This Boocock_GenomicEpidemiologyLACOVID2020_BMCReadme.txt file was generated on 2021-12-14 by James Boocock 

GENERAL INFORMATION

1. Title of Dataset: Genomic epidemiology of the Los Angeles COVID-19 outbreak and the early history of the B.1.43 strain in the US.

2. Author Information
	A. Principal Investigator Contact Information
		Name: Leonid Kruglyak 
		Institution: UCLA
		Address: Department of Human Genetics, David Geffen School of Medicine
		Email: lkruglyak@mednet.ucla.edu

	C. Alternate Contact Information
		Name: James Boocock 
		Institution: UCLA
		Address: Department of Human Genetics, David Geffen School of Medicine
		Email: james.boocock@ucla.edu

3. Date of data collection (single date, range, approximate date):
    2020 

4. Geographic location of data collection: 
    Los Angeles County

5. Information about funding sources that supported the collection of the data:
    We thank the UCLA David Geffen School of Medicine Dean Office for their support, the Fast Grants, Inc for funding of this work. A generous donation was provided by Jane Semel. This work was supported by funding from the Howard Hughes Medical Institute (to LK) and Damon Runyon Cancer Research Foundation (DFS-43-20 to YY). 


DATA & FILE OVERVIEW

1. File List: 
data
├── Duplicate\ Sent\ Genomes_Deidentified.csv
├── all.fasta (Our LA processed V-seq and NEB genomes)
├── all_3_none.fasta
├── all_sequences2.fasta (Our LA genomes that were submitted to gisaid)
├── b_1_43_lockdown.log (Beast log file for estimating the effective population size before and after LA's lockdown)
├── branch_lengths.json
├── gisaid
│   ├── good_genomes.txt
│   ├── metadata_2020-07-10_23-53.tsv (metadata for the gisaid sequences used in our analysis)
│   └── sequences_2020-07-10_23-53.fasta (gisaid sequences used in analysis)
├── lineages.csv (Phased B.1.43 genome lineages)
├── lineages_merged.csv (Gisaid and LA genome pangolin lineages)
├── long_sample_list_august19th.csv (Sample contamination list)
├── nextstrain_ncov_la_all_b_one_two_timetree.nwk (B.1.43 timetree with LA and other genomes)
├── nextstrain_ncov_la_all_b_one_two_tree.nwk (B.1.43 mutation tree with LA and other genomes)
├── nextstrain_ncov_north-america_usa_los-angeles_hets_curate_three_timetree.nwk (Timetree of all LA genomes along with worldwide samples)
├── nextstrain_ncov_north-america_usa_los-angeles_hets_curate_three_tree.nwk (Mutation tree of all LA genomes along  with worldwide samples)
├── nt_muts.json (json mutation list for all the LA and other strains)
├── phased.fasta (Phased B.1.43 genomes LA)
├── phased_genomes_two_lineages.fasta (Phased B.1.43 genomes)
├── qc_report.tsv (QC report for our datasets, used to filter genomes)
└── tree_json_b_1_43.json (B.1.43 tree in JSON format)

METHODOLOGICAL INFORMATION

1. Description of methods used for collection/generation of data: 
Refer to the methods section of the paper "Genomic epidemiology of the Los Angeles COVID-19 outbreak and the early history of the B.1.43 strain in the US" for a detailed description of how the data was generated.

2. Methods for processing the data: 
Refer to the methods section of the paper "Genomic epidemiology of the Los Angeles COVID-19 outbreak and the early history of the B.1.43 strain in the US" for a detailed description of how the data was generated.

3. Instrument- or software-specific information needed to interpret the data: 
The 'analysis_scripts' folder that can be found at our github has scripts for processing everything in this dataset https://github.com/theboocock/COVID-NGS2


DATA-SPECIFIC INFORMATION FOR: Duplicate\ Sent\ Genomes_Deidentified.csv

1. Number of variables:  6

2. Number of cases/rows: 66

3. Variable List: 
<list variable name(s), description(s), unit(s)and value labels as appropriate for each>
id, unique idenntifier, string
test, type of test, string
specdate, data specimen collected, date
spec, type of specimen, string
date, date test taken, date
group, duplicate group, string

4. Missing data codes: 

5. Specialized formats or other abbreviations used: 


DATA-SPECIFIC INFORMATION FOR: gisaid/good_genomes.txt 
<repeat this section for each dataset, folder or file, as appropriate>

List of GISAID genomes that passed our filter

1. Number of variables: 1

2. Number of cases/rows: 59982 

3. Variable List: 
<list variable name(s), description(s), unit(s)and value labels as appropriate for each>
gisaid id, gisaid IDs,  string
4. Missing data codes: 
<list code/symbol and definition>n

5. Specialized formats or other abbreviations used: 

DATA-SPECIFIC INFORMATION FOR: gisaid/metadata_2020-07-10_23-53.tsv 
<repeat this section for each dataset, folder or file, as appropriate>

1. Number of variables:  26

2. Number of cases/rows: 62,644

3. Variable List: 
<list variable name(s), description(s), unit(s)and value labels as appropriate for each>

strain, strain name, string
virus, virus name, string
gisaid_epi_isl, gisaid epi isl, string
genbank_accession, genbank accession if it exists, string
date, date genome collected, string
region, region where genome was collected, string
country, country where genome was collected, string
division, division where genome was collected, string
location, location where genome was collected, string
region_exposure, region where exposure occurred, string
conutry_exposure, countryy where exposure occurred, string
division_exposure, division where exposure occurred, string
segment, sequence segement usually genome, string
length, length of sequence, number
host, host where virus was collected, string
age, age of host, number
sex, sex of host, string
pangolin_lineage, pangolin lineage, string
GISAID_clade, GISAID clade assignment, string
originating_lab, lab that collected the specimen, string
submitiing_lab, lab that submitted the specimen, string
authors, authors of the genome, string
url, url where genome was downloaded, string
title, manuscript title, string
paper_url, url of paper that goes with the genomes, string
date_submitted, date genomes where submitted to GISAID, string

