QC statistics for lane 7


Date Flowcell Lane Platform Unit Readgroup Sample Library Type Project Genome Centre
2016-10-27 HF5KTBBXX 7 161021_K00198_0118_AHF5KTBBXX_7 WTCHG_323580 30 samples 444/16_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 4365291 100.0 384.15 28810.92 27906.81 92.9 8.2 0.00 1.9 5.83 ± 0.00 .0121 10.64 10.49 53.13 13.06 back
7.2 75 88 4378843 100.0 385.34 28900.37 27430.94 92.5 8.3 0.00 1.9 6.40 ± 0.00 .0126 10.42 10.42 48.15 12.81

  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 47.6 ± 10.1 46.6 ± 9.5 4.65 213 ± 245 18.6 76.2 0.0 1.0 0.0 0.0 34.0
7.2 47.4 ± 10.6 46.4 ± 10.0 2.64 213 ± 225 19.7 79.3 0.0 1.1 0.0 0.0 31.5

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_323580_211 07C_DARK_RET_LEFT PAR3810A71 Our indexes RNA-Seq PolyA galGal4 P160354
212 GCTCCTCT WTCHG_323580_212 07D_DARK_RET_RIGHT PAR3810A72 Our indexes RNA-Seq PolyA galGal4 P160354
213 GAGTTAGT WTCHG_323580_213 10A_DARK_TEL_LEFT PAR3810A73 Our indexes RNA-Seq PolyA galGal4 P160354
214 CTTGTGGT WTCHG_323580_214 10B_DARK_TEL_RIGHT PAR3810A74 Our indexes RNA-Seq PolyA galGal4 P160354
215 CTATTGTG WTCHG_323580_215 10C_DARK_RET_LEFT PAR3810A75 Our indexes RNA-Seq PolyA galGal4 P160354
216 CATTGGCT WTCHG_323580_216 10D_DARK_RET_RIGHT PAR3810A76 Our indexes RNA-Seq PolyA galGal4 P160354
217 TGCCAATC WTCHG_323580_217 14A_DARK_TEL_LEFT PAR3810A77 Our indexes RNA-Seq PolyA galGal4 P160354
218 TCCAATTG WTCHG_323580_218 14B_DARK_TEL_RIGHT PAR3810A78 Our indexes RNA-Seq PolyA galGal4 P160354
219 TACTTCGA WTCHG_323580_219 14C_DARK_RET_LEFT PAR3810A79 Our indexes RNA-Seq PolyA galGal4 P160354
220 GCGAAGTC WTCHG_323580_220 14D_DARK_RET_RIGHT PAR3810A80 Our indexes RNA-Seq PolyA galGal4 P160354
233 TGAATTCT WTCHG_323580_233 29A_6HLIGHT_TEL_LEFT PAR3810A93 Our indexes RNA-Seq PolyA galGal4 P160354
234 TCCAGCCA WTCHG_323580_234 29B_6HLIGHT_TEL_RIGHT PAR3810A94 Our indexes RNA-Seq PolyA galGal4 P160354
235 TAAGAGGA WTCHG_323580_235 29C_6HLIGHT_RET_LEFT PAR3810A95 Our indexes RNA-Seq PolyA galGal4 P160354
236 GCCTTCCT WTCHG_323580_236 29D_6HLIGHT_RET_RIGHT PAR3810A96 Our indexes RNA-Seq PolyA galGal4 P160354
237 GACGACGT WTCHG_323580_237 31A_6HLIGHT_TEL_LEFT PAR3810A97 Our indexes RNA-Seq PolyA galGal4 P160354
238 CTGCATGT WTCHG_323580_238 31B_6HLIGHT_TEL_RIGHT PAR3810A98 Our indexes RNA-Seq PolyA galGal4 P160354
239 CGTCTCGA WTCHG_323580_239 31C_6HLIGHT_RET_LEFT PAR3810A99 Our indexes RNA-Seq PolyA galGal4 P160354
240 CACCAACT WTCHG_323580_240 31D_6HLIGHT_RET_RIGHT PAR3810A100 Our indexes RNA-Seq PolyA galGal4 P160354
251 GTGGTTGA WTCHG_323580_251 49C_24HLIGHT_RET_LEFT PAR3810A111 Our indexes RNA-Seq PolyA galGal4 P160354
