Consensus sequences
All consensus sequences will be deposited on GISAID and on NCBI under BioProject ID PRJNA612578. metadata.csv contains collection dates, location, originating labs and sequencing metrics: coverage and average depth.
| Location | Number of Sequences |
|---|---|
| 21 | |
| Alabama/Madison | 1 |
| Arizona/Maricopa | 3 |
| Arizona/Yuma | 1 |
| California/Alameda | 8 |
| California/Contra Costa | 3 |
| California/El Dorado | 1 |
| California/Fresno | 1 |
| California/Kern | 1 |
| California/Merced | 1 |
| California/Nevada | 2 |
| California/Placer | 1 |
| California/Sacramento | 1 |
| California/San Francisco | 3 |
| California/San Mateo | 1 |
| California/Santa Barbara | 3 |
| California/Santa Clara | 10 |
| California/Stanislaus | 1 |
| California/Ventura | 1 |
| Florida/Orange | 2 |
| Florida/Volusia | 1 |
| Illinois/Champaign | 1 |
| Iraq/Kurdistan/Duhok | 535 |
| Jordan/Amman | 483 |
| Jordan/Aqaba | 41 |
| Jordan/Irbid | 58 |
| Jordan/Mafraq | 2 |
| Jordan/Zarqa | 5 |
| Maryland/Montgomery | 1 |
| Mexico/Baja California | 26 |
| Mexico/Baja California Sur/Los Cabos | 1 |
| Mexico/Baja California/ | 1 |
| Mexico/Baja California/Ensenada | 58 |
| Mexico/Baja California/Mexicali | 426 |
| Mexico/Baja California/Reforma | 1 |
| Mexico/Baja California/Rosarito | 12 |
| Mexico/Baja California/San Quintin | 1 |
| Mexico/Baja California/Tecate | 9 |
| Mexico/Baja California/Tijuana | 1449 |
| Mexico/Chiapas/Baja California | 1 |
| Mexico/Chihuahua | 9 |
| Mexico/Chihuahua/Chihuahua | 40 |
| Mexico/Chihuahua/Ciudad Juarez | 61 |
| Mexico/Coahuila/Saltillo | 135 |
| Mexico/Coahuila/Torreon | 170 |
| Mexico/Durango/Durango | 4 |
| Mexico/Jalisco/Guadalajara | 93 |
| Mexico/Jalisco/Guadalajara Tetlan | 1 |
| Mexico/Jalisco/Puerto Vallarta | 53 |
| Mexico/Jalisco/Vallarta | 14 |
| Mexico/Jalisco/Zapopan | 4 |
| Mexico/Nuevo Leon/Guadalupe | 75 |
| Mexico/Nuevo Leon/Monterrey | 195 |
| Mexico/Nuevo Leon/San Nicolas De Los Garza | 116 |
| Mexico/Nuevo Leon/San Nicolas de los Garza | 65 |
| Mexico/Nuevo Leon/Santa Catarina | 45 |
| Mexico/Sinaloa/Culiacan | 453 |
| Mexico/Sinaloa/Los Mochis | 123 |
| Mexico/Sinaloa/Mazatlan | 107 |
| Mexico/Sonora | 32 |
| Mexico/Sonora/Hermosillo | 62 |
| Mexico/Sonora/Obregon | 66 |
| Mexico/Sonora/San Luis Rio Colorado | 35 |
| Mexico/Sonora/San Luis R������o Colorado | 2 |
| Mexico/Tamaulipas/Reynosa | 1 |
| Mexico/Tijuana | 1 |
| Mexico/Tlaxcala/Chiautempan | 1 |
| Michigan/Genesee | 1 |
| Minnesota/Dakota | 1 |
| Nebraska/Sarpy | 2 |
| Nevada/Clark | 4 |
| New Jersey/Union | 1 |
| New York/Bronx | 1 |
| New York/Kings | 1 |
| New York/New York | 1 |
| New York/Rensselaer | 1 |
| Oregon/Benton | 1 |
| Pakistan/Islamabad Capital Territory/Islamabad | 51 |
| Pakistan/Punjab/Lahore | 7 |
| Pennsylvania/Philadelphia | 1 |
| Texas/Collin | 1 |
| Texas/Fort Bend | 1 |
| USA/Alaska/Anchorage Municipality | 1 |
| USA/Arizona/Maricopa | 2 |
| USA/Arizona/Pima | 3 |
| USA/Arizona/Yuma | 1 |
| USA/California/ | 2 |
| USA/California/Alameda | 13 |
| USA/California/Bellflower | 1 |
| USA/California/City and County of San Francisco | 1 |
| USA/California/Contra Costa | 6 |
| USA/California/Cruise_Ship_1 | 8 |
| USA/California/Cruise_Ship_2 | 32 |
| USA/California/Davis | 1 |
| USA/California/Downey | 1 |
| USA/California/El Dorado | 5 |
| USA/California/Fresno | 2 |
| USA/California/Glenn | 1 |
| USA/California/Humboldt | 1 |
| USA/California/Imperial | 283 |
| USA/California/Inglewood | 1 |
| USA/California/Kern | 5 |
