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PPD_0039BY5.1

Display Name: Georgia/PPD_0039BY5.1/2023-01-01
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
2024-11-19 16:17:00 UTC
Date released
2024-11-19 16:30:17 UTC

Data use terms

Data use terms
OPEN

Data Use Terms History

ChangedUserData Use Terms
2024-11-19 16:17insdc_ingest_userOPEN
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
PRJNA1063190
Biosample accession
SAMN39328239
INSDC accession L
PP116320.1
INSDC accession M
PP116319.1
INSDC accession S
PP116318.1
NCBI release date
2024-02-10
SRA run accession
SRR27477368

Alignment states and QC metrics L

Completeness L
99.87%
Length L
12124
Total ambiguous nucs L
0
Total deleted nucs L
12
Total frame shifts L
0
Total inserted nucs L
44
Total SNPs L
1304
Total unknown nucs L
0

Alignment states and QC metrics M

Completeness M
99.59%
Frame shifts M
GPC:31-32(nt:183-188)
Length M
5342
Total ambiguous nucs M
0
Total deleted nucs M
10
Total frame shifts M
1
Total inserted nucs M
8
Total SNPs M
1034
Total unknown nucs M
0

Alignment states and QC metrics S

Completeness S
98.86%
Length S
1658
Total ambiguous nucs S
0
Total deleted nucs S
10
Total frame shifts S
0
Total inserted nucs S
15
Total SNPs S
241
Total unknown nucs S
0

Sample details

Collection country
Georgia
Collection date
2023-01-01
Isolate name
GE/Ser-H/2023

Host

Host name scientific
Homo sapiens
Host taxon id
9606

Nucleotide mutations

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

    Amino acid mutations

    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