QC statistics for lane 7


Date Flowcell Lane Platform Unit Readgroup Sample Library Type Project Genome Centre
2016-10-13 HF3WCBBXX 7 161011_K00198_0114_AHF3WCBBXX_7 WTCHG_320657 30 samples 394/16_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
7.1 75 88 4012773 100.0 353.12 26484.30 26185.14 80.4 7.8 0.00 1.3 2.17 ± 0.00 .0037 9.12 10.68 45.50 10.27 back
7.2 75 88 4012773 100.0 353.12 26484.30 25415.92 79.3 7.9 0.00 1.3 4.06 ± 0.62 .0035 8.85 10.58 39.44 9.36

  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
7.1 47.7 ± 10.1 46.4 ± 9.8 4.58 192 ± 57 15.6 71.2 0.0 0.3 0.0 0.0 33.9
7.2 47.5 ± 10.7 45.9 ± 10.2 2.69 193 ± 57 16.9 74.0 0.0 0.2 0.0 0.0 31.0

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_320657_209 07A_DARK_TEL_LEFT PAR3810A69 Our indexes RNA-Seq PolyA galGal4 P160354
210 TCGCCACA WTCHG_320657_210 07B_DARK_TEL_RIGHT PAR3810A70 Our indexes RNA-Seq PolyA galGal4 P160354
221 GAGTGTCA WTCHG_320657_221 22A_6HLIGHT_TEL_LEFT PAR3810A81 Our indexes RNA-Seq PolyA galGal4 P160354
222 CTTGGCCA WTCHG_320657_222 22B_6HLIGHT_TEL_RIGHT PAR3810A82 Our indexes RNA-Seq PolyA galGal4 P160354
223 CTATGCGT WTCHG_320657_223 22C_6HLIGHT_RET_LEFT PAR3810A83 Our indexes RNA-Seq PolyA galGal4 P160354
224 CAGGTTCT WTCHG_320657_224 22D_6HLIGHT_RET_RIGHT PAR3810A84 Our indexes RNA-Seq PolyA galGal4 P160354
241 TGAACCTC WTCHG_320657_241 42A_24HLIGHT_TEL_LEFT PAR3810A101 Our indexes RNA-Seq PolyA galGal4 P160354
242 TCCACAAC WTCHG_320657_242 42B_24HLIGHT_TEL_RIGHT PAR3810A102 Our indexes RNA-Seq PolyA galGal4 P160354
243 TAAGGAAG WTCHG_320657_243 42C_24HLIGHT_RET_LEFT PAR3810A103 Our indexes RNA-Seq PolyA galGal4 P160354
244 GCCTCTTC WTCHG_320657_244 42D_24HLIGHT_RET_RIGHT PAR3810A104 Our indexes RNA-Seq PolyA galGal4 P160354
245 GACGTACA WTCHG_320657_245 44A_24HLIGHT_TEL_LEFT PAR3810A105 Our indexes RNA-Seq PolyA galGal4 P160354
246 CTGCTGCA WTCHG_320657_246 44B_24HLIGHT_TEL_RIGHT PAR3810A106 Our indexes RNA-Seq PolyA galGal4 P160354
247 CGTCCTAG WTCHG_320657_247 44C_24HLIGHT_RET_LEFT PAR3810A107 Our indexes RNA-Seq PolyA galGal4 P160354
248 CACCGGTC WTCHG_320657_248 44D_24HLIGHT_RET_RIGHT PAR3810A108 Our indexes RNA-Seq PolyA galGal4 P160354
249 TCTGATCA WTCHG_320657_249 49A_24HLIGHT_TEL_LEFT PAR3810A109 Our indexes RNA-Seq PolyA galGal4 P160354
250 TCATATGT WTCHG_320657_250 49B_24HLIGHT_TEL_RIGHT PAR3810A110 Our indexes RNA-Seq PolyA galGal4 P160354
273 TCTGCAGT WTCHG_320657_273 02A_DARK_TEL_LEFT PAR3810A61 Our indexes RNA-Seq PolyA galGal4 P160354
274 TCATCATG WTCHG_320657_274 02B_DARK_TEL_RIGHT PAR3810A62 Our indexes RNA-Seq PolyA galGal4 P160354
275 GTCCGGAG WTCHG_320657_275 02C_DARK_RET_LEFT PAR3810A63 Our indexes RNA-Seq PolyA galGal4 P160354
