Salmonella pangenome graph and variant call data for 539,283 genomesDescription:Salmonella enterica causes human disease and decreases agricultural production. The overall goals of this project is to generate a large database of S. enterica variants with 539,283 samples and 236,069 features for applications in machine learning and genomics. We transformed single nucleotide polymorphism (SNP) data into reduced dimensional representations which are tolerant of missing data based on disentangled variational autoencoders. TFRecord files were made with custom Python scripts that parsed the variant call formats (VCF) into sparse tensors and combined them with the Salmonella In Silico Typing Resource (SISTR) serotype data.The data directory contains:The tar file of TFRecords: tfrecords.tar (103 GB). The TFRecords are organized first by how they were genotyped. mpileup records were created with Mpileup, and the gvg records were created with graph variant calling. In each of these directories batches of ~10,000 sequence reads named Sra10k_XX.tfrecord.gz (00--54). File Sra10k_99.tfrecord.gz contains incomplete SRAs. Each TFRecord contains the shape of the tensor, the indices of non-zero variants, sample name, serotype, and sparse values. Value 99 was assigned to '.' records.The file output.tar (11.4 TB) contains the .vcf files used to create the TFRecords above. The data in here is contained more succinctly in the TTFrecord format. This data will not normally be used.A tar file of metadata files for the samples, metadata (95 MB). Sequence read archive (SRA) accessions were downloaded using edirect/eutilities and saved as SraAccList.txt.esearch -db sra -query "txid28901[Organism:exp] AND (cluster_public[prop] AND 'biomol dna'[Properties] AND 'library layout paired'[Properties] AND 'platform illumina'[Properties] AND 'strategy wgs'[Properties] OR 'strategy wga'[Properties] OR 'strategy wcs'[Properties] OR 'strategy clone'[Properties] OR 'strategy finishing'[Properties] OR 'strategy validation'[Properties])" | efetch -format runinfo -mode xml | xtract -pattern Row -element Run > SraAccList.txtGoogle BigQuery was used to download metadata for the SRA accessions from the National Institute of Health (NIH).SELECT * FROM nih-sra-datastore.sra.metadata as metadata INNER JOIN {table_id} as leiacc ON metadata.acc = leiacc.accID;Files were processed into batches of ~10,000 and named Sra_completed_XX.csv (00--53).A VCF document mapping the TFRecord data to the positions in the graph subjected to the Type strain LT2: mapping/DRR452337.gvg.vcf-with_TFRecord_in_1st_column.txtScripts for creating and reading TFRecord data: code.reading_and_parsing_fns.py defines functions for converting VCFs of variants called using gvg to sparse tensors and makes the TFRecord files.gvg_to_tfrecord.py creates TFRecords from from the sparse tensors.Tutorial for using the TFRecords: Example_logistic_regression.mdPangenome graph files and references used for variant calling and genotyping: pangenome.refPlus100.fasta.gz which contains the genomes of the 101 Salmonella strains without plasmids used for construction of the pangenome graph.salm.100.NC_003197_v2.d2_complete.gfa.gz The complete 101 Salmonella strain pangenome graph in Graphical Fragment Assembly (GFA2) Format 2.0 including alt nodes used for genotypingsalm.100.NC_003197_v2.full.gfa.gz the full graph including alt nodes.salm.100.NC_003197_v2.full.vcf.gz A VCF of the file abovegenotyped.gvg.vcf the genotype calls in vcf formatpaths.txt the paths of the graphSCINet users: The data folder can be accessed/retrieved with valid SCINet account at this location: /LTS/ADCdatastorage/NAL/published/node28083194/See the SCINet File Transfer guide for more information on moving large files: https://scinet.usda.gov/guides/data/datatransferGlobus users: The files can also be accessed through Globus by following this data link. The user will need to log in to Globus in order to access this data. User accounts are free of charge with several options for signing on. Instructions for creating an account are on the login page.

Jordan: PISA science scores: The latest value from 2022 is 374.527 index points, a decline from 429.252 index points in 2018. In comparison, the world average is 449.005 index points, based on data from 78 countries. Historically, the average for Jordan from 2006 to 2022 is 409.863 index points. The minimum value, 374.527 index points, was reached in 2022 while the maximum of 429.252 index points was recorded in 2018.

Business Applications for Michigan was 47.86000 % Chg. from Yr. Ago in August of 2025, according to the United States Federal Reserve. Historically, Business Applications for Michigan reached a record high of 700.00000 in January of 2013 and a record low of -88.85000 in January of 2025. Trading Economics provides the current actual value, an historical data chart and related indicators for Business Applications for Michigan - last updated from the United States Federal Reserve on November of 2025.

Business Applications for Kentucky was 1280.00000 Number in August of 2025, according to the United States Federal Reserve. Historically, Business Applications for Kentucky reached a record high of 1520.00000 in August of 2025 and a record low of 30.00000 in January of 2012. Trading Economics provides the current actual value, an historical data chart and related indicators for Business Applications for Kentucky - last updated from the United States Federal Reserve on November of 2025.

The Philippines: Political corruption index: The latest value from 2024 is 0.849 index points, an increase from 0.83 index points in 2023. In comparison, the world average is 0.483 index points, based on data from 171 countries. Historically, the average for the Philippines from 1960 to 2024 is 0.782 index points. The minimum value, 0.711 index points, was reached in 1992 while the maximum of 0.89 index points was recorded in 1979.

