PP_000R8XE.1

Display Name: Turkey/PP_000R8XE.1/2021-01-01
Kalaycioglu, A. T.; Oguzoglu, T. C.; Ari, O.; Durmaz, R.; Engin, A.; Bakir, M.; Erdem, E.

Submission details

Submission ID
ON623088.1.L/ON623082.1.M
Submitting group
Automated Ingest from INSDC/NCBI Virus by Loculus
Date submitted
2024-08-27 12:10:45 UTC
Date released
2024-08-27 12:15:34 UTC

Data use terms

Data use terms
OPEN

Data Use Terms History

ChangedUserData Use Terms
2024-08-27 12:11insdc_ingest_userOPEN
Data use terms URL
https://pathoplexus.org/about/terms-of-use/open-data

Authors

Author affiliations
Karadeniz Technical University, Faculty of Pharmacy Department of Pharmaceutical Microbiology

Alignment states and QC metrics L

Completeness L
69.62%
Length L
8430
Total ambiguous nucs L
0
Total deleted nucs L
0
Total frame shifts L
0
Total inserted nucs L
0
Total SNPs L
876
Total unknown nucs L
1

Alignment states and QC metrics M

Completeness M
99.96%
Length M
5362
Total ambiguous nucs M
0
Total deleted nucs M
28
Total frame shifts M
0
Total inserted nucs M
26
Total SNPs M
1020
Total unknown nucs M
0

Sample details

Collection subdivision level 2
Asia
Collection country
Turkey
Collection date
2021-01-01
Isolate name
TR-SIVAS-C5F-2021

Host

Host name scientific
Homo sapiens
Host taxon id
9606

INSDC

INSDC accession L
ON623088.1
INSDC accession M
ON623082.1
NCBI release date
2023-02-20

Nucleotide mutations

Substitutions

L

  • L:T3505C
  • L:G3523A
  • L:T3529C
  • L:G3568A
  • L:C3571T
  • L:C3572T
  • L:A3583G
  • L:C3586T
  • L:T3589G
  • L:C3595T
  • L:T3607C
  • L:G3627A
  • L:G3628A
  • L:A3630G
  • L:T3646C
  • L:G3652A
  • L:G3676A
  • L:A3679G

    • M

  • M:T40A
  • M:G50A
  • M:A51G
  • M:T67C
  • M:T68C
  • M:A69G
  • M:T71A
  • M:G76C
  • M:A80G
  • M:G84A
  • M:T86C
  • M:A88G
  • M:C92T
  • M:T94C
  • M:T100C
  • M:T102C
  • M:C103T
  • M:A108G
    • Deletions
    M:165-167, M:327-329, M:593-595, M:5172, M:5173, M:5180, M:5181, M:5187-5191, M:5238, M:5246-5250, M:5277-5280
    Insertions
    ins_M:5202:CTT, ins_M:599:ATA, ins_M:158:CAG, ins_M:5231:TTACAG, ins_M:5286:TAAG, ins_M:5194:CGTCTAG

    Amino acid mutations

    Substitutions

    GPC

  • GPC:M1T
  • GPC:I3T
  • GPC:S4L
  • GPC:M6V
  • GPC:Y7C
  • GPC:A8F
  • GPC:C11Y
  • GPC:C15L
  • GPC:L17R
  • GPC:E19G
  • GPC:T20A
  • GPC:S23Q
  • GPC:H24S
  • GPC:E26A
  • GPC:R28E
  • GPC:K31G
  • GPC:D33N
  • GPC:M35T

    • RdRp

  • RdRp:D1171E
  • RdRp:R1184K
  • RdRp:K1185R
  • RdRp:R1212K
  • RdRp:V1228I
  • RdRp:K1282M
  • RdRp:V1317I
  • RdRp:I1363V
  • RdRp:N1367D
  • RdRp:L1386I
  • RdRp:S1436N
  • RdRp:M1448L
  • RdRp:S1454A
  • RdRp:R1456K
  • RdRp:I1458L
  • RdRp:R1478K
  • RdRp:V1495I
  • RdRp:V1577I
    • Deletions
    GPC:90
    Insertions
    None