276 GATATATG WTCHG_320657_276 02D_DARK_RET_RIGHT PAR3810A64 Our indexes RNA-Seq PolyA galGal4 P160354
277 GAACTAAC WTCHG_320657_277 03A_DARK_TEL_LEFT PAR3810A65 Our indexes RNA-Seq PolyA galGal4 P160354
278 CTCATGAC WTCHG_320657_278 03B_DARK_TEL_RIGHT PAR3810A66 Our indexes RNA-Seq PolyA galGal4 P160354
279 CGCTCTGA WTCHG_320657_279 03C_DARK_RET_LEFT PAR3810A67 Our indexes RNA-Seq PolyA galGal4 P160354
280 ATGAGATC WTCHG_320657_280 03D_DARK_RET_RIGHT PAR3810A68 Our indexes RNA-Seq PolyA galGal4 P160354
289 TCGCTGTG WTCHG_320657_289 24A_6HLIGHT_TEL_LEFT PAR3810A85 Our indexes RNA-Seq PolyA galGal4 P160354
290 TATCCTGA WTCHG_320657_290 24B_6HLIGHT_TEL_RIGHT PAR3810A86 Our indexes RNA-Seq PolyA galGal4 P160354
291 GTAACCGA WTCHG_320657_291 24C_6HLIGHT_RET_LEFT PAR3810A87 Our indexes RNA-Seq PolyA galGal4 P160354
292 GATACGCA WTCHG_320657_292 24D_6HLIGHT_RET_RIGHT PAR3810A88 Our indexes RNA-Seq PolyA galGal4 P160354
293 GAACCGGT WTCHG_320657_293 25A_6HLIGHT_TEL_LEFT PAR3810A89 Our indexes RNA-Seq PolyA galGal4 P160354
294 CTCACAGT WTCHG_320657_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
7 209 07A_DARK_TEL_LEFT PAR3810A69 5.37 2 1.0 0.4 11.02 5 22.9 10.9
7 210 07B_DARK_TEL_RIGHT PAR3810A70 4.09 2 0.6 0.2 7.62 4 13.5 5.9
7 221 22A_6HLIGHT_TEL_LEFT PAR3810A81 3.87 2 0.5 0.2 7.44 4 13.1 5.7
7 222 22B_6HLIGHT_TEL_RIGHT PAR3810A82 6.77 2 1.7 0.9 17.18 8 36.1 20.1
7 223 22C_6HLIGHT_RET_LEFT PAR3810A83 6.88 2 2.1 1.1 18.56 10 41.0 23.1
7 224 22D_6HLIGHT_RET_RIGHT PAR3810A84 7.37 2 2.2 1.2 20.48 10 43.2 25.4
7 241 42A_24HLIGHT_TEL_LEFT PAR3810A101 8.26 2 2.2 1.2 21.96 10 43.3 26.3
7 242 42B_24HLIGHT_TEL_RIGHT PAR3810A102 9.02 2 2.3 1.3 24.34 11 46.4 29.0
7 243 42C_24HLIGHT_RET_LEFT PAR3810A103 6.20 2 1.8 0.8 15.77 8 35.6 18.7
7 244 42D_24HLIGHT_RET_RIGHT PAR3810A104 5.56 2 1.6 0.7 14.05 7 32.5 16.2
7 245 44A_24HLIGHT_TEL_LEFT PAR3810A105 6.47 2 1.6 0.8 15.79 7 33.7 18.3
7 246 44B_24HLIGHT_TEL_RIGHT PAR3810A106 3.58 2 0.5 0.2 7.37 4 12.2 5.5
7 247 44C_24HLIGHT_RET_LEFT PAR3810A107 4.41 2 1.0 0.4 9.94 5 21.9 9.4
7 248 44D_24HLIGHT_RET_RIGHT PAR3810A108 6.36 2 2.0 1.0 17.44 9 39.3 21.5
7 249 49A_24HLIGHT_TEL_LEFT PAR3810A109 5.64 2 1.1 0.5 11.88 6 24.7 12.2
7 250 49B_24HLIGHT_TEL_RIGHT PAR3810A110 7.39 2 1.9 1.0 18.78 9 38.7 22.3
7 273 02A_DARK_TEL_LEFT PAR3810A61 9.34 2 2.3 1.3 24.03 11 45.5 28.3
7 274 02B_DARK_TEL_RIGHT PAR3810A62 3.67 2 0.4 0.2 6.77 4 11.1 4.7
7 275 02C_DARK_RET_LEFT PAR3810A63 6.38 2 1.8 0.9 16.19 8 36.6 19.4
7 276 02D_DARK_RET_RIGHT PAR3810A64 7.11 2 2.3 1.2 19.99 10 43.2 25.2
7 277 03A_DARK_TEL_LEFT PAR3810A65 3.86 2 0.4 0.2 6.98 4 11.4 4.9