| USA/California/Long Beach | 1 |
| USA/California/Los Angeles | 503 |
| USA/California/Los Angeles | 1 |
| USA/California/Los Angeles County | 72 |
| USA/California/Madera | 1 |
| USA/California/Marin | 2 |
| USA/California/Mariposa | 1 |
| USA/California/Modesto | 1 |
| USA/California/Monterey | 2 |
| USA/California/Murrieta | 2 |
| USA/California/Napa | 1 |
| USA/California/Orange | 281 |
| USA/California/Orange County | 9 |
| USA/California/Placer | 11 |
| USA/California/RIverside | 1 |
| USA/California/Riverside | 651 |
| USA/California/Sacramento | 7 |
| USA/California/San Bernardino | 86 |
| USA/California/San Diego | 97948 |
| USA/California/San Francisco | 20 |
| USA/California/San Mateo | 59 |
| USA/California/Santa Barbara | 6 |
| USA/California/Santa Clara | 10 |
| USA/California/Santa Cruz | 1 |
| USA/California/Solano | 3 |
| USA/California/Sonoma | 1 |
| USA/California/Stanislaus | 1 |
| USA/California/Sutter | 1 |
| USA/California/Temecula | 1 |
| USA/California/Tulare | 1 |
| USA/California/Ventura | 5 |
| USA/Colorado/Boulder | 1 |
| USA/Florida/Saint Johns | 1 |
| USA/Hawaii/Honolulu | 1 |
| USA/Idaho/Ada | 1 |
| USA/Illinois/Cook | 2 |
| USA/Illinois/DuPage | 2 |
| USA/Illinois/Rock Island | 1 |
| USA/Indiana/Johnson | 1 |
| USA/Kentucky/Jefferson | 1 |
| USA/Louisiana/New Orleans | 143 |
| USA/Maryland/Anne Arundel | 1 |
| USA/Maryland/Montgomery | 1 |
| USA/Massachusetts/Middlesex | 1 |
| USA/Michigan/Wayne | 1 |
| USA/Minnesota/Anoka | 1 |
| USA/Minnesota/Ramsey | 1 |
| USA/Missouri/St. Louis | 1 |
| USA/Nevada/Clark | 1 |
| USA/Nevada/Douglas | 1 |
| USA/New Jersey/Monmouth | 1 |
| USA/New York/Dutchess | 1 |
| USA/New York/Orange | 1 |
| USA/New York/Warren | 1 |
| USA/New York/Westchester | 1 |
| USA/North Carolina/Durham | 1 |
| USA/Ohio/Clark | 1 |
| USA/Ohio/Hamilton | 1 |
| USA/Oklahoma/Tulsa | 1 |
| USA/Oregon/Klamath | 1 |
| USA/Pennsylvania/Allegheny | 1 |
| USA/Pennsylvania/Erie | 1 |
| USA/Pennsylvania/Montgomery | 1 |
| USA/South Carolina/Spartanburg | 1 |
| USA/Tennessee/Grainger | 1 |
| USA/Tennessee/Sumner | 1 |
| USA/Texas/Bell | 1 |
| USA/Texas/Montgomery | 2 |
| USA/Utah/Salt Lake | 1 |
| USA/Virginia/Fairfax | 1 |
| USA/Washington/King | 3 |
| USA/Washington/Kitsap | 1 |
| USA/West Virginia/Kanawha | 1 |
| USA/Wisconsin/Bayfield | 1 |
| USA/Wisconsin/Dane | 1 |
| USA/Wyoming/Albany | 1 |
| Utah/Utah | 1 |
| Virginia/Arlington | 2 |
| Virginia/Northumberland | 1 |
Raw read files
Raw read files for both Illumina and Oxford Nanopore data are available on,
- Google cloud.
- SRA under BioProject ID: PRJNA612578.
The sequencing is being performed using an amplicon-based sequencing scheme using PrimalSeq with artic nCoV-2019 scheme.
Nanopore data was processed using the artic-nCoV019 pipeline with minimap2 and medaka. Illumina data was processed using iVar (Grubaguh et al. Genome Biology 2019) with bwa.
Disclaimer. Please note that this data is still based on work in progress and should be considered preliminary. If you intend to include any of these data in publications, please let us know – otherwise please feel free to download and use without restrictions. We have shared this data with the hope that people will download and use it, as well as scrutinize it so we can improve our methods and analyses. Please contact us if you have any questions or comments – we’ll buy beers for #ResearchParasites that spot flaws and faults in the data and come up with improvements!
Andersen Lab The Scripps Research Institute La Jolla, CA, USA [email protected]