252 GCAGAGCT WTCHG_323580_252 49D_24HLIGHT_RET_RIGHT PAR3810A112 Our indexes RNA-Seq PolyA galGal4 P160354
253 GACGGTAC WTCHG_323580_253 50A_24HLIGHT_TEL_LEFT PAR3810A113 Our indexes RNA-Seq PolyA galGal4 P160354
254 CTGCGCAC WTCHG_323580_254 50B_24HLIGHT_TEL_RIGHT PAR3810A114 Our indexes RNA-Seq PolyA galGal4 P160354
255 CGGAAGGA WTCHG_323580_255 50C_24HLIGHT_RET_LEFT PAR3810A115 Our indexes RNA-Seq PolyA galGal4 P160354
256 ATTCTCCT WTCHG_323580_256 50D_24HLIGHT_RET_RIGHT PAR3810A116 Our indexes RNA-Seq PolyA galGal4 P160354
257 TCTGTGAC WTCHG_323580_257 54A_24HLIGHT_TEL_LEFT PAR3810A117 Our indexes RNA-Seq PolyA galGal4 P160354
258 TCATTGCA WTCHG_323580_258 54B_24HLIGHT_TEL_RIGHT PAR3810A118 Our indexes RNA-Seq PolyA galGal4 P160354
259 GTGGCCAG WTCHG_323580_259 54C_24HLIGHT_RET_LEFT PAR3810A119 Our indexes RNA-Seq PolyA galGal4 P160354
295 CGAGGAGA WTCHG_323580_295 25C_6HLIGHT_RET_LEFT PAR3810A91 Our indexes RNA-Seq PolyA galGal4 P160354
296 ATCTCTCT WTCHG_323580_296 25D_6HLIGHT_RET_RIGHT PAR3810A92 Our indexes RNA-Seq PolyA galGal4 P160354
301 ATAGAGTC WTCHG_323580_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
7 211 07C_DARK_RET_LEFT PAR3810A71 10.79 3 3.5 2.2 40.85 22 69.5 52.6
7 212 07D_DARK_RET_RIGHT PAR3810A72 10.82 3 3.4 2.2 41.20 22 68.3 51.7
7 213 10A_DARK_TEL_LEFT PAR3810A73 7.07 3 1.5 0.7 17.46 8 39.6 21.9
7 214 10B_DARK_TEL_RIGHT PAR3810A74 11.70 2 3.0 1.9 39.73 18 65.1 46.7
7 215 10C_DARK_RET_LEFT PAR3810A75 4.12 2 0.7 0.2 9.25 5 21.4 8.6
7 216 10D_DARK_RET_RIGHT PAR3810A76 3.78 2 0.6 0.2 8.22 5 17.7 7.0
7 217 14A_DARK_TEL_LEFT PAR3810A77 2.88 2 0.2 0.1 5.40 3 7.7 3.0
7 218 14B_DARK_TEL_RIGHT PAR3810A78 4.20 2 0.6 0.2 8.69 5 18.1 8.0
7 219 14C_DARK_RET_LEFT PAR3810A79 10.07 2 3.3 2.1 38.15 21 66.7 49.2
7 220 14D_DARK_RET_RIGHT PAR3810A80 9.37 2 3.2 1.9 34.66 19 64.6 46.2
7 233 29A_6HLIGHT_TEL_LEFT PAR3810A93 6.71 2 1.6 0.8 17.29 9 40.4 22.2
7 234 29B_6HLIGHT_TEL_RIGHT PAR3810A94 3.15 2 0.3 0.1 6.00 3 9.8 4.0
7 235 29C_6HLIGHT_RET_LEFT PAR3810A95 3.16 2 0.3 0.1 6.30 4 11.3 4.3
7 236 29D_6HLIGHT_RET_RIGHT PAR3810A96 6.07 2 1.7 0.7 16.96 9 42.7 22.2
7 237 31A_6HLIGHT_TEL_LEFT PAR3810A97 4.45 2 0.8 0.3 10.45 5 22.6 10.7
7 238 31B_6HLIGHT_TEL_RIGHT PAR3810A98 4.85 2 0.9 0.3 10.86 6 24.5 11.5
7 239 31C_6HLIGHT_RET_LEFT PAR3810A99 7.56 2 2.3 1.2 23.59 13 53.8 32.9
7 240 31D_6HLIGHT_RET_RIGHT PAR3810A100 7.77 2 2.5 1.3 25.23 14 55.2 34.6
7 251 49C_24HLIGHT_RET_LEFT PAR3810A111 9.56 2 3.1 1.9 35.04 19 64.1 45.8
7 252 49D_24HLIGHT_RET_RIGHT PAR3810A112 9.35 2 3.1 1.9 34.69 19 63.9 45.6
7 253 50A_24HLIGHT_TEL_LEFT PAR3810A113 3.16 2 0.3 0.1 6.09 3 10.0 4.1
7 254 50B_24HLIGHT_TEL_RIGHT PAR3810A114 4.25 2 0.7 0.2 9.26 5 20.4 9.1
