0.06 46.8 ± 10.5 45.8 ± 9.9 2.75 205 ± 185 0.1 29.9
1.2 276 14.88 1050.45 92.3 6.86 .0131 19.5 88.4 9.86 AAAAAAAAAA 0.04 46.8 ± 10.4 45.8 ± 9.8 2.73 200 ± 175 0.1 30.1
1.2 277 3.34 234.85 92.5 7.22 .0068 20.9 64.4 7.46 TTTTTTTTTT 0.06 47.2 ± 10.5 46.2 ± 10.0 2.65 203 ± 191 0.1 30.1
1.2 278 12.29 859.60 92.3 7.19 .0104 20.9 87.8 11.02 TTTTTTTTTT 0.06 47.1 ± 10.6 46.0 ± 10.0 2.66 201 ± 182 0.1 29.9
1.2 279 3.75 261.65 92.1 7.10 .0088 19.4 68.5 6.68 TTTTTTTTTT 0.07 46.8 ± 10.6 45.9 ± 10.1 2.75 202 ± 178 0.1 29.7
1.2 280 16.74 1180.86 92.2 6.99 .0133 20.1 89.8 11.25 TTTTTTTTTT 0.05 47.2 ± 10.5 46.1 ± 10.0 2.81 202 ± 185 0.1 30.2
1.2 289 6.73 472.26 92.0 7.02 .0086 20.0 78.2 8.74 TTTTTTTTTT 0.06 47.1 ± 10.7 46.0 ± 10.1 2.71 197 ± 171 0.1 30.0
1.2 290 14.39 1008.59 92.0 6.99 .0116 19.8 89.1 11.02 TTTTTTTTTT 0.06 47.1 ± 10.7 46.0 ± 10.0 2.73 201 ± 172 0.1 29.9
1.2 291 4.17 292.93 91.9 6.95 .0092 19.3 70.3 7.16 TTTTTTTTTT 0.06 47.2 ± 10.6 46.1 ± 10.0 2.77 199 ± 173 0.1 30.0
1.2 292 15.83 1115.89 91.9 6.81 .0134 19.2 88.4 10.33 TTTTTTTTTT 0.04 47.2 ± 10.6 46.1 ± 10.0 2.78 198 ± 168 0.1 30.1
1.2 293 12.53 883.11 91.8 7.03 .0106 20.6 87.9 11.47 TTTTTTTTTT 0.04 47.6 ± 10.8 46.5 ± 10.1 2.74 198 ± 176 0.1 30.1
1.2 294 11.32 795.44 91.7 7.09 .0104 20.7 86.4 10.97 TTTTTTTTTT 0.06 47.6 ± 10.7 46.5 ± 10.0 2.75 200 ± 180 0.1 30.0

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 (%)
1.1 1 2.776 5.60 92.95 38.97 0.01 0.01 0.00
1.1 2 2.852 5.57 92.92 39.08 0.01 0.01 0.00
1.1 3 2.865 5.58 92.92 39.11 0.01 0.01 0.00
1.1 4 2.893 5.59 92.93 39.14 0.01 0.01 0.00
1.1 5 2.896 5.57 92.90 39.13 0.02 0.02 0.00
1.1 6 2.902 5.58 92.91 39.13 0.02 0.02 0.00
1.1 7 2.920 5.55 92.87 39.13 0.02 0.02 0.00
1.1 8 2.922 5.56 92.85 39.13 0.02 0.02 0.00
1.1 9 2.946 5.59 92.86 39.14 0.02 0.02 0.00
1.1 10 2.955 5.58 92.85 39.20 0.02 0.02 0.00
1.1 11 2.954 5.59 92.86 39.20 0.02 0.02 0.00
1.1 12 2.976 5.55 92.84 39.19 0.02 0.02 0.00
1.1 13 2.960 5.57 92.86 39.15 0.02 0.02 0.00
1.1 14 2.940 5.57 92.84 39.12 0.02 0.02 0.00
1.1 15 2.953 5.57 92.86 39.13 0.02 0.02 0.00
1.1 16 2.945 5.56 92.86 39.11 0.02 0.02 0.00
1.1 17 2.976 5.58 92.83 39.11 0.02 0.02 0.00
1.1 18 2.962 5.56 92.81 39.12 0.02 0.02 0.00
1.1 19 2.993 5.56 92.82 39.13 0.02 0.02 0.00
1.1 20 3.014 5.53 92.80 39.20 0.02 0.02 0.00
1.1 21 5.647 5.56 92.91 39.08 0.02 0.02 0.00
1.1 22 5.698 5.56 92.91 39.11 0.02 0.02 0.00