7 278 03B_DARK_TEL_RIGHT PAR3810A66 7.40 2 1.7 0.9 17.18 8 35.8 19.9
7 279 03C_DARK_RET_LEFT PAR3810A67 3.53 2 0.5 0.2 6.99 4 12.6 5.0
7 280 03D_DARK_RET_RIGHT PAR3810A68 7.75 2 2.4 1.3 22.51 11 46.3 28.4
7 289 24A_6HLIGHT_TEL_LEFT PAR3810A85 5.24 2 1.0 0.4 10.70 5 22.3 10.5
7 290 24B_6HLIGHT_TEL_RIGHT PAR3810A86 7.41 2 1.9 1.0 18.88 9 38.9 22.4
7 291 24C_6HLIGHT_RET_LEFT PAR3810A87 3.64 2 0.6 0.2 7.40 4 14.0 5.5
7 292 24D_6HLIGHT_RET_RIGHT PAR3810A88 7.16 2 2.3 1.2 20.75 11 44.3 26.4
7 293 25A_6HLIGHT_TEL_LEFT PAR3810A89 7.27 2 1.7 0.9 17.20 8 35.8 20.1
7 294 25B_6HLIGHT_TEL_RIGHT PAR3810A90 6.85 2 1.6 0.8 15.90 7 33.4 18.2

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
7.1 All 353.12 26185.14 80.4 2.17 .0037 15.6 71.2 10.27 N/A 0.00 47.7 ± 10.1 46.4 ± 9.8 4.58 192 ± 57 0.0 33.9
7.1 209 7.63 565.50 80.3 2.11 .0034 15.7 66.6 8.23 TTTTTTTTTT 0.05 47.7 ± 10.1 46.2 ± 9.7 4.54 195 ± 58 0.0 33.9
7.1 210 4.42 327.38 80.1 2.18 .0032 15.8 56.7 7.36 TTTTTTTTTT 0.04 47.9 ± 10.1 46.5 ± 9.6 4.56 192 ± 58 0.0 33.9
7.1 221 4.34 321.75 80.5 2.17 .0032 15.5 56.5 6.98 TTTTTTTTTT 0.04 47.8 ± 10.0 46.4 ± 9.5 4.60 188 ± 55 0.0 33.9
7.1 222 13.76 1020.44 79.7 2.23 .0037 16.1 77.0 10.36 TTTTTTTTTT 0.04 48.3 ± 10.1 46.9 ± 9.8 4.58 187 ± 54 0.0 33.9
7.1 223 15.25 1130.59 80.5 2.20 .0038 15.4 78.0 10.88 TTTTTTTTTT 0.05 47.6 ± 10.2 46.1 ± 9.8 4.57 191 ± 56 0.0 33.9
7.1 224 16.97 1259.11 80.2 2.21 .0039 15.7 78.8 11.06 TTTTTTTTTT 0.03 47.8 ± 10.2 46.4 ± 9.8 4.55 191 ± 55 0.0 33.9
7.1 241 18.94 1404.60 80.1 2.14 .0039 15.7 81.0 12.01 TTTTTTTTTT 0.04 48.0 ± 10.3 46.6 ± 9.8 4.55 192 ± 57 0.0 34.0
7.1 242 20.94 1552.73 80.5 2.17 .0039 15.9 82.3 12.98 TTTTTTTTTT 0.05 47.6 ± 10.1 46.2 ± 9.7 4.60 191 ± 58 0.0 33.9
7.1 243 12.40 919.89 81.2 2.20 .0037 15.4 75.0 9.23 TTTTTTTTTT 0.03 47.4 ± 10.1 46.0 ± 9.7 4.64 192 ± 57 0.0 33.9
7.1 244 11.01 816.78 80.8 2.19 .0037 15.3 73.8 8.22 TTTTTTTTTT 0.04 47.7 ± 10.1 46.4 ± 9.8 4.64 192 ± 55 0.0 33.9
7.1 245 12.49 925.94 80.5 2.20 .0037 15.7 75.5 9.91 TTTTTTTTTT 0.03 47.9 ± 10.1 46.6 ± 9.7 4.62 187 ± 54 0.0 33.9
7.1 246 4.59 340.13 82.4 2.04 .0031 14.7 55.2 8.32 TTTTTTTTTT 0.05 47.1 ± 9.4 46.0 ± 9.1 4.63 187 ± 56 0.0 34.0
7.1 247 7.03 521.19 80.9 2.22 .0034 15.1 66.8 7.23 TTTTTTTTTT 0.04 47.5 ± 10.1 46.1 ± 9.7 4.62 189 ± 55 0.0 33.9
7.1 248 14.53 1077.31 80.9 2.17 .0038 15.0 77.2 9.29 TTTTTTTTTT 0.04 47.5 ± 10.2 46.1 ± 9.8 4.59 193 ± 57 0.0 33.9
7.1 249 8.42 624.55 80.2 2.18 .0034 15.9 68.6 9.15 TTTTTTTTTT 0.03 47.7 ± 10.1 46.3 ± 9.8 4.53 191 ± 57 0.0 33.9
7.1 250 15.72 1166.24 80.3 2.14 .0037 15.5 78.4 11.51 TTTTTTTTTT 0.02 47.8 ± 10.1 46.4 ± 9.7 4.57 193 ± 58 0.0 33.9