7 255 50C_24HLIGHT_RET_LEFT PAR3810A115 10.04 2 3.4 2.1 38.48 21 66.3 49.3
7 256 50D_24HLIGHT_RET_RIGHT PAR3810A116 9.40 2 3.1 1.9 34.30 19 63.7 45.5
7 257 54A_24HLIGHT_TEL_LEFT PAR3810A117 2.61 2 0.2 0.0 4.74 3 5.9 2.2
7 258 54B_24HLIGHT_TEL_RIGHT PAR3810A118 10.34 2 2.8 1.7 35.30 16 62.6 43.4
7 259 54C_24HLIGHT_RET_LEFT PAR3810A119 4.91 2 1.2 0.4 12.23 7 30.8 13.8
7 295 25C_6HLIGHT_RET_LEFT PAR3810A91 3.09 2 0.3 0.1 6.34 4 11.3 4.3
7 296 25D_6HLIGHT_RET_RIGHT PAR3810A92 5.52 2 1.5 0.6 15.04 8 39.1 19.2
7 301 54D_24HLIGHT_RET_RIGHT PAR3810A120 6.02 2 1.8 0.8 17.01 9 42.5 22.2

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 384.15 27906.81 92.9 5.69 .0121 18.6 76.2 13.06 N/A 0.00 47.6 ± 10.1 46.6 ± 9.5 4.65 213 ± 245 0.0 34.0
7.1 211 28.14 2044.71 93.0 5.67 .0147 18.7 93.1 14.57 TTTTTTTTTT 0.05 47.5 ± 10.1 46.5 ± 9.5 4.68 221 ± 258 0.0 34.0
7.1 212 28.02 2035.73 93.0 5.69 .0144 18.6 91.2 15.19 TTTTTTTTTT 0.04 47.6 ± 10.0 46.6 ± 9.5 4.68 213 ± 244 0.0 34.0
7.1 213 10.12 735.17 93.0 5.89 .0097 19.6 81.2 11.61 TTTTTTTTTT 0.04 48.1 ± 10.0 47.1 ± 9.6 4.62 212 ± 262 0.0 34.0
7.1 214 27.07 1966.57 93.1 5.75 .0132 19.1 92.8 16.34 TTTTTTTTTT 0.04 47.7 ± 10.0 46.7 ± 9.5 4.64 214 ± 260 0.0 34.0
7.1 215 4.73 343.43 93.4 5.65 .0092 18.2 68.6 7.96 TTTTTTTTTT 0.05 47.2 ± 9.9 46.2 ± 9.4 4.66 216 ± 250 0.0 34.0
7.1 216 4.01 291.16 93.1 5.66 .0085 18.2 65.3 8.68 TTTTTTTTTT 0.05 47.4 ± 9.9 46.5 ± 9.5 4.64 214 ± 244 0.0 34.0
7.1 217 1.88 136.36 92.6 5.80 .0058 18.2 47.9 6.78 TTTTTTTTTT 0.05 47.9 ± 10.2 46.9 ± 9.6 4.60 212 ± 258 0.0 34.0
7.1 218 4.09 297.36 92.8 5.75 .0072 18.6 64.7 8.28 TTTTTTTTTT 0.04 47.8 ± 10.1 46.8 ± 9.5 4.64 217 ± 268 0.0 34.0
7.1 219 26.20 1902.95 93.0 5.67 .0143 18.6 91.1 13.91 TTTTTTTTTT 0.04 47.5 ± 10.1 46.6 ± 9.5 4.67 212 ± 241 0.0 34.0
7.1 220 23.68 1720.45 92.7 5.67 .0143 18.5 90.4 12.95 CACACACACA 0.01 47.7 ± 10.1 46.8 ± 9.6 4.65 212 ± 237 0.0 34.0
7.1 233 10.50 762.47 92.7 5.70 .0102 18.7 82.1 11.78 TTTTTTTTTT 0.06 47.8 ± 10.1 46.9 ± 9.7 4.57 214 ± 253 0.0 34.0
7.1 234 2.35 170.80 92.8 5.73 .0062 18.3 53.9 7.66 TTTTTTTTTT 0.05 47.8 ± 10.1 46.9 ± 9.6 4.64 218 ± 265 0.0 34.0
7.1 235 2.80 203.45 92.7 5.60 .0076 17.9 58.5 7.62 TTTTTTTTTT 0.05 47.6 ± 10.2 46.7 ± 9.7 4.67 212 ± 229 0.0 34.0
7.1 236 10.23 743.09 92.7 5.71 .0115 18.6 80.9 10.50 TTTTTTTTTT 0.04 47.8 ± 10.1 46.9 ± 9.6 4.68 212 ± 243 0.0 33.9
7.1 237 5.56 404.38 93.9 5.51 .0086 18.2 69.7 10.55 TTTTTTTTTT 0.05 47.3 ± 9.8 46.4 ± 9.2 4.69 211 ± 255 0.0 34.0
7.1 238 5.77 419.02 92.9 5.63 .0082 18.4 71.1 10.44 TTTTTTTTTT 0.06 47.7 ± 10.0 46.8 ± 9.4 4.66 213 ± 254 0.0 34.0