1.1 23 5.699 5.56 92.91 39.10 0.02 0.02 0.00
1.1 24 5.717 5.56 92.91 39.11 0.02 0.02 0.00
1.1 25 5.686 5.64 92.89 38.98 0.02 0.02 0.00
1.1 26 5.714 5.73 92.87 38.93 0.02 0.02 0.00
1.1 27 5.698 5.66 92.88 39.03 0.02 0.02 0.00
1.1 28 5.803 5.54 92.87 39.18 0.02 0.02 0.00
1.1 29 2.753 6.45 92.89 37.92 0.01 0.01 0.00
1.1 30 2.767 6.04 92.85 38.58 0.01 0.01 0.00
1.1 31 2.766 5.76 92.93 38.89 0.01 0.01 0.00
1.1 32 2.797 5.56 92.94 39.11 0.01 0.01 0.00
1.1 33 2.793 5.80 92.87 38.91 0.01 0.01 0.00
1.1 34 2.823 5.74 92.90 38.98 0.01 0.01 0.00
1.1 35 2.832 5.71 92.92 39.02 0.01 0.01 0.00
1.1 36 2.841 5.71 92.94 39.09 0.01 0.01 0.00
1.1 37 2.851 5.53 92.89 39.18 0.01 0.01 0.00
1.1 38 2.827 5.54 92.90 39.17 0.01 0.01 0.00
1.1 39 2.835 5.52 92.92 39.16 0.01 0.01 0.00
1.1 40 2.840 5.55 92.92 39.17 0.01 0.01 0.00
1.1 41 5.663 5.56 92.91 39.13 0.01 0.01 0.00
1.1 42 5.740 5.56 92.90 39.17 0.02 0.02 0.00
1.1 43 5.767 5.55 92.87 39.20 0.02 0.02 0.00
1.1 44 5.789 5.61 92.88 39.17 0.02 0.02 0.00
1.1 45 5.774 5.60 92.88 39.09 0.02 0.02 0.00
1.1 46 5.768 5.54 92.90 39.20 0.02 0.02 0.00
1.1 47 5.760 5.58 92.90 39.21 0.02 0.02 0.00
1.1 48 5.831 5.55 92.89 39.23 0.02 0.02 0.00
1.1 49 2.957 5.56 92.84 39.20 0.02 0.02 0.00
1.1 50 2.962 5.55 92.80 39.25 0.02 0.02 0.00
1.1 51 2.967 5.56 92.85 39.25 0.02 0.02 0.00
1.1 52 2.979 5.55 92.80 39.24 0.02 0.02 0.00
1.1 53 2.984 5.56 92.85 39.25 0.02 0.02 0.00
1.1 54 2.981 5.55 92.86 39.24 0.03 0.03 0.00
1.1 55 2.985 5.56 92.77 39.24 0.02 0.02 0.00
1.1 56 3.008 5.56 92.83 39.26 0.03 0.03 0.00
1.1 57 3.026 5.57 92.79 39.28 0.03 0.03 0.00
1.1 58 3.028 5.56 92.77 39.28 0.03 0.03 0.00
1.1 59 3.034 5.55 92.81 39.29 0.03 0.03 0.00
1.1 60 3.036 5.53 92.80 39.31 0.03 0.03 0.00
1.1 61 5.723 5.56 92.90 39.15 0.02 0.02 0.00
1.1 62 5.727 5.57 92.89 39.15 0.02 0.02 0.00
1.1 63 5.740 5.55 92.89 39.16 0.02 0.02 0.00
1.1 64 5.772 5.55 92.89 39.18 0.02 0.02 0.00
1.1 65 5.771 5.56 92.87 39.11 0.02 0.02 0.00
1.1 66 5.776 5.56 92.89 39.20 0.02 0.02 0.00
1.1 67 5.800 5.57 92.87 39.20 0.02 0.02 0.00
1.1 68 5.846 5.55 92.87 39.24 0.02 0.02 0.00
1.1 69 2.771 5.57 92.96 39.08 0.02 0.02 0.00
1.1 70 2.773 5.57 92.95 39.08 0.02 0.02 0.00
1.1 71 2.792 5.55 92.97 39.10 0.02 0.02 0.00
1.1 72 2.815 5.55 92.92 39.12 0.02 0.02 0.00
1.1 73 2.834 5.56 92.94 39.15 0.02 0.02 0.00
1.1 74 2.826 5.57 92.94 39.14 0.02 0.02 0.00
