Completed Genetic Samples

Results of rapid genetic identification of outmigrating juvenile Chinook salmon (Oncorhynchus tshawytscha) collected at RST sites across the Sacramento River Basin (water years 2022–2026). Run assignments are derived from SHERLOCK and GT-seq analyses, with associated capture metadata and length-at-date (LAD)-based field assignments.

completed_genetic_samples

Format

A data frame with 7,477 rows and 24 variables:

sample_id

character. Unique identifier of the sample processed. Composed of location code, season, sample event, sample bin (size class), and sample number separated by an underscore.

datetime_collected

POSIXct. Date and time of sample collection (format: YYYY-MM-DD hh:mm:ss). Range: 2022-01-10 to 2025-05-11.

fork_length_mm

numeric. Fork length of the sampled fish, in millimeters. Range: 23–176.

field_run_type

character. Run type assigned in the field using length-at-date (LAD) criteria. One of: FALL, LATEFALL, SPRING, WINTER, UNKNOWN, NA.

final_run_designation

character. Final run type assigned via combined SHERLOCK and GT-seq analysis. One of: FALL OR LATE FALL, SPRING, GREB1L HETEROZYGOTE, WINTER.

shlk_chr28_genotype

character. SHERLOCK genotype result at the Greb1L locus on chromosome 28 (OTS28), indicating early- vs. late-migration timing. One of: EARLY, LATE, HETEROZYGOTE, NA.

shlk_chr16_genotype

character. SHERLOCK genotype result at the OTS16 locus on chromosome 16, used to differentiate spring-run and winter-run individuals among early-migrating fish. One of: SPRING, WINTER, INDETERMINATE, NA.

shlk_run_designation

character. Run designation derived from SHERLOCK genetic assay results and decision logic. One of: SPRING, EARLY/LATE HETEROZYGOUS, SPRING/WINTER, FALL/LATEFALL, WINTER, NA.

gtseq_chr28_geno

character. GT-seq genotype at the Greb1L locus on chromosome 28, indicating early- vs. late-migration timing. One of: EARLY, LATE, HETEROZYGOTE, NA.

pop_structure_id

character. Central Valley salmonid population structure assignment from GT-seq (RUBIAS). One of: FALL, LATEFALL, SPRING, WINTER, NA.

cv_fall

numeric. Summed posterior assignment probability (PofZ) to the Central Valley Fall reporting unit. Range: 0–1.

cv_late_fall

numeric. Summed posterior assignment probability (PofZ) to the Central Valley Late Fall reporting unit. Range: 0–1.

cv_spring

numeric. Summed posterior assignment probability (PofZ) to the Central Valley Spring reporting unit. Range: 0–1.

cv_winter

numeric. Summed posterior assignment probability (PofZ) to the Central Valley (Sacramento River) Winter reporting unit. Range: 0–1.

tributary

character. Spring-run tributary assignment from RUBIAS. One of: ButteSp, Feather River Lineage Spring, MillDeerSp, NA.

buttefall

numeric. Posterior assignment probability (PofZ) to the Butte River Fall reporting unit. Range: 0–1.

frh_fall

numeric. Posterior assignment probability (PofZ) to the Feather River Hatchery Fall reporting unit. Range: 0–1.

frh_sp

numeric. Posterior assignment probability (PofZ) to the Feather River Hatchery Spring reporting unit. Range: 0–1.

mill_deer_fall

numeric. Posterior assignment probability (PofZ) to the Mill/Deer Fall reporting unit. Range: 0–0.999.

san_joaquin_fall

numeric. Posterior assignment probability (PofZ) to the San Joaquin Fall reporting unit. Range: 0–1.

butte_sp

numeric. Posterior assignment probability (PofZ) to the Butte River Spring reporting unit. Range: 0–1.

mill_deer_sp

numeric. Posterior assignment probability (PofZ) to the Mill/Deer Spring reporting unit. Range: 0–1.

coleman_f

numeric. Posterior assignment probability (PofZ) to the Coleman Hatchery Fall reporting unit. Range: 0–1.

sac_win

numeric. Posterior assignment probability (PofZ) to the Sacramento River Winter reporting unit. Range: 0–1.

Source

California Department of Water Resources (DWR) and partners. EDI Data Package edi.2335.1. https://portal.edirepository.org/nis/mapbrowse?packageid=edi.2335.1