7.1 273 20.55 1524.09 80.1 2.14 .0040 16.0 81.4 13.39 TTTTTTTTTT 0.03 48.0 ± 10.2 46.6 ± 9.9 4.52 195 ± 59 0.0 33.9
7.1 274 3.70 274.21 80.4 2.13 .0032 15.5 53.2 6.38 TTTTTTTTTT 0.03 47.8 ± 10.1 46.4 ± 9.8 4.54 196 ± 60 0.0 33.9
7.1 275 12.81 950.16 80.9 2.14 .0037 15.5 75.4 9.24 TTTTTTTTTT 0.04 47.4 ± 10.0 46.0 ± 9.7 4.60 197 ± 59 0.0 33.9
7.1 276 16.77 1241.42 80.9 2.18 .0039 15.3 79.0 9.77 CACACACACA 0.01 47.5 ± 10.1 46.2 ± 9.6 4.61 193 ± 57 0.0 33.9
7.1 277 3.65 270.53 80.3 2.19 .0031 16.3 52.8 6.84 TTTTTTTTTT 0.05 47.6 ± 10.0 46.3 ± 9.7 4.55 194 ± 59 0.0 33.9
7.1 278 13.45 997.58 80.5 2.17 .0037 16.2 75.9 10.82 TTTTTTTTTT 0.04 47.6 ± 10.0 46.2 ± 9.7 4.56 193 ± 58 0.0 33.9
7.1 279 4.13 306.32 80.8 2.17 .0032 15.3 57.5 6.17 TTTTTTTTTT 0.04 47.4 ± 10.0 46.1 ± 9.7 4.58 193 ± 57 0.0 33.9
7.1 280 18.62 1381.37 80.4 2.19 .0039 15.9 80.1 10.94 CACACACACA 0.01 47.8 ± 10.1 46.4 ± 9.7 4.56 193 ± 56 0.0 33.9
7.1 289 7.40 548.93 80.3 2.14 .0034 15.5 66.3 8.32 TTTTTTTTTT 0.05 47.7 ± 10.2 46.3 ± 9.8 4.59 191 ± 57 0.0 33.9
7.1 290 15.72 1165.79 80.5 2.12 .0038 15.3 78.0 10.85 TTTTTTTTTT 0.04 47.7 ± 10.1 46.2 ± 9.7 4.62 194 ± 58 0.0 33.9
7.1 291 4.51 334.47 80.5 2.22 .0032 15.3 59.0 6.42 TTTTTTTTTT 0.03 47.8 ± 10.1 46.5 ± 9.8 4.63 191 ± 55 0.0 33.9
7.1 292 17.53 1299.54 80.6 2.20 .0040 15.2 79.4 10.01 TTTTTTTTTT 0.02 47.8 ± 10.1 46.5 ± 9.8 4.63 190 ± 54 0.0 33.9
7.1 293 13.62 1009.87 79.9 2.19 .0038 16.0 76.3 11.19 TTTTTTTTTT 0.04 48.1 ± 10.3 46.7 ± 9.8 4.59 191 ± 57 0.0 33.9
7.1 294 12.23 906.71 79.7 2.18 .0037 16.2 74.7 10.68 TTTTTTTTTT 0.04 48.1 ± 10.2 46.8 ± 9.8 4.58 192 ± 57 0.0 33.9
7.2 All 353.12 25415.92 79.3 4.06 .0035 16.9 74.0 9.36 N/A 0.00 47.5 ± 10.7 45.9 ± 10.2 2.69 193 ± 57 0.0 31.0
7.2 209 7.63 547.28 79.0 4.09 .0032 17.2 69.8 7.36 TTTTTTTTTT 0.08 47.4 ± 10.8 45.9 ± 10.2 2.68 196 ± 58 0.0 30.9
7.2 210 4.42 317.44 78.9 4.09 .0030 17.3 59.8 6.70 TTTTTTTTTT 0.07 47.7 ± 10.7 46.1 ± 10.2 2.63 193 ± 58 0.0 31.0
7.2 221 4.34 312.88 79.3 3.97 .0030 16.9 59.5 6.31 TTTTTTTTTT 0.07 47.6 ± 10.6 46.0 ± 10.1 2.73 190 ± 55 0.0 31.1
7.2 222 13.76 992.01 78.5 4.08 .0035 17.3 79.7 9.42 TTTTTTTTTT 0.06 48.2 ± 10.8 46.6 ± 10.3 2.73 188 ± 54 0.0 31.1
7.2 223 15.25 1096.84 79.3 4.07 .0036 16.6 80.4 9.97 TTTTTTTTTT 0.08 47.4 ± 10.7 45.8 ± 10.3 2.66 192 ± 56 0.0 31.0
7.2 224 16.97 1221.87 79.1 4.12 .0036 16.8 81.0 10.15 TTTTTTTTTT 0.07 47.6 ± 10.8 46.0 ± 10.3 2.71 191 ± 56 0.0 31.0
7.2 241 18.94 1363.57 78.9 4.02 .0036 17.0 83.4 10.93 TTTTTTTTTT 0.08 47.8 ± 10.9 46.2 ± 10.4 2.75 193 ± 57 0.0 31.1
7.2 242 20.94 1506.42 79.3 4.05 .0037 17.3 84.7 11.84 TTTTTTTTTT 0.08 47.4 ± 10.7 45.8 ± 10.2 2.62 192 ± 58 0.0 31.0
