Sequencing data

We have an open data release policy and links to datasets will be made available as soon as we produce them.

Validation data

MP1751

We have sequenced the MP1751 strain of Zika virus. This virus was originally described by Haddow [1] and has undergone several rounds of passage. This work was performed in collaboration with Public Health England. The Illumina-generated consensus sequence is available from this site (data generated by Steve Pullan, Richard Vipond, Miles Carroll and colleagues at Public Health England)

WHO reference strain

We have sequenced the proposed WHO reference strain from French Polynesia (closely related to Brazilian strains) using the latest version of our multiplexed PCR protocol. The strain was kindly supplied by Sally Baylis from the Paul-Ehrlich-Instiut. The Illumina generated consensus sequence is available in Genbank (accession KX369547.1).

Road trip data

Below are links to MinION R9 reads basecalled with Metrichor that fall into the ‘pass’ folder, i.e. meet a quality threshold and are successfully demultiplexed. Only reads that map to the Zika genome are included. Not all runs have yet completed basecalling, so they may represent a subset of the total available reads. Each PCR run contains a negative water control which is sequenced (not necessarily on each flowcell).

Flowcell 1

Date: 4th June Location: Natal

Barcode 2D pass reads Mapped reads Covered bases (cov>=1) Covered bases (cov>=20) link
NB01 5952 676 3719 2070 FAST5 mapped
NB02 2361 822 2859 708 FAST5 mapped
NB03 4082 1258 4481 2601 FAST5 mapped
NB04 1554 311 4750 356 FAST5 mapped
NB05 4256 1584 4934 2265 FAST5 mapped
NB06 2406 477 5145 1853 FAST5 mapped
NB07 2442 492 5572 2499 FAST5 mapped
NB08 4246 700 4785 834 FAST5 mapped
NB09 3049 1014 5233 2698 FAST5 mapped
NB10 6446 1148 6416 3859 FAST5 mapped
NB11 7078 1602 6147 3837 FAST5 mapped
NB12 2231 860 5043 1182 FAST5 mapped

Flowcell 2

Date: 4th June Location: Natal

Barcode 2D pass reads Mapped reads Covered bases (cov>=1) Covered bases (cov>=20) link
NB01 2496 433 4783 1704 FAST5 mapped
NB02 1675 602 7347 1836 FAST5 mapped
NB03 1821 344 5158 1351 FAST5 mapped
NB04 98 22 4458 0 FAST5 mapped
NB05 2604 541 7048 2572 FAST5 mapped
NB06 2424 68 5216 308 FAST5 mapped
NB07 2788 2059 9408 6891 FAST5 mapped
NB08 3016 2878 10332 8789 FAST5 mapped
NB09 2291 2235 10333 8957 FAST5 mapped
NB10 2660 479 6396 2466 FAST5 mapped
NB11 2442 122 7611 303 FAST5 mapped
NB12 2015 364 8002 2746 FAST5 mapped

Flowcell 3

Date: 6th June Location: Joao Pessoa

Barcode 2D pass reads Mapped reads Covered bases (cov>=1) Covered bases (cov>=20) link
NB01 3414 1717 8236 6254 FAST5 mapped
NB02 3565 1421 7708 4251 FAST5 mapped
NB03 2606 1401 8653 4834 FAST5 mapped
NB04 4609 1164 7892 5326 FAST5 mapped
NB05 4001 2363 8359 6590 FAST5 mapped
NB06 4683 1511 8566 5385 FAST5 mapped
NB07 3160 361 6657 2377 FAST5 mapped
NB08 3275 46 4337 0 FAST5 mapped
NB09 288 121 7108 326 FAST5 mapped
NB10 2277 293 6064 2108 FAST5 mapped
NB11 56 13 3190 0 FAST5 mapped

Flowcell 4

Date: 7th June Location: Joao Pessoa

Barcode 2D pass reads Mapped reads Covered bases (cov>=1) Covered bases (cov>=20) link
NB01 293 56 3527 54 FAST5 mapped
NB02 3592 329 4117 1477 FAST5 mapped
NB03 2617 108 3299 737 FAST5 mapped
NB04 3670 991 8300 5379 FAST5 mapped
NB05 14586 704 3281 746 FAST5 mapped
NB06 4231 53 3742 224 FAST5 mapped
NB07 6881 470 4390 1890 FAST5 mapped
NB08 27 3 755 0 FAST5 mapped
NB09 25 0 0 0 FAST5 mapped
NB10 3527 703 7671 3354 FAST5 mapped
NB11 2939 250 4741 1489 FAST5 mapped
NB12 647 68 2469 318 FAST5 mapped

Flowcell 5

Date: 10th June Location: Recife

Barcode 2D pass reads Mapped reads Covered bases (cov>=1) Covered bases (cov>=20) link
NB01 2073 452 4236 1308 FAST5 mapped
NB02 3152 612 2912 1862 FAST5 mapped
NB03 2597 258 3384 351 FAST5 mapped
NB04 2398 277 2069 628 FAST5 mapped
NB05 2770 272 3522 669 FAST5 mapped
NB06 2903 319 4187 1060 FAST5 mapped
NB07 3112 132 3837 319 FAST5 mapped
NB08 954 432 339 329 FAST5 mapped

References

[1] Haddow, A. J., Williams, M. C., Woodall, J. P., Simpson, D. I. H., & Goma, L. K. H. (1964). Twelve isolations of Zika virus from Aedes (Stegomyia) africanus (Theobald) taken in and above a Uganda forest. Bulletin of the World Health Organization, 31(1), 57–69.