7.1 239 15.01 1090.08 92.8 5.74 .0128 18.9 86.3 11.39 TTTTTTTTTT 0.04 47.7 ± 10.1 46.8 ± 9.7 4.67 208 ± 234 0.0 34.0
7.1 240 16.12 1170.26 92.6 5.73 .0132 18.8 85.9 12.25 CCTGCATCTG 0.01 47.7 ± 10.1 46.8 ± 9.7 4.63 213 ± 244 0.0 34.0
7.1 251 23.33 1694.81 93.2 5.69 .0140 18.7 89.6 13.58 TTTTTTTTTT 0.04 47.5 ± 10.1 46.5 ± 9.5 4.69 210 ± 237 0.0 34.0
7.1 252 23.43 1702.59 92.8 5.65 .0139 18.5 89.4 14.73 TTTTTTTTTT 0.04 47.6 ± 10.1 46.6 ± 9.5 4.69 211 ± 233 0.0 34.0
7.1 253 2.42 176.05 92.7 5.71 .0063 18.2 54.1 8.11 TTTTTTTTTT 0.04 47.9 ± 10.1 47.0 ± 9.6 4.65 208 ± 242 0.0 34.0
7.1 254 4.65 337.49 92.7 5.75 .0078 18.9 68.5 9.39 TTTTTTTTTT 0.04 47.9 ± 10.1 46.9 ± 9.5 4.63 210 ± 248 0.0 34.0
7.1 255 26.05 1892.03 92.9 5.64 .0146 18.2 90.2 14.11 TTTTTTTTTT 0.05 47.4 ± 10.1 46.3 ± 9.6 4.70 211 ± 239 0.0 34.0
7.1 256 22.80 1656.34 92.7 5.68 .0140 18.3 88.9 14.18 TTTTTTTTTT 0.04 47.5 ± 10.1 46.5 ± 9.5 4.64 212 ± 242 0.0 34.0
7.1 257 1.56 113.29 92.6 5.60 .0052 17.0 43.1 7.26 TTTTTTTTTT 0.06 47.8 ± 10.1 46.8 ± 9.7 4.64 212 ± 242 0.0 34.0
7.1 258 24.39 1772.16 92.8 5.65 .0130 18.7 92.2 14.91 TTTTTTTTTT 0.05 47.8 ± 10.0 46.8 ± 9.5 4.65 216 ± 258 0.0 34.0
7.1 259 7.05 512.08 92.8 5.58 .0097 17.9 75.2 8.74 TTTTTTTTTT 0.04 47.5 ± 10.1 46.6 ± 9.6 4.70 210 ± 230 0.0 34.0
7.1 295 2.74 199.24 92.4 5.78 .0078 18.4 59.0 7.21 TTTTTTTTTT 0.03 48.1 ± 10.1 47.1 ± 9.7 4.61 210 ± 240 0.0 34.0
7.1 296 8.93 648.41 91.6 5.88 .0115 19.2 80.9 10.51 TTTTTTTTTT 0.07 48.5 ± 10.3 47.4 ± 9.8 4.24 218 ± 254 0.0 34.0
7.1 301 10.52 764.89 92.6 5.61 .0112 18.1 80.8 10.60 TTTTTTTTTT 0.05 47.7 ± 10.1 46.7 ± 9.6 4.71 207 ± 225 0.0 34.0
7.2 All 385.34 27430.94 92.5 6.24 .0126 19.7 79.3 12.81 N/A 0.00 47.4 ± 10.6 46.4 ± 10.0 2.64 213 ± 225 0.0 31.5
7.2 211 28.24 2006.71 92.7 6.26 .0153 19.9 95.6 14.30 TTTTTTTTTT 0.09 47.2 ± 10.6 46.2 ± 10.1 2.67 222 ± 242 0.0 31.4
7.2 212 28.11 2003.65 92.7 6.21 .0149 19.6 93.5 14.95 TTTTTTTTTT 0.05 47.3 ± 10.6 46.3 ± 10.0 2.68 213 ± 231 0.0 31.6
7.2 213 10.16 724.45 92.6 6.38 .0100 20.9 84.9 11.35 TTTTTTTTTT 0.05 47.8 ± 10.6 46.8 ± 10.1 2.72 210 ± 230 0.0 31.7
7.2 214 27.16 1932.52 92.7 6.33 .0135 20.4 95.9 16.02 TTTTTTTTTT 0.06 47.5 ± 10.6 46.4 ± 10.1 2.62 213 ± 230 0.0 31.5
7.2 215 4.74 337.19 93.1 6.25 .0096 19.5 72.5 7.87 TTTTTTTTTT 0.09 46.9 ± 10.5 46.0 ± 10.0 2.57 216 ± 233 0.0 31.5
7.2 216 4.02 286.24 92.8 6.26 .0090 19.5 69.1 8.62 TTTTTTTTTT 0.08 47.1 ± 10.5 46.1 ± 10.0 2.66 214 ± 230 0.0 31.5
7.2 217 1.88 134.10 92.2 6.31 .0059 19.5 50.6 6.64 TTTTTTTTTT 0.08 47.8 ± 10.8 46.7 ± 10.2 2.72 210 ± 224 0.0 31.6
7.2 218 4.11 291.87 92.4 6.34 .0077 20.0 68.3 8.08 TTTTTTTTTT 0.08 47.6 ± 10.6 46.7 ± 10.1 2.64 215 ± 232 0.0 31.4