1.1 75 2.840 5.55 92.94 39.16 0.02 0.02 0.00
1.1 76 2.842 5.55 92.95 39.15 0.02 0.02 0.00
1.1 77 2.844 5.57 92.94 39.17 0.02 0.02 0.00
1.1 78 2.835 5.54 92.96 39.15 0.02 0.02 0.00
1.1 79 2.835 5.55 92.93 39.14 0.02 0.02 0.00
1.1 80 2.842 5.53 92.94 39.16 0.02 0.02 0.00
1.1 81 2.843 5.53 92.96 39.16 0.02 0.02 0.00
1.1 82 2.863 5.53 92.92 39.18 0.02 0.02 0.00
1.1 83 2.871 5.54 92.93 39.19 0.02 0.02 0.00
1.1 84 2.870 5.54 92.93 39.22 0.02 0.02 0.00
1.1 85 2.868 5.57 92.93 39.07 0.02 0.02 0.00
1.1 86 2.855 5.54 92.92 39.23 0.02 0.02 0.00
1.1 87 2.827 5.58 92.93 39.20 0.02 0.02 0.00
1.1 88 2.876 5.53 92.91 39.23 0.02 0.02 0.00

Lane Tile Yield (pf, Mrd) Variant rate (%) Mapped (%) Average Q N bases (%) LowQ (%) Last base lowQ (%)
1.2 1 2.776 6.86 91.86 35.60 0.07 0.07 0.01
1.2 2 2.852 6.45 92.13 36.01 0.08 0.08 0.00
1.2 3 2.865 6.46 92.09 36.09 0.07 0.07 0.00
1.2 4 2.893 6.43 92.15 36.23 0.08 0.08 0.00
1.2 5 2.896 6.48 92.11 36.31 0.07 0.07 0.00
1.2 6 2.902 6.49 92.10 36.34 0.07 0.07 0.00
1.2 7 2.920 6.34 92.18 36.62 0.08 0.08 0.00
1.2 8 2.922 6.34 92.19 36.63 0.07 0.07 0.00
1.2 9 2.946 6.35 92.15 36.60 0.08 0.08 0.00
1.2 10 2.955 6.35 92.14 36.59 0.08 0.08 0.00
1.2 11 2.954 6.37 92.16 36.57 0.08 0.08 0.00
1.2 12 2.976 6.29 92.18 36.79 0.08 0.08 0.00
1.2 13 2.960 6.23 92.26 37.04 0.07 0.07 0.00
1.2 14 2.940 6.20 92.27 37.19 0.06 0.06 0.00
1.2 15 2.953 6.23 92.25 37.05 0.06 0.06 0.00
1.2 16 2.945 6.22 92.28 37.18 0.07 0.07 0.00
1.2 17 2.976 6.22 92.24 37.16 0.07 0.07 0.00
1.2 18 2.962 6.20 92.22 37.13 0.07 0.07 0.00
1.2 19 2.993 6.19 92.22 37.14 0.08 0.08 0.00
1.2 20 3.014 6.22 92.20 37.16 0.08 0.08 0.00
1.2 21 5.647 6.30 92.23 36.52 0.06 0.06 0.00
1.2 22 5.698 6.27 92.24 36.69 0.06 0.06 0.00
1.2 23 5.699 6.27 92.25 36.75 0.06 0.06 0.00
1.2 24 5.717 6.30 92.23 36.67 0.06 0.06 0.00
1.2 25 5.686 6.31 92.22 36.67 0.06 0.06 0.00
1.2 26 5.714 6.37 92.15 36.57 0.06 0.06 0.00
1.2 27 5.698 6.25 92.21 36.69 0.06 0.06 0.00
1.2 28 5.803 6.28 92.16 36.65 0.06 0.06 0.00
1.2 29 2.753 6.47 92.18 36.30 0.04 0.04 0.00
1.2 30 2.767 6.67 92.02 35.88 0.05 0.05 0.00
1.2 31 2.766 6.70 92.10 36.08 0.05 0.05 0.00
1.2 32 2.797 6.41 92.16 36.30 0.04 0.04 0.00
1.2 33 2.793 6.77 92.09 36.14 0.04 0.04 0.00
1.2 34 2.823 6.36 92.13 36.43 0.05 0.05 0.00
1.2 35 2.832 6.75 92.07 35.97 0.05 0.05 0.00
1.2 36 2.841 6.50 92.17 36.31 0.04 0.04 0.00
1.2 37 2.851 6.37 92.16 36.47 0.05 0.05 0.00