7.2 243 12.40 891.78 80.1 4.11 .0035 16.6 77.5 8.44 TTTTTTTTTT 0.09 47.0 ± 10.7 45.5 ± 10.2 2.65 192 ± 58 0.0 31.0
7.2 244 11.01 793.75 79.7 4.01 .0035 16.3 76.7 7.50 TTTTTTTTTT 0.06 47.3 ± 10.7 45.7 ± 10.2 2.75 192 ± 56 0.0 31.1
7.2 245 12.49 901.15 79.4 3.97 .0034 16.9 78.3 9.01 TTTTTTTTTT 0.06 47.7 ± 10.7 46.0 ± 10.2 2.74 188 ± 54 0.0 31.1
7.2 246 4.59 330.82 80.9 3.79 .0029 16.2 58.1 7.53 TTTTTTTTTT 0.07 47.0 ± 10.2 45.7 ± 9.6 2.57 189 ± 54 0.0 31.1
7.2 247 7.03 505.81 79.8 4.05 .0032 16.2 69.8 6.61 TTTTTTTTTT 0.07 47.3 ± 10.7 45.7 ± 10.2 2.67 190 ± 56 0.0 31.0
7.2 248 14.53 1045.12 79.7 4.04 .0036 16.1 79.6 8.48 TTTTTTTTTT 0.08 47.3 ± 10.7 45.7 ± 10.3 2.72 194 ± 57 0.0 31.1
7.2 249 8.42 606.45 79.0 4.08 .0032 17.2 71.6 8.29 TTTTTTTTTT 0.08 47.4 ± 10.8 45.9 ± 10.3 2.57 192 ± 58 0.0 31.0
7.2 250 15.72 1130.81 79.1 4.07 .0035 16.8 81.2 10.52 TTTTTTTTTT 0.08 47.6 ± 10.8 45.9 ± 10.3 2.56 194 ± 58 0.0 31.0
7.2 273 20.55 1477.89 78.8 4.12 .0037 17.4 84.2 12.27 TTTTTTTTTT 0.08 47.9 ± 10.9 46.3 ± 10.4 2.73 196 ± 59 0.0 31.0
7.2 274 3.70 265.74 79.1 4.08 .0030 16.9 56.3 5.75 TTTTTTTTTT 0.08 47.6 ± 10.7 46.0 ± 10.2 2.65 197 ± 60 0.0 31.0
7.2 275 12.81 919.94 79.7 4.10 .0035 16.7 78.3 8.40 TTTTTTTTTT 0.08 47.1 ± 10.5 45.7 ± 10.2 2.70 198 ± 61 0.0 30.9
7.2 276 16.77 1208.31 79.8 3.96 .0037 16.5 81.5 8.92 TTTTTTTTTT 0.05 47.2 ± 10.5 45.7 ± 10.2 2.69 193 ± 57 0.0 31.0
7.2 277 3.65 262.62 79.0 4.08 .0029 17.8 55.9 6.16 TTTTTTTTTT 0.08 47.6 ± 10.6 46.1 ± 10.2 2.59 195 ± 59 0.0 31.0
7.2 278 13.45 966.07 79.1 4.14 .0034 17.6 79.2 9.80 TTTTTTTTTT 0.08 47.4 ± 10.6 45.9 ± 10.2 2.61 194 ± 59 0.0 30.9
7.2 279 4.13 296.63 79.6 4.15 .0030 16.6 60.5 5.63 TTTTTTTTTT 0.08 47.2 ± 10.7 45.7 ± 10.3 2.71 194 ± 58 0.0 30.9
7.2 280 18.62 1342.86 79.2 4.04 .0037 17.1 82.4 10.00 TTTTTTTTTT 0.07 47.5 ± 10.5 46.0 ± 10.2 2.75 194 ± 57 0.0 31.1
7.2 289 7.40 532.24 79.1 4.05 .0031 16.9 69.6 7.47 TTTTTTTTTT 0.08 47.4 ± 10.8 45.8 ± 10.3 2.67 192 ± 57 0.0 31.0
7.2 290 15.72 1130.24 79.3 4.05 .0035 16.6 80.7 9.86 TTTTTTTTTT 0.08 47.5 ± 10.7 45.9 ± 10.2 2.69 195 ± 58 0.0 30.9
7.2 291 4.51 324.73 79.4 4.08 .0031 16.5 62.0 5.87 TTTTTTTTTT 0.07 47.5 ± 10.7 46.0 ± 10.3 2.72 192 ± 55 0.0 31.1
7.2 292 17.53 1264.16 79.6 4.02 .0038 16.3 81.6 9.20 TTTTTTTTTT 0.05 47.6 ± 10.7 46.1 ± 10.3 2.74 191 ± 54 0.0 31.1
7.2 293 13.62 980.70 78.7 4.08 .0035 17.4 79.2 10.20 TTTTTTTTTT 0.06 48.0 ± 10.9 46.3 ± 10.4 2.67 192 ± 57 0.0 31.1
7.2 294 12.23 879.78 78.5 4.12 .0035 17.7 77.7 9.70 TTTTTTTTTT 0.07 48.1 ± 10.8 46.5 ± 10.3 2.70 193 ± 57 0.0 31.0

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 (%)
7.1 1 3.119 1.76 80.55 39.31 0.00 0.00 0.00
7.1 2 3.156 1.76 80.51 39.34 0.00 0.00 0.00