7.2 219 26.28 1870.10 92.7 6.22 .0150 19.6 93.5 13.67 TTTTTTTTTT 0.08 47.3 ± 10.6 46.2 ± 10.1 2.65 213 ± 227 0.0 31.5
7.2 220 23.75 1693.73 92.4 6.15 .0149 19.6 92.9 12.74 TTTTTTTTTT 0.05 47.5 ± 10.7 46.5 ± 10.2 2.71 212 ± 224 0.0 31.7
7.2 233 10.52 748.65 92.3 6.28 .0104 20.0 85.7 11.46 TTTTTTTTTT 0.10 47.7 ± 10.8 46.6 ± 10.2 2.52 212 ± 220 0.0 31.4
7.2 234 2.36 167.88 92.4 6.30 .0064 19.6 57.1 7.52 TTTTTTTTTT 0.09 47.7 ± 10.8 46.6 ± 10.1 2.70 216 ± 231 0.0 31.5
7.2 235 2.81 199.78 92.4 6.18 .0081 19.3 62.1 7.55 TTTTTTTTTT 0.11 47.3 ± 10.8 46.2 ± 10.2 2.64 213 ± 216 0.0 31.4
7.2 236 10.27 731.62 92.4 6.30 .0124 19.8 84.3 10.33 CGTATGCCGT 0.29 47.6 ± 10.6 46.6 ± 10.1 2.85 212 ± 227 0.0 31.6
7.2 237 5.58 398.27 93.5 6.07 .0091 19.6 73.2 10.29 TTTTTTTTTT 0.07 47.0 ± 10.3 46.1 ± 9.7 2.70 206 ± 190 0.0 31.6
7.2 238 5.78 411.63 92.5 6.21 .0086 19.7 74.9 10.21 TTTTTTTTTT 0.07 47.6 ± 10.6 46.5 ± 10.0 2.62 210 ± 207 0.0 31.5
7.2 239 15.06 1071.14 92.5 6.25 .0132 20.0 89.3 11.16 TTTTTTTTTT 0.08 47.4 ± 10.7 46.4 ± 10.3 2.67 208 ± 221 0.0 31.5
7.2 240 16.17 1150.07 92.2 6.27 .0137 19.9 88.8 12.02 TTTTTTTTTT 0.08 47.6 ± 10.7 46.6 ± 10.2 2.68 213 ± 229 0.0 31.5
7.2 251 23.40 1663.52 92.8 6.25 .0147 19.8 92.1 13.34 TTTTTTTTTT 0.07 47.1 ± 10.6 46.0 ± 10.1 2.67 211 ± 225 0.0 31.4
7.2 252 23.51 1674.10 92.5 6.17 .0146 19.5 92.1 14.48 TTTTTTTTTT 0.07 47.3 ± 10.6 46.3 ± 10.0 2.61 211 ± 220 0.0 31.5
7.2 253 2.43 173.08 92.3 6.21 .0065 19.4 57.3 7.98 TTTTTTTTTT 0.07 47.6 ± 10.7 46.5 ± 10.1 2.72 207 ± 206 0.0 31.5
7.2 254 4.66 331.91 92.3 6.28 .0082 20.2 72.1 9.17 TTTTTTTTTT 0.07 47.7 ± 10.7 46.7 ± 10.2 2.69 208 ± 215 0.0 31.6
7.2 255 26.12 1858.12 92.6 6.18 .0149 19.3 92.8 13.83 TTTTTTTTTT 0.09 47.0 ± 10.7 46.0 ± 10.1 2.68 211 ± 220 0.0 31.4
7.2 256 22.87 1629.55 92.4 6.21 .0145 19.4 91.5 13.93 TTTTTTTTTT 0.07 47.3 ± 10.6 46.2 ± 10.1 2.63 213 ± 226 0.0 31.5
7.2 257 1.56 111.03 92.2 6.17 .0054 18.3 46.0 7.13 TTTTTTTTTT 0.09 47.4 ± 10.8 46.3 ± 10.2 2.70 210 ± 209 0.0 31.3
7.2 258 24.47 1741.56 92.4 6.22 .0132 20.0 95.1 14.55 TTTTTTTTTT 0.09 47.5 ± 10.6 46.5 ± 10.1 2.65 213 ± 217 0.0 31.5
7.2 259 7.07 503.35 92.5 6.09 .0105 19.0 78.6 8.60 TTTTTTTTTT 0.08 47.1 ± 10.7 46.0 ± 10.2 2.74 210 ± 218 0.0 31.5
7.2 295 2.75 195.86 92.1 6.30 .0083 19.5 62.2 7.15 TTTTTTTTTT 0.06 47.9 ± 10.8 46.8 ± 10.2 2.75 210 ± 226 0.0 31.5
7.2 296 8.95 636.93 91.1 6.55 .0123 20.2 84.2 10.28 TTTTTTTTTT 0.10 48.7 ± 11.0 47.5 ± 10.4 1.62 218 ± 238 0.0 31.5
7.2 301 10.55 752.33 92.3 6.12 .0118 19.2 84.0 10.42 TTTTTTTTTT 0.09 47.4 ± 10.7 46.4 ± 10.2 2.74 207 ± 211 0.0 31.6

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 (%)
7.1 1 3.497 5.46 92.84 39.60 0.03 0.03 0.00
7.1 2 3.562 5.40 92.85 39.67 0.03 0.03 0.01