1.2 38 2.827 7.07 92.01 35.80 0.04 0.04 0.00
1.2 39 2.835 6.62 92.12 36.08 0.05 0.05 0.00
1.2 40 2.840 7.39 92.06 35.68 0.05 0.05 0.00
1.2 41 5.663 6.66 91.51 35.94 0.04 0.04 0.03
1.2 42 5.740 6.72 91.64 35.85 0.05 0.05 0.03
1.2 43 5.767 7.00 91.73 35.75 0.05 0.05 0.02
1.2 44 5.789 6.49 91.84 36.12 0.05 0.05 0.02
1.2 45 5.774 6.59 91.84 36.06 0.05 0.05 0.02
1.2 46 5.768 6.48 91.85 36.27 0.04 0.04 0.02
1.2 47 5.760 6.43 91.98 36.28 0.04 0.04 0.02
1.2 48 5.831 6.55 91.89 36.21 0.04 0.04 0.02
1.2 49 2.957 6.57 91.75 36.14 0.05 0.05 0.04
1.2 50 2.962 6.64 91.57 35.98 0.05 0.05 0.04
1.2 51 2.967 6.59 91.75 36.02 0.05 0.05 0.03
1.2 52 2.979 6.57 91.80 36.18 0.05 0.05 0.03
1.2 53 2.984 6.46 91.96 36.43 0.05 0.05 0.02
1.2 54 2.981 6.39 92.06 36.64 0.05 0.05 0.02
1.2 55 2.985 6.58 91.65 36.26 0.04 0.04 0.04
1.2 56 3.008 6.40 92.01 36.65 0.05 0.05 0.02
1.2 57 3.026 6.38 91.99 36.61 0.05 0.05 0.02
1.2 58 3.028 6.38 91.99 36.59 0.05 0.05 0.02
1.2 59 3.034 6.36 92.01 36.56 0.05 0.05 0.02
1.2 60 3.036 6.42 91.97 36.46 0.05 0.05 0.02
1.2 61 5.723 6.44 92.01 36.19 0.06 0.06 0.15
1.2 62 5.727 6.48 91.97 36.23 0.06 0.06 0.16
1.2 63 5.740 6.45 91.96 36.28 0.06 0.06 0.16
1.2 64 5.772 6.45 91.96 36.35 0.06 0.06 0.16
1.2 65 5.771 6.42 92.03 36.35 0.06 0.06 0.16
1.2 66 5.776 6.35 92.12 36.44 0.06 0.06 0.15
1.2 67 5.800 6.40 92.06 36.27 0.06 0.06 0.16
1.2 68 5.846 6.47 91.88 36.20 0.06 0.06 0.17
1.2 69 2.771 6.32 92.19 36.41 0.09 0.09 0.32
1.2 70 2.773 6.32 92.17 36.40 0.09 0.09 0.32
1.2 71 2.792 6.32 92.20 36.42 0.09 0.09 0.33
1.2 72 2.815 6.27 92.15 36.51 0.09 0.09 0.32
1.2 73 2.834 6.28 92.19 36.56 0.09 0.09 0.33
1.2 74 2.826 6.28 92.20 36.58 0.09 0.09 0.33
1.2 75 2.840 6.31 92.17 36.48 0.09 0.09 0.33
1.2 76 2.842 6.30 92.18 36.52 0.09 0.09 0.34
1.2 77 2.844 6.28 92.18 36.54 0.09 0.09 0.33
1.2 78 2.835 6.30 92.19 36.44 0.09 0.09 0.34
1.2 79 2.835 6.31 92.08 36.41 0.09 0.09 0.33
1.2 80 2.842 6.33 92.07 36.42 0.09 0.09 0.33
1.2 81 2.843 6.28 92.20 36.53 0.09 0.09 0.33
1.2 82 2.863 6.28 92.12 36.50 0.09 0.09 0.32
1.2 83 2.871 6.32 92.12 36.46 0.09 0.09 0.32
1.2 84 2.870 6.32 92.12 36.49 0.09 0.09 0.32
1.2 85 2.868 6.37 92.10 36.35 0.09 0.09 0.31
1.2 86 2.855 6.27 92.13 36.56 0.08 0.08 0.30
1.2 87 2.827 6.33 92.12 36.39 0.08 0.08 0.28
1.2 88 2.876 6.29 92.07 36.45 0.08 0.08 0.30


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