United States - Covered Employment was 153186715.00000 Number in November of 2025, according to the United States Federal Reserve. Historically, United States - Covered Employment reached a record high of 153186715.00000 in October of 2025 and a record low of 52631500.00000 in January of 1972. Trading Economics provides the current actual value, an historical data chart and related indicators for United States - Covered Employment - last updated from the United States Federal Reserve on November of 2025.

Global trade data of Graph under 293399, 293399 global trade data, trade data of Graph from 80+ Countries.

Information Earnings in Nevada was 3186151.00000 Thous. of $ in April of 2025, according to the United States Federal Reserve. Historically, Information Earnings in Nevada reached a record high of 3186151.00000 in April of 2025 and a record low of 738452.00000 in January of 1998. Trading Economics provides the current actual value, an historical data chart and related indicators for Information Earnings in Nevada - last updated from the United States Federal Reserve on December of 2025.

Spain: Internet users, percent of population: The latest value from 2023 is 95.4 percent, an increase from 94.5 percent in 2022. In comparison, the world average is 72.46 percent, based on data from 177 countries. Historically, the average for Spain from 1990 to 2023 is 46.36 percent. The minimum value, 0.01 percent, was reached in 1990 while the maximum of 95.4 percent was recorded in 2023.

Graph and download economic data for Market Yield on U.S. Treasury Securities at 30-Year Constant Maturity, Quoted on an Investment Basis (DGS30) from 1977-02-15 to 2025-11-28 about 30-year, maturity, Treasury, interest rate, interest, rate, and USA.

United States - M1 (DISCONTINUED) was 18105.10000 Bil. of $ in February of 2021, according to the United States Federal Reserve. Historically, United States - M1 (DISCONTINUED) reached a record high of 18151.40000 in January of 2021 and a record low of 273.40000 in January of 1975. Trading Economics provides the current actual value, an historical data chart and related indicators for United States - M1 (DISCONTINUED) - last updated from the United States Federal Reserve on November of 2025.

San Marino: PISA math scores: The latest value from is index points, unavailable from index points in . In comparison, the world average is 0.000 index points, based on data from countries. Historically, the average for San Marino from to is index points. The minimum value, index points, was reached in while the maximum of index points was recorded in .

Consumption as percent of GDP in the USA, June, 2025 The most recent value is 68.13 percent as of Q2 2025, an increase compared to the previous value of 67.81 percent. Historically, the average for the USA from Q1 1960 to Q2 2025 is 64.03 percent. The minimum of 58.06 percent was recorded in Q1 1967, while the maximum of 68.97 percent was reached in Q4 2024. | TheGlobalEconomy.com

Hungary: Rural population, percent of total population: The latest value from 2024 is 26.82 percent, a decline from 27.14 percent in 2023. In comparison, the world average is 38.30 percent, based on data from 196 countries. Historically, the average for Hungary from 1960 to 2024 is 34.92 percent. The minimum value, 26.82 percent, was reached in 2024 while the maximum of 44.09 percent was recorded in 1960.

Business confidence survey in Belgium, October, 2025 The most recent value is -9.1 points as of October 2025, a decline compared to the previous value of -7.9 points. Historically, the average for Belgium from September 2017 to October 2025 is -6.64 points. The minimum of -36.1 points was recorded in April 2020, while the maximum of 10.1 points was reached in July 2021. | TheGlobalEconomy.com

Initial Claims in Minnesota was 4228.00000 Number in October of 2025, according to the United States Federal Reserve. Historically, Initial Claims in Minnesota reached a record high of 115773.00000 in March of 2020 and a record low of 1820.00000 in September of 1999. Trading Economics provides the current actual value, an historical data chart and related indicators for Initial Claims in Minnesota - last updated from the United States Federal Reserve on November of 2025.

Vietnam: Forest area, percent of total land area: The latest value from 2023 is 47.4 percent, an increase from 47.2 percent in 2022. In comparison, the world average is 31.6 percent, based on data from 194 countries. Historically, the average for Vietnam from 1990 to 2023 is 40 percent. The minimum value, 28.8 percent, was reached in 1990 while the maximum of 47.4 percent was recorded in 2023.

Homeownership Rate for Missouri was 70.50% in January of 2024, according to the United States Federal Reserve. Historically, Homeownership Rate for Missouri reached a record high of 74.80 in January of 2002 and a record low of 63.70 in January of 1989. Trading Economics provides the current actual value, an historical data chart and related indicators for Homeownership Rate for Missouri - last updated from the United States Federal Reserve on November of 2025.

Turkey: Financial markets development, depth: The latest value from 2021 is 0.421 index points, a decline from 0.449 index points in 2020. In comparison, the world average is 0.255 index points, based on data from 157 countries. Historically, the average for Turkey from 1985 to 2021 is 0.228 index points. The minimum value, 0.021 index points, was reached in 1985 while the maximum of 0.449 index points was recorded in 2020.

Vietnam: Gold production in kilograms: The latest value from 2023 is 956 kilograms, an increase from 600 kilograms in 2022. In comparison, the world average is 35695 kilograms, based on data from 91 countries. Historically, the average for Vietnam from 2001 to 2023 is 1863 kilograms. The minimum value, 164 kilograms, was reached in 2014 while the maximum of 3500 kilograms was recorded in 2010.