7.1 3 3.562 5.41 92.84 39.68 0.03 0.03 0.00
7.1 4 3.565 5.41 92.82 39.70 0.03 0.03 0.00
7.1 5 3.580 5.40 92.86 39.71 0.04 0.04 0.01
7.1 6 3.573 5.40 92.86 39.68 0.03 0.03 0.01
7.1 7 3.567 5.40 92.86 39.68 0.03 0.03 0.01
7.1 8 3.562 5.40 92.86 39.68 0.03 0.03 0.00
7.1 9 3.550 5.39 92.85 39.67 0.03 0.03 0.01
7.1 10 3.536 5.39 92.86 39.67 0.03 0.03 0.00
7.1 11 3.515 5.39 92.85 39.64 0.04 0.04 0.01
7.1 12 3.465 5.40 92.88 39.59 0.03 0.03 0.01
7.1 13 3.437 5.39 92.91 39.55 0.03 0.03 0.00
7.1 14 3.455 5.41 92.88 39.57 0.03 0.03 0.00
7.1 15 3.495 5.40 92.86 39.62 0.03 0.03 0.01
7.1 16 3.548 5.39 92.86 39.67 0.04 0.04 0.01
7.1 17 3.583 5.39 92.80 39.71 0.04 0.04 0.01
7.1 18 3.602 5.38 92.83 39.71 0.04 0.04 0.01
7.1 19 3.615 5.40 92.82 39.74 0.04 0.04 0.01
7.1 20 3.619 5.39 92.80 39.74 0.04 0.04 0.01
7.1 21 6.893 5.40 92.86 39.59 0.02 0.02 0.00
7.1 22 6.928 5.39 92.85 39.63 0.02 0.02 0.00
7.1 23 6.942 5.40 92.86 39.63 0.02 0.02 0.00
7.1 24 6.941 5.40 92.84 39.64 0.02 0.02 0.00
7.1 25 6.904 5.54 92.80 39.45 0.02 0.02 0.00
7.1 26 6.905 5.41 92.84 39.62 0.02 0.02 0.00
7.1 27 6.928 5.47 92.81 39.54 0.02 0.02 0.00
7.1 28 6.932 5.40 92.83 39.64 0.02 0.02 0.00
7.1 29 3.281 5.40 92.94 39.46 0.01 0.01 0.00
7.1 30 3.311 5.39 92.93 39.49 0.01 0.01 0.00
7.1 31 3.303 5.40 92.93 39.48 0.01 0.01 0.00
7.1 32 3.306 5.40 92.95 39.48 0.01 0.01 0.00
7.1 33 3.308 5.39 92.90 39.47 0.01 0.01 0.00
7.1 34 3.310 5.39 92.92 39.46 0.01 0.01 0.00
7.1 35 3.319 5.38 92.87 39.51 0.01 0.01 0.00
7.1 36 3.339 5.52 92.86 39.41 0.01 0.01 0.00
7.1 37 3.358 5.40 92.89 39.54 0.01 0.01 0.00
7.1 38 3.362 5.39 92.89 39.53 0.01 0.01 0.00
7.1 39 3.382 5.40 92.85 39.57 0.01 0.01 0.00
7.1 40 3.378 5.39 92.87 39.56 0.01 0.01 0.00
7.1 41 6.776 5.41 92.87 39.54 0.01 0.01 0.00
7.1 42 6.835 5.41 92.86 39.55 0.01 0.01 0.00
7.1 43 6.885 5.39 92.83 39.58 0.01 0.01 0.00
7.1 44 6.903 5.39 92.85 39.59 0.01 0.01 0.00
7.1 45 6.907 5.40 92.85 39.54 0.01 0.01 0.00
7.1 46 6.876 5.39 92.87 39.60 0.01 0.01 0.02
7.1 47 6.847 5.40 92.88 39.57 0.01 0.01 0.03
7.1 48 6.838 5.40 92.89 39.56 0.01 0.01 0.02
7.1 49 3.438 5.38 92.87 39.54 0.01 0.01 0.03
7.1 50 3.435 5.38 92.85 39.52 0.01 0.01 0.04
7.1 51 3.433 5.40 92.88 39.52 0.01 0.01 0.06
7.1 52 3.413 5.38 92.89 39.51 0.01 0.01 0.04
7.1 53 3.395 5.38 92.90 39.48 0.01 0.01 0.05
7.1 54 3.388 5.38 92.87 39.47 0.01 0.01 0.03
7.1 55 3.457 5.39 92.89 39.55 0.02 0.02 0.04
7.1 56 3.511 5.38 92.86 39.60 0.02 0.02 0.05
7.1 57 3.543 5.37 92.83 39.64 0.02 0.02 0.05
7.1 58 3.528 5.38 92.83 39.62 0.02 0.02 0.04
7.1 59 3.553 5.37 92.83 39.67 0.02 0.02 0.04
7.1 60 3.549 5.37 92.85 39.63 0.02 0.02 0.04
7.1 61 6.788 5.41 92.88 39.50 0.01 0.01 0.02