4. Missing data codes: 
<list code/symbol and definition>
?, missing

5. Specialized formats or other abbreviations used: 

DATA-SPECIFIC INFORMATION FOR: lineages.csv
<repeat this section for each dataset, folder or file, as appropriate>

1. Number of variables: 6

2. Number of cases/rows: 22

3. Variable List: 
<list variable name(s), description(s), unit(s)and value labels as appropriate for each>
taxon, sample name, string
lineage, pangolin lineage, string
probability, probability of assignment, number
pangoLEARN_version, version of pangoLEARN used to assign lineage, string
status, status of lineage assignment, string
note, note about sample, string

4. Missing data codes: 
<list code/symbol and definition>n

5. Specialized formats or other abbreviations used: 

DATA-SPECIFIC INFORMATION FOR: lineages_merged.csv
<repeat this section for each dataset, folder or file, as appropriate>

1. Number of variables: 6

2. Number of cases/rows: 22

3. Variable List: 
<list variable name(s), description(s), unit(s)and value labels as appropriate for each>
taxon, sample name, string
lineage, pangolin lineage, string
probability, probability of assignment, number
pangoLEARN_version, version of pangoLEARN used to assign lineage, string
status, status of lineage assignment, string
note, note about sample, string

4. Missing data codes: 
<list code/symbol and definition>n

5. Specialized formats or other abbreviations used: 

DATA-SPECIFIC INFORMATION FOR: lineages_merged.csv 
<repeat this section for each dataset, folder or file, as appropriate>

1. Number of variables: 

2. Number of cases/rows: 

3. Variable List: 
<list variable name(s), description(s), unit(s)and value labels as appropriate for each>

4. Missing data codes: 
<list code/symbol and definition>n

5. Specialized formats or other abbreviations used: 


DATA-SPECIFIC INFORMATION FOR: long_sample_list_august19th.csv
<repeat this section for each dataset, folder or file, as appropriate>

1. Number of variables: 7 

2. Number of cases/rows: 15

3. Variable List: 
<list variable name(s), description(s), unit(s)and value labels as appropriate for each>
merged_id, sample id, string
uid, universal identifier, string
ct, qPCR ct value, strig
het_sample_count, number of het sites, number
date_fix, date of collection, date
lib_type, sequencing library type, string
p1, sequencing primer 1, strig

4. Missing data codes: 
<list code/symbol and definition>n

5. Specialized formats or other abbreviations used: 

DATA-SPECIFIC INFORMATION FOR: qc_report.tsv 
<repeat this section for each dataset, folder or file, as appropriate>

1. Number of variables: 107

2. Number of cases/rows: 260

3. Variable List: 
<list variable name(s), description(s), unit(s)and value labels as appropriate for each>
merged_id, sample id, string
mapped_human, number of reads mapping to the human genome, number
mapped_rrna, number of reads mapping to the human rRNA locus, number
mapped_sars2_dedup, number of reads mapping to the sars2 genome after PCR deduplication, number
mapped_sars2_dedup, number of reads mapping to the sars2 genome without PCR deduplication, number
unmapped, number of unmapped reads, number of unmappped reads, number
total_read_count, total number of reads, number
sars2_percent_dup, percentage of reads mapping to the sars2 genome after PCR deduplication, number
sars2_percent_dedup, percentage of reads mapping to the sars2 genome without PCR deduplication, number
coverage_3x, coverage of the sars2 genome at >= 3x, number
read_group_name, read group name in bam, string
uid_lib, unique sample identifier and library type combination, string
lib_names, library names mapped, string
fastqs_one, read one fastq location, string
fastqs_two, read two  fastq location, string
library_id_internal, internal library id, string 
coverage_mean_dedup, mean sars2 genome coverage after PCR deduplication, number
coverage_mean_no_dedup, mean sars2 genome coverage without PCR deduplication, number
coverage_5x, coverage of the sars2 genome at >= 5x, number
taxon, sample name alternative, string
lineage, pangolin lineage, string
probability, pangolin assignment probability, number
pangoLEARN_version, version of pangoLEARN used to assign lineages, string
status, status of the pangoLEARN analysis, string
note, note from the pangoLEARN analysis, string
pangolin_phased, pangolin lineage from the phased data, string
prob_phased, probability of assignment from the phased data, string
gisaid_phased, gisaid lineage for the phased genomes, string
uid, unique sample identifier, string
lib_name_short, short library name, string
uid.x, uid duplicate column, string
sample_type, sample type, string
virus, virus type, string
gisaid_epi_isl, gisaid id, string
gennbak_accession, genbank accession, string
region, region where genome was collected, string
division, division where genome was collected, string
location, location where genome was collected, string
region_exposure, region where person was exposed, string
country_exposure, country where genome was exposed, string
division_exposure, division where genome was exposed, string
segment, sequenced segment, string
length, sequence length, string
host, virus host, string
age, host age, number
sex, host sex, string
originating_lab, lab where sample originated, string
submitting_lab, lab where sample was submitted, string
authors, authors of paper, string
url, url where samples were found, string
title, paper title, string
date_submitted, date sample submitted, string
library_type, sequencing library type, string
uid_sample_type, uid combined with the library type, string
id_library_type, uid combied with the library type, string
sample_name_fasta, sample name of strain in the fasta files, string 

4. Missing data codes: 
<list code/symbol and definition>n

5. Specialized formats or other abbreviations used: