Sig_COVID19

Sig_COVID19 is a repository to share mutational signature data constructed from evolution of virus sequences (mainly SARS-CoV-2). Because virus genomes are often single stranded, this signature consists of 192-context, which is twice that of the COSMIC signature. This Repository also provides mutational signatures of various viruses in addition to SARS-CoV-2. The full lists of mutations and phylogenetic tree is also available.

You can download

• selected data
• all data of therepository

# Download phylogenetic tree data

wget https://github.com/ju-lab/SC2_evol_signature/raw/master/data/msa_0117.tree.gz
gzip -d msa_0117.tree.gz


# Download per sample information

wget https://github.com/ju-lab/SC2_evol_signature/raw/master/data/Per_sample_mutation_list.csv.gz
wget https://github.com/ju-lab/SC2_evol_signature/raw/master/data/GISAID_metadata.csv
wget https://github.com/ju-lab/SC2_evol_signature/raw/master/data/loglikelihood_to_be_root_and_outgroup_distance.csv


# Download annotated mutation information

wget https://github.com/ju-lab/SC2_evol_signature/raw/master/data/All_mutation_information.csv.gz


# Download all data

git clone https://github.com/ju-lab/SC2_evol_signature.git

Data format

The phylogenetic tree file is in the newick format with sample IDs (tip labels) and node names. These names are useful for indexing the mutation data. The tree file can be loaded on R with read.tree function in the ape package. The tree object can be further explored using ape, phangorn, and other R packages and softwares.

library(ape)
tree <- read.tree("msa_0117.tree")
plot(tree)

The mutation data is catalogued in Per_sample_mutation_list.csv.gz and All_mutation_information.csv.gz. And the specific mutations can be explored by their unique identifers matched through the dataset including the tree file.

# Per_sample_mutation_list.csv.gz

|ID             |Sampling_date |Country |...|Mutation_IDs 
|:--------------|:-------------|:-------|...|:-------------------------------------------------------------
|EPI_ISL_507764 |2020-03-26    |USA     |   |sbs_1059_AC>TC_351794_351743,sbs_25563_AG>TA_351795_351794, ..
|EPI_ISL_495656 |2020-04-16    |USA     |   |sbs_23374_CT>CT_351538_2,sbs_1059_AC>TC_351794_351743,sbs_2 ..
|EPI_ISL_483143 |2020-04-21    |Germany |...|ind_24685_T>-_351539_3,sbs_13011_AC>TA_351538_351539,sbs_18 ..
|EPI_ISL_483144 |2020-04-21    |Germany |   |sbs_13011_AC>TA_351538_351539,sbs_18326_GC>TT_351538_351539 ..
|EPI_ISL_738254 |2020-04-14    |USA     |   |sbs_1059_AC>TC_351794_351743,sbs_25563_AG>TA_351795_351794, ..
|EPI_ISL_507762 |2020-03-27    |USA     |   |sbs_1059_AC>TC_351794_351743,sbs_25563_AG>TA_351795_351794, ..



# All_mutation_information.csv.gz

|mutID                      |type |status 1   |status 2                                                                   |...
|:--------------------------|:----|:----------|:--------------------------------------------------------------------------|
|sbs_10_TT>GT_633183_329639 |SBS  |node281658 |hCoV-19/USA/LA-EVTL071/2020|EPI_ISL_451232|2020-05-04&|NorthAmerica        |
|sbs_11_TT>CA_357288_6016   |SBS  |node5763   |hCoV-19/USA/UT-UPHL-2012146142/2020|EPI_ISL_746962|2020-12-01|NorthAmerica |
|sbs_13_AT>AA_649653_348274 |SBS  |node298128 |hCoV-19/USA/CA-CSMC203/2020|EPI_ISL_824612|2020-12-27|NorthAmerica         |...
|sbs_13_AT>CA_631201_327314 |SBS  |node279676 |hCoV-19/USA/LA-EVTL1196/2020|EPI_ISL_768465|2020-12-11|NorthAmerica        |
|sbs_13_AT>CA_611678_611679 |SBS  |node260153 |node260154                                                                 |
|sbs_13_AT>CA_622041_317640 |SBS  |node270516 |hCoV-19/USA/LA-EVTL1375/2020|EPI_ISL_779041|2020-12-11|NorthAmerica        |

Citation

If you use Sig_COVID19, please cite: (will be updated)

Yi K. et al, 2021, Mutational spectrum of SARS-CoV-2 during the global pandemic, XXXXXXXXX XXX-XXXX