7.1 62 6.829 5.41 92.87 39.52 0.01 0.01 0.02
7.1 63 6.814 5.40 92.86 39.54 0.01 0.01 0.02
7.1 64 6.832 5.39 92.87 39.54 0.01 0.01 0.03
7.1 65 6.855 5.40 92.88 39.53 0.01 0.01 0.02
7.1 66 6.830 5.39 92.86 39.56 0.01 0.01 0.02
7.1 67 6.830 5.40 92.86 39.54 0.01 0.01 0.02
7.1 68 6.823 5.39 92.84 39.54 0.01 0.01 0.02
7.1 69 3.268 5.42 92.94 39.41 0.01 0.01 0.00
7.1 70 3.259 5.41 92.92 39.40 0.01 0.01 0.00
7.1 71 3.272 5.40 92.95 39.42 0.01 0.01 0.00
7.1 72 3.278 5.39 92.94 39.42 0.01 0.01 0.00
7.1 73 3.296 5.40 92.87 39.43 0.01 0.01 0.00
7.1 74 3.286 5.42 92.90 39.41 0.01 0.01 0.00
7.1 75 3.300 5.41 92.92 39.45 0.01 0.01 0.00
7.1 76 3.347 5.41 92.88 39.50 0.01 0.01 0.00
7.1 77 3.349 5.38 92.89 39.49 0.01 0.01 0.00
7.1 78 3.343 5.39 92.90 39.49 0.01 0.01 0.00
7.1 79 3.351 5.40 92.90 39.50 0.01 0.01 0.00
7.1 80 3.358 5.42 92.87 39.50 0.01 0.01 0.00
7.1 81 3.364 5.40 92.85 39.51 0.01 0.01 0.00
7.1 82 3.395 5.41 92.85 39.53 0.01 0.01 0.00
7.1 83 3.411 5.39 92.82 39.56 0.01 0.01 0.00
7.1 84 3.408 5.40 92.85 39.56 0.01 0.01 0.00
7.1 85 3.396 5.41 92.84 39.47 0.01 0.01 0.00
7.1 86 3.376 5.42 92.87 39.56 0.01 0.01 0.00
7.1 87 3.379 5.41 92.87 39.53 0.01 0.01 0.00
7.1 88 3.381 5.40 92.86 39.52 0.01 0.01 0.00

Lane Tile Yield (pf, Mrd) Variant rate (%) Mapped (%) Average Q N bases (%) LowQ (%) Last base lowQ (%)
7.2 1 3.508 5.90 92.57 38.71 0.03 0.03 0.01
7.2 2 3.574 5.82 92.61 39.01 0.04 0.04 0.01
7.2 3 3.575 5.81 92.63 39.13 0.04 0.04 0.01
7.2 4 3.577 5.80 92.60 39.14 0.04 0.04 0.01
7.2 5 3.592 5.81 92.63 39.13 0.04 0.04 0.01
7.2 6 3.585 5.83 92.64 39.10 0.04 0.04 0.01
7.2 7 3.581 5.81 92.64 39.17 0.04 0.04 0.01
7.2 8 3.575 5.80 92.64 39.21 0.04 0.04 0.01
7.2 9 3.563 5.80 92.63 39.20 0.04 0.04 0.01
7.2 10 3.549 5.81 92.64 39.16 0.04 0.04 0.01
7.2 11 3.528 5.81 92.63 39.11 0.04 0.04 0.01
7.2 12 3.478 5.81 92.66 39.03 0.04 0.04 0.01
7.2 13 3.448 5.84 92.66 39.00 0.03 0.03 0.01
7.2 14 3.467 5.83 92.64 39.01 0.04 0.04 0.01
7.2 15 3.507 5.83 92.61 39.03 0.04 0.04 0.01
7.2 16 3.560 5.80 92.62 39.06 0.04 0.04 0.01
7.2 17 3.595 5.80 92.57 39.16 0.04 0.04 0.01
7.2 18 3.614 5.83 92.59 39.06 0.04 0.04 0.01
7.2 19 3.627 5.81 92.58 39.11 0.04 0.04 0.01
7.2 20 3.631 5.81 92.55 39.15 0.04 0.04 0.01
7.2 21 6.911 5.98 92.50 38.37 0.03 0.03 0.01
7.2 22 6.942 5.98 92.49 38.40 0.03 0.03 0.01
7.2 23 6.962 5.89 92.52 38.54 0.03 0.03 0.01
7.2 24 6.961 5.91 92.49 38.51 0.03 0.03 0.01
7.2 25 6.936 5.93 92.45 38.34 0.03 0.03 0.01
7.2 26 6.927 5.91 92.48 38.48 0.03 0.03 0.01
7.2 27 6.955 5.90 92.46 38.51 0.03 0.03 0.01
7.2 28 6.952 5.89 92.48 38.52 0.03 0.03 0.01
7.2 29 3.289 5.99 92.50 37.90 0.01 0.01 0.02
7.2 30 3.314 6.14 92.46 37.83 0.01 0.01 0.01
