Barcode-Lane Summary Information For Experiment (Demo)

Project Summary

Project Name Demo
Machine HWI-BRUNOP20X
Run Folder 110120_P20_0993_A805CKABXX
Flow Cell ID A805CKABXX
Platform
Control Software SCS
Primary Analysis RTA 1.10.36.0
Secondary Analysis CASAVA-1.8.2

Project Results Summary

Clusters (Raw) Clusters(PF) Yield (MBases)
1,567,312 1,567,312 235

Barcode-Lane summary

Barcode-Lane Sample Barcode Lane Species Analysis Type Length Num Tiles Genome Directory
AR008_ACTTGA_L1 AR008 ACTTGA 1 human eland rna 75 75 1 /illumina/development/casava/Version_1_8_branch/share/CASAVA-1.8.2/examples/iGenomes/Homo_sapiens/UCSC/hg18/Sequence/Chromosomes/chr22.fa
PhiX_TTAGGC_L1 PhiX TTAGGC 1 phix eland pair 75 75 1 /illumina/development/casava/Version_1_8_branch/share/CASAVA-1.8.2/examples/iGenomes/PhiX/NCBI/1993-04-28/Sequence/Chromosomes/phix.fa

Barcode-Lane Results Summary : Read 1

Barcode-Lane Info
Barcode lane Barcode lane Yield (Mbases) Clusters (raw) Clusters (PF) 1st Cycle Int (PF) % intensity after 20 cycles (PF) % PF Clusters % Align (PF) Alignment Score (PF) % Mismatch Rate (PF) % >=Q30 bases (PF) Mean Quality SCore (PF)
AR008_ACTTGA_L1 114 1,518,208 1,518,208 472 +/-0 98.55 +/-0 100.00 4.15 10.15 3.51 90.95 35.59
PhiX_TTAGGC_L1 4 49,104 49,104 472 +/-0 98.55 +/-0 100.00 94.26 379.07 0.29 92.90 36.15

Barcode-Lane Results Summary : Read 2

Barcode-Lane Info
Barcode lane Barcode lane Yield (Mbases) Clusters (raw) Clusters (PF) 1st Cycle Int (PF) % intensity after 20 cycles (PF) % PF Clusters % Align (PF) Alignment Score (PF) % Mismatch Rate (PF) % >=Q30 bases (PF) Mean Quality SCore (PF)
AR008_ACTTGA_L1 114 1,518,208 1,518,208 329 +/-0 83.72 +/-0 100.00 4.03 9.61 4.00 82.93 33.29
PhiX_TTAGGC_L1 4 49,104 49,104 329 +/-0 83.72 +/-0 100.00 93.38 368.98 0.58 86.36 34.37

Expanded Barcode-Lane Summary : Read 1

Barcode lane Info Phasing Info Raw data Filtered data
Barcode lane Clusters (raw) % Phasing % Prephasing % Mismatch Rate (raw) % PF Clusters Cycle 2-4 Av Int (PF) Cycle 2-10 Av % Loss (PF) Cycle 10-20 Av % Loss (PF) % Align (PF) % Mismatch Rate (PF) % >=Q30 bases (PF) Mean Quality SCore (PF)
AR008_ACTTGA_L1 1,518,208 0.18 0.25 3.51 100.00 579.66 +/-0.00 2.35 +/-0.00 0.91 +/-0.00 4.15 3.51 90.95 35.59
PhiX_TTAGGC_L1 49,104 0.18 0.25 0.29 100.00 579.66 +/-0.00 2.35 +/-0.00 0.91 +/-0.00 94.26 0.29 92.90 36.15

Expanded Barcode-Lane Summary : Read 2

Barcode lane Info Phasing Info Raw data Filtered data
Barcode lane Clusters (raw) % Phasing % Prephasing % Mismatch Rate (raw) % PF Clusters Cycle 2-4 Av Int (PF) Cycle 2-10 Av % Loss (PF) Cycle 10-20 Av % Loss (PF) % Align (PF) % Mismatch Rate (PF) % >=Q30 bases (PF) Mean Quality SCore (PF)
AR008_ACTTGA_L1 1,518,208 0.13 0.22 4.00 100.00 311.45 +/-0.00 2.35 +/-0.00 0.91 +/-0.00 4.03 4.00 82.93 33.29
PhiX_TTAGGC_L1 49,104 0.13 0.22 0.58 100.00 311.45 +/-0.00 2.35 +/-0.00 0.91 +/-0.00 93.38 0.58 86.36 34.37

IVC Plots

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All Intensity Plots

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Mismatch Graphs

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Mismatch Curves

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Additional Paired Statistics

Barcode-Lane Info Relative Orientation Statistics Insert Size Statistics (for relative orientation R+) Insert Statistics (% of individually uniquely alignable pairs)
Barcode-Lane F-:
>R2 R1>		 F+:
>R1 R2>		 R-:
<R2 R1>		 R+:
>R1 R2<		 Total Median Below-median SD Above-median SD Low thresh. High thresh. Too small Too large Orientation and size OK
PhiX_TTAGGC_L1 13
(0.03%) 		8
(0.02%) 		993
(2.16%) 		44,862
(97.79%) 		45,876 196 26 31 84 272 58
(0.13%) 		62
(0.14%) 		44,742
(97.53%)

CASAVA-1.8.2