7.1 3 3.190 1.75 80.51 39.41 0.00 0.00 0.00
7.1 4 3.212 1.75 80.49 39.43 0.01 0.01 0.00
7.1 5 3.184 1.75 80.46 39.40 0.00 0.00 0.00
7.1 6 3.188 1.76 80.51 39.38 0.01 0.01 0.00
7.1 7 3.199 1.75 80.52 39.44 0.01 0.01 0.01
7.1 8 3.218 1.75 80.45 39.44 0.01 0.01 0.01
7.1 9 3.229 1.75 80.47 39.46 0.01 0.01 0.01
7.1 10 3.237 1.76 80.42 39.46 0.01 0.01 0.00
7.1 11 3.255 1.75 80.45 39.49 0.01 0.01 0.01
7.1 12 3.257 1.75 80.49 39.49 0.01 0.01 0.01
7.1 13 3.249 1.75 80.50 39.47 0.01 0.01 0.00
7.1 14 3.221 1.74 80.47 39.44 0.01 0.01 0.00
7.1 15 3.235 1.75 80.48 39.46 0.01 0.01 0.00
7.1 16 3.278 1.75 80.45 39.52 0.01 0.01 0.00
7.1 17 3.285 1.75 80.48 39.53 0.01 0.01 0.00
7.1 18 3.273 1.74 80.43 39.51 0.01 0.01 0.00
7.1 19 3.291 1.74 80.50 39.54 0.01 0.01 0.00
7.1 20 3.283 1.75 80.44 39.53 0.01 0.01 0.00
7.1 21 6.326 1.74 80.43 39.42 0.01 0.01 0.01
7.1 22 6.351 1.74 80.43 39.44 0.01 0.01 0.01
7.1 23 6.350 1.69 80.23 39.43 0.01 0.01 0.01
7.1 24 6.345 1.74 80.47 39.44 0.01 0.01 0.01
7.1 25 6.356 1.75 80.46 39.39 0.01 0.01 0.01
7.1 26 6.318 1.74 80.48 39.44 0.01 0.01 0.01
7.1 27 6.342 1.76 80.47 39.41 0.01 0.01 0.01
7.1 28 6.376 1.74 80.46 39.46 0.01 0.01 0.01
7.1 29 3.071 1.73 80.48 39.38 0.01 0.01 0.01
7.1 30 3.095 1.72 80.45 39.39 0.01 0.01 0.01
7.1 31 3.097 1.73 80.46 39.40 0.01 0.01 0.01
7.1 32 3.089 1.73 80.45 39.36 0.01 0.01 0.01
7.1 33 3.076 1.73 80.40 39.35 0.01 0.01 0.01
7.1 34 3.082 1.73 80.46 39.37 0.01 0.01 0.01
7.1 35 3.070 1.74 80.51 39.38 0.01 0.01 0.01
7.1 36 3.104 1.73 80.49 39.41 0.01 0.01 0.01
7.1 37 3.122 1.73 80.46 39.42 0.01 0.01 0.01
7.1 38 3.104 1.74 80.45 39.42 0.01 0.01 0.01
7.1 39 3.128 1.73 80.47 39.44 0.01 0.01 0.01
7.1 40 3.136 1.73 80.45 39.44 0.01 0.01 0.01
7.1 41 6.165 1.74 80.43 39.34 0.01 0.01 0.01
7.1 42 6.191 1.87 80.41 39.26 0.01 0.01 0.01
7.1 43 6.196 1.74 80.44 39.35 0.01 0.01 0.01
7.1 44 6.111 1.74 80.32 39.34 0.01 0.01 0.01
7.1 45 6.053 1.76 80.31 39.18 0.01 0.01 0.01
7.1 46 5.991 1.75 80.39 39.31 0.01 0.01 0.01
7.1 47 6.069 1.75 80.32 39.26 0.01 0.01 0.01
7.1 48 6.223 1.74 80.40 39.36 0.01 0.01 0.01
7.1 49 3.205 1.76 80.46 39.39 0.01 0.01 0.01
7.1 50 3.207 1.76 80.49 39.42 0.01 0.01 0.01
7.1 51 3.229 1.76 80.47 39.43 0.01 0.01 0.01
7.1 52 3.232 1.75 80.41 39.43 0.01 0.01 0.01
7.1 53 3.216 1.76 80.47 39.41 0.01 0.01 0.01
7.1 54 3.187 1.75 80.48 39.38 0.01 0.01 0.01
7.1 55 3.185 1.76 80.45 39.39 0.01 0.01 0.01
7.1 56 3.228 1.76 80.44 39.44 0.01 0.01 0.01
7.1 57 3.257 1.75 80.44 39.49 0.01 0.01 0.01
7.1 58 3.252 1.76 80.44 39.47 0.01 0.01 0.01
7.1 59 3.266 1.75 80.44 39.49 0.01 0.01 0.01
7.1 60 3.265 1.76 80.45 39.50 0.01 0.01 0.01
7.1 61 6.316 1.77 80.42 39.36 0.00 0.00 0.01