7.2 31 3.312 6.00 92.49 37.95 0.01 0.01 0.03
7.2 32 3.315 5.99 92.52 37.93 0.01 0.01 0.02
7.2 33 3.317 5.97 92.48 37.95 0.01 0.01 0.03
7.2 34 3.319 5.98 92.48 37.91 0.01 0.01 0.02
7.2 35 3.328 5.99 92.44 37.95 0.02 0.02 0.03
7.2 36 3.348 5.98 92.42 37.98 0.02 0.02 0.03
7.2 37 3.366 5.98 92.46 38.05 0.02 0.02 0.04
7.2 38 3.371 6.00 92.44 37.93 0.01 0.01 0.03
7.2 39 3.390 6.14 92.37 37.88 0.02 0.02 0.04
7.2 40 3.387 6.01 92.44 38.01 0.02 0.02 0.04
7.2 41 6.797 5.91 92.54 38.52 0.01 0.01 0.03
7.2 42 6.856 5.91 92.53 38.57 0.01 0.01 0.02
7.2 43 6.907 5.91 92.51 38.61 0.01 0.01 0.03
7.2 44 6.924 5.90 92.51 38.61 0.01 0.01 0.03
7.2 45 6.927 5.93 92.50 38.51 0.02 0.02 0.03
7.2 46 6.899 5.90 92.55 38.63 0.01 0.01 0.03
7.2 47 6.868 5.91 92.53 38.55 0.01 0.01 0.03
7.2 48 6.859 5.92 92.53 38.55 0.01 0.01 0.03
7.2 49 3.451 5.81 92.66 39.19 0.01 0.01 0.00
7.2 50 3.447 5.79 92.64 39.19 0.01 0.01 0.00
7.2 51 3.446 5.79 92.67 39.17 0.01 0.01 0.00
7.2 52 3.425 5.81 92.68 39.13 0.01 0.01 0.00
7.2 53 3.408 5.81 92.69 39.11 0.01 0.01 0.00
7.2 54 3.400 5.81 92.64 39.08 0.01 0.01 0.00
7.2 55 3.470 5.82 92.66 39.10 0.02 0.02 0.00
7.2 56 3.524 5.80 92.64 39.18 0.02 0.02 0.00
7.2 57 3.556 5.80 92.61 39.26 0.02 0.02 0.00
7.2 58 3.542 5.81 92.61 39.21 0.01 0.01 0.00
7.2 59 3.566 5.78 92.60 39.23 0.02 0.02 0.00
7.2 60 3.562 5.80 92.63 39.26 0.01 0.01 0.00
7.2 61 6.810 5.91 92.54 38.49 0.01 0.01 0.00
7.2 62 6.851 5.90 92.52 38.53 0.01 0.01 0.00
7.2 63 6.836 5.89 92.52 38.59 0.01 0.01 0.00
7.2 64 6.854 5.89 92.52 38.60 0.01 0.01 0.00
7.2 65 6.878 5.91 92.53 38.53 0.01 0.01 0.00
7.2 66 6.852 5.89 92.52 38.60 0.01 0.01 0.00
7.2 67 6.851 5.90 92.49 38.55 0.01 0.01 0.00
7.2 68 6.843 5.90 92.49 38.60 0.01 0.01 0.00
7.2 69 3.277 5.99 92.49 37.92 0.01 0.01 0.00
7.2 70 3.267 6.03 92.45 37.86 0.01 0.01 0.00
7.2 71 3.281 6.01 92.50 37.93 0.01 0.01 0.00
7.2 72 3.286 6.05 92.42 37.71 0.01 0.01 0.00
7.2 73 3.305 6.03 92.41 37.88 0.01 0.01 0.00
7.2 74 3.295 6.03 92.44 37.85 0.01 0.01 0.00
7.2 75 3.309 6.02 92.47 37.94 0.01 0.01 0.00
7.2 76 3.356 6.01 92.44 38.03 0.01 0.01 0.00
7.2 77 3.358 5.99 92.45 38.04 0.00 0.00 0.00
7.2 78 3.352 6.01 92.44 37.87 0.01 0.01 0.00
7.2 79 3.360 6.01 92.44 37.94 0.01 0.01 0.00
7.2 80 3.367 6.03 92.41 37.95 0.01 0.01 0.00
7.2 81 3.372 6.03 92.38 37.93 0.01 0.01 0.00
7.2 82 3.404 6.00 92.39 38.05 0.01 0.01 0.00
7.2 83 3.421 6.00 92.37 38.08 0.00 0.00 0.00
7.2 84 3.418 5.99 92.39 38.08 0.00 0.00 0.00
7.2 85 3.404 6.07 92.34 37.77 0.00 0.00 0.00
7.2 86 3.385 6.02 92.39 38.02 0.00 0.00 0.00
7.2 87 3.387 6.03 92.39 37.88 0.00 0.00 0.00
7.2 88 3.389 6.06 92.36 37.90 0.01 0.01 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