PPD_0039BY5.2

Display Name: Georgia/PPD_0039BY5.2/2023-01-01

Karan, L. S.; Perekopskaya, N. E.; Morozkin, E. S.; Roev, G. V.

Submission details

Submission ID

PP116320.1.L/PP116319.1.M/PP116318.1.S

Submitting group

Automated Ingest from INSDC/NCBI Virus by Loculus

Date submitted

2025-02-03 16:47:40 UTC

Date released

2025-02-03 16:48:04 UTC

Data use terms

Changed	User	Data Use Terms
2024-11-19 16:17	insdc_ingest_user	OPEN

OPEN

Data use terms URL

https://pathoplexus.org/about/terms-of-use/open-data

Authors

Author affiliations

Central Research Institute of Epidemiology, Department of Molecular Diagnostic and Epidemiology

INSDC

Bioproject accession

Biosample accession

INSDC accession L

INSDC accession M

INSDC accession S

Raw reads accession

NCBI release date

2024-02-10

Alignment and QC metrics L

Completeness L

99.87%

Length L

12124

Total ambiguous nucs L

Total deleted nucs L

Total frame shifts L

Total inserted nucs L

Total SNPs L

1304

Total unknown nucs L

Alignment and QC metrics M

Completeness M

99.59%

Frame shifts M

GPC:31-32(nt:183-188)

Length M

5342

Total ambiguous nucs M

Total deleted nucs M

Total frame shifts M

Total inserted nucs M

Total SNPs M

1034

Total unknown nucs M

Alignment and QC metrics S

Completeness S

98.86%

Length S

1658

Total ambiguous nucs S

Total deleted nucs S

Total frame shifts S

Total inserted nucs S

Total SNPs S

241

Total unknown nucs S

Sample details

Earliest release date

2024-02-10

Collection country

Georgia

Collection date

2023

Collection date (lower bound)

2023-01-01

Collection date (upper bound)

2023-12-31

Isolate name

GE/Ser-H/2023

Host

Host name scientific

Homo sapiens

Host taxon id

9606

Nucleotide mutations

Mutations called relative to the NC_005301.3, NC_005300.2 & NC_005302.1 references

Substitutions

L

L:G23T

L:A35G

L:A42T

L:G43C

L:T47G

L:T49C

L:A53G

L:T58C

L:C59T

L:C63G

L:C64G

L:T66C

L:A72G

L:A73C

L:A91G

L:G93A

L:C100T

L:A109G

M

M:T40A

M:G50A

M:A51G

M:G62C

M:T65C

M:T67C

M:T68C

M:A69G

M:T71A

M:G76T

M:A80G

M:T83C

M:G84A

M:T86C

M:C92T

M:T100C

M:T102C

M:C103T

S

S:T49C

S:A50T

S:G54A

S:G76A

S:T79C

S:A81G

S:G99A

S:G100A

S:A109G

S:C115T

S:A121G

S:G134A

S:C142T

S:T157C

S:C166T

S:G171A

S:T175A

S:C178A

Deletions

L:11975-11982, L:12029, L:12078, L:12084, L:12099, M:167-169, M:189, M:197-199, M:321-323, S:1542-1547, S:1630-1633

Insertions

ins_S:1667:CTTC, ins_S:1563:TATG, ins_S:1566:AT, ins_S:1577:A, ins_S:1620:C, ins_S:1609:TTC, ins_M:5171:T, ins_M:158:CAG, ins_M:182:GGGA, ins_L:12033:A, ins_L:11971:CCATACCA, ins_L:12104:CCAGTTTCATTATTTGCAGGGTGTGGG, ins_L:11924:G, ins_L:12108:ACGATT, ins_L:67:C

Amino acid mutations

Mutations called relative to the NC_005301.3, NC_005300.2 & NC_005302.1 references

Substitutions

GPC

GPC:I3T

GPC:S4L

GPC:M6V

GPC:Y7C

GPC:A8F

GPC:C11Y

GPC:Q13R

GPC:C15L

GPC:E19G

GPC:T20A

GPC:S23Q

GPC:H24S

GPC:E26T

GPC:R28E

GPC:M35T

GPC:T36I

GPC:T37A

GPC:D40T

NP

NP:N9S

NP:R15K

NP:V27M

NP:S39N

NP:R45K

NP:A100S

NP:S109N

NP:T111A

NP:T124A

NP:G125N

NP:H195R

NP:D199E

NP:I246V

NP:K265R

NP:R270K

NP:I277T

NP:S301G

NP:A307P

RdRp

RdRp:S6N

RdRp:S19T

RdRp:D55A

RdRp:Y60N

RdRp:R63H

RdRp:S67L

RdRp:R80K

RdRp:K91E

RdRp:R156K

RdRp:M172V

RdRp:R174K

RdRp:S205P

RdRp:N206Y

RdRp:T215I

RdRp:K218R

RdRp:K275R

RdRp:I279V

RdRp:V352I

Deletions

GPC:33, GPC:77, GPC:157-168, GPC:215-218

Insertions

ins_GPC:221:SPPV, ins_GPC:152:SSPKTVTTPAS, ins_GPC:172:E

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