7.1 62 6.312 1.74 80.47 39.39 0.00 0.00 0.01
7.1 63 6.323 1.74 80.48 39.41 0.00 0.00 0.00
7.1 64 6.336 1.75 80.43 39.42 0.00 0.00 0.01
7.1 65 6.335 1.76 80.46 39.35 0.00 0.00 0.01
7.1 66 6.323 1.76 80.47 39.46 0.01 0.01 0.01
7.1 67 6.356 1.77 80.49 39.38 0.01 0.01 0.01
7.1 68 6.359 1.75 80.48 39.45 0.01 0.01 0.01
7.1 69 3.094 1.74 80.48 39.39 0.00 0.00 0.00
7.1 70 3.115 1.73 80.46 39.40 0.00 0.00 0.00
7.1 71 3.118 1.74 80.44 39.42 0.00 0.00 0.00
7.1 72 3.119 1.73 80.47 39.42 0.00 0.00 0.00
7.1 73 3.109 1.74 80.52 39.40 0.00 0.00 0.00
7.1 74 3.096 1.74 80.52 39.38 0.00 0.00 0.00
7.1 75 3.087 1.73 80.54 39.39 0.00 0.00 0.00
7.1 76 3.104 1.74 80.46 39.39 0.01 0.01 0.00
7.1 77 3.132 1.74 80.45 39.42 0.01 0.01 0.00
7.1 78 3.135 1.73 80.43 39.44 0.01 0.01 0.00
7.1 79 3.130 1.73 80.43 39.41 0.00 0.00 0.00
7.1 80 3.130 1.74 80.41 39.43 0.01 0.01 0.00
7.1 81 3.142 1.73 80.45 39.44 0.01 0.01 0.00
7.1 82 3.123 1.74 80.46 39.42 0.01 0.01 0.00
7.1 83 3.129 1.77 80.41 39.38 0.01 0.01 0.00
7.1 84 3.123 1.79 80.47 39.39 0.01 0.01 0.00
7.1 85 3.131 1.77 80.38 39.25 0.00 0.00 0.00
7.1 86 3.077 1.75 80.44 39.44 0.01 0.01 0.00
7.1 87 3.039 1.77 80.41 39.29 0.00 0.00 0.01
7.1 88 3.105 1.74 80.37 39.39 0.00 0.00 0.01

Lane Tile Yield (pf, Mrd) Variant rate (%) Mapped (%) Average Q N bases (%) LowQ (%) Last base lowQ (%)
7.2 1 3.119 3.41 79.43 37.53 0.01 0.01 0.00
7.2 2 3.156 3.32 79.38 37.68 0.01 0.01 0.00
7.2 3 3.190 3.24 79.38 37.78 0.01 0.01 0.00
7.2 4 3.212 3.18 79.42 37.85 0.01 0.01 0.00
7.2 5 3.184 3.15 79.39 37.88 0.01 0.01 0.00
7.2 6 3.188 3.10 79.43 37.97 0.01 0.01 0.00
7.2 7 3.199 3.08 79.43 38.02 0.01 0.01 0.00
7.2 8 3.218 3.05 79.34 38.00 0.01 0.01 0.00
7.2 9 3.229 3.05 79.39 38.01 0.01 0.01 0.00
7.2 10 3.237 3.03 79.38 38.09 0.01 0.01 0.00
7.2 11 3.255 3.01 79.36 38.07 0.01 0.01 0.00
7.2 12 3.257 3.03 79.40 38.09 0.01 0.01 0.00
7.2 13 3.249 3.00 79.42 38.06 0.01 0.01 0.00
7.2 14 3.221 2.98 79.38 38.03 0.01 0.01 0.00
7.2 15 3.235 2.97 79.41 38.14 0.01 0.01 0.00
7.2 16 3.278 2.93 79.40 38.21 0.01 0.01 0.00
7.2 17 3.285 2.92 79.40 38.20 0.01 0.01 0.00
7.2 18 3.273 2.96 79.35 38.08 0.01 0.01 0.00
7.2 19 3.291 2.90 79.42 38.20 0.01 0.01 0.01
7.2 20 3.283 2.91 79.37 38.21 0.01 0.01 0.01
7.2 21 6.326 3.47 79.13 37.37 0.03 0.03 0.01
7.2 22 6.351 3.34 79.19 37.55 0.03 0.03 0.01
7.2 23 6.350 3.74 78.47 37.06 0.03 0.03 0.01
7.2 24 6.345 3.27 79.23 37.66 0.02 0.02 0.01
7.2 25 6.356 3.35 79.28 37.61 0.02 0.02 0.01
7.2 26 6.318 3.23 79.26 37.60 0.02 0.02 0.01
7.2 27 6.342 3.15 79.29 37.76 0.02 0.02 0.00
7.2 28 6.376 3.11 79.32 37.83 0.02 0.02 0.01
7.2 29 3.071 3.31 79.24 37.45 0.02 0.02 0.01
7.2 30 3.095 3.29 79.24 37.54 0.03 0.03 0.01
7.2 31 3.097 3.27 79.23 37.57 0.02 0.02 0.01
7.2 32 3.089 3.43 79.08 37.37 0.02 0.02 0.01
7.2 33 3.076 3.46 79.05 37.37 0.01 0.01 0.01
7.2 34 3.082 3.23 79.29 37.57 0.02 0.02 0.02
7.2 35 3.070 3.12 79.37 37.70 0.02 0.02 0.01
7.2 36 3.104 3.19 79.32 37.72 0.01 0.01 0.02
7.2 37 3.122 6.61 79.25 37.46 0.01 0.01 0.02
7.2 38 3.104 3.20 79.23 37.52 0.01 0.01 0.01
7.2 39 3.128 3.24 79.24 37.50 0.01 0.01 0.02
7.2 40 3.136 3.25 79.24 37.55 0.01 0.01 0.02
7.2 41 6.165 3.35 79.26 37.51 0.01 0.01 0.01
7.2 42 6.191 3.24 79.31 37.66 0.01 0.01 0.01
7.2 43 6.196 3.27 79.22 37.66 0.01 0.01 0.01
7.2 44 6.111 3.41 78.99 37.48 0.01 0.01 0.01
7.2 45 6.053 3.58 78.98 37.37 0.01 0.01 0.01
7.2 46 5.991 3.34 79.06 37.51 0.01 0.01 0.01
7.2 47 6.069 3.37 78.99 37.44 0.01 0.01 0.01
7.2 48 6.223 3.26 79.11 37.67 0.01 0.01 0.01
7.2 49 3.205 2.99 79.40 38.15 0.01 0.01 0.01
7.2 50 3.207 2.97 79.45 38.23 0.01 0.01 0.01
7.2 51 3.229 2.96 79.40 38.20 0.01 0.01 0.01
7.2 52 3.232 2.96 79.36 38.20 0.00 0.00 0.01
7.2 53 3.216 2.96 79.42 38.21 0.00 0.00 0.01
7.2 54 3.187 2.95 79.45 38.14 0.00 0.00 0.01
7.2 55 3.185 2.94 79.38 38.18 0.00 0.00 0.01
7.2 56 3.228 2.91 79.36 38.22 0.00 0.00 0.01
7.2 57 3.257 2.91 79.39 38.27 0.00 0.00 0.01
7.2 58 3.252 2.89 79.38 38.21 0.00 0.00 0.01
7.2 59 3.266 2.87 79.42 38.28 0.00 0.00 0.01
7.2 60 3.265 2.86 79.39 38.33 0.00 0.00 0.01
7.2 61 6.316 3.28 79.28 37.65 0.00 0.00 0.00
7.2 62 6.312 3.25 79.31 37.68 0.00 0.00 0.00
7.2 63 6.323 3.23 79.29 37.70 0.00 0.00 0.00
7.2 64 6.336 3.18 79.26 37.71 0.00 0.00 0.00
7.2 65 6.335 3.20 79.30 37.70 0.00 0.00 0.00
7.2 66 6.323 3.08 79.35 37.87 0.00 0.00 0.00
7.2 67 6.356 3.03 79.41 38.00 0.00 0.00 0.00
7.2 68 6.359 3.01 79.37 38.04 0.00 0.00 0.00
7.2 69 3.094 3.19 79.35 37.69 0.00 0.00 0.00
7.2 70 3.115 3.20 79.30 37.62 0.00 0.00 0.00
7.2 71 3.118 3.18 79.27 37.69 0.00 0.00 0.00
7.2 72 3.119 3.18 79.28 37.71 0.00 0.00 0.00
7.2 73 3.109 3.17 79.34 37.71 0.00 0.00 0.00
7.2 74 3.096 3.18 79.34 37.67 0.00 0.00 0.00
7.2 75 3.087 3.14 79.34 37.75 0.01 0.01 0.00
7.2 76 3.104 3.13 79.30 37.73 0.01 0.01 0.02
7.2 77 3.132 3.10 79.32 37.80 0.01 0.01 0.04
7.2 78 3.135 3.15 79.27 37.67 0.01 0.01 0.05
7.2 79 3.130 3.20 79.25 37.63 0.01 0.01 0.04
7.2 80 3.130 3.12 79.24 37.70 0.02 0.02 0.05
7.2 81 3.142 3.16 79.23 37.62 0.02 0.02 0.05
7.2 82 3.123 3.16 79.21 37.59 0.02 0.02 0.06
7.2 83 3.129 3.19 79.19 37.53 0.02 0.02 0.08
7.2 84 3.123 3.16 79.25 37.64 0.02 0.02 0.06
7.2 85 3.131 3.62 79.09 37.24 0.02 0.02 0.08
7.2 86 3.077 3.31 79.16 37.34 0.02 0.02 0.08
7.2 87 3.039 3.36 79.07 37.24 0.02 0.02 0.09
7.2 88 3.105 3.32 79.11 37.40 0.02 0.02 0.09


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