PP_000RFJZ.2

Display Name: North_Macedonia/PP_000RFJZ.2/2023-01-01
Bosevska, G.; Emmerich, P.; von Possel, R.; Toth, E. G.; Osmani, D.; Cadar, D.

Submission details

Submission ID
PP963968.1.L/PP963969.1.M/PP963970.1.S
Submitting group
Automated Ingest from INSDC/NCBI Virus by Loculus
Date submitted
2024-09-26 15:01:57 UTC
Date released
2024-09-26 15:22:15 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
Bernhard Nocht Institute for Tropical Medicine, Virus Genomics and Evolution

Alignment states and QC metrics L

Completeness L
100.00%
Length L
12347
Total ambiguous nucs L
0
Total deleted nucs L
9
Total frame shifts L
0
Total inserted nucs L
248
Total SNPs L
1287
Total unknown nucs L
0

Alignment states and QC metrics M

Completeness M
100.00%
Length M
5388
Total ambiguous nucs M
0
Total deleted nucs M
7
Total frame shifts M
0
Total inserted nucs M
29
Total SNPs M
1056
Total unknown nucs M
0

Alignment states and QC metrics S

Completeness S
100.00%
Length S
1814
Total ambiguous nucs S
0
Total deleted nucs S
18
Total frame shifts S
0
Total inserted nucs S
160
Total SNPs S
243
Total unknown nucs S
0

Sample details

Collection country
North Macedonia
Collection date
2023-01-01
Isolate name
Kuchica-2713

Host

Host name scientific
Homo sapiens
Host taxon id
9606

INSDC

INSDC accession L
PP963968.1
INSDC accession M
PP963969.1
INSDC accession S
PP963970.1
NCBI release date
2024-07-06

Nucleotide mutations

Substitutions

L

  • L:T10C
  • L:A35G
  • L:A42T
  • L:G43C
  • L:T49C
  • L:A53G
  • L:C59T
  • L:C63G
  • L:C64T
  • L:T65C
  • L:T67C
  • L:A72G
  • L:A73T
  • L:A91G
  • L:G93A
  • L:C100T
  • L:A109G
  • L:T131A

    • M

  • M:A6G
  • M:A7C
  • M:A10C
  • M:A11C
  • M:A13C
  • M:T40C
  • M:G50A
  • M:A51G
  • M:A61T
  • M:T67C
  • M:T68C
  • M:T71A
  • M:G76C
  • M:A80G
  • M:T83C
  • M:G84A
  • M:C85T
  • M:T86C

    • S

  • S:A7G
  • S:G8C
  • S:A9G
  • S:A11C
  • S:A13T
  • S:T16A
  • S:G17C
  • S:C19A
  • S:G20T
  • S:T23A
  • S:A24G
  • S:C27A
  • S:T49C
  • S:A50T
  • S:G54A
  • S:T79C
  • S:A81G
  • S:G99A
    • Deletions
    L:11982-11990, M:4, M:318-323, S:4, S:5, S:1542-1547, S:1610-1619
    Insertions
    ins_S:1672:ATGGACTTGGTATGTCCAGATCCCTGAGCAGCGTCATCAGGATTGGCAACAGGGATTGTTCCAAAGCAGACACCCATTTCACTGATTCTACCGGCTGTCAACACAGCAGGGTGCATGTAGATCCTGTTCTGCTGG, ins_S:1563:TATG, ins_S:1566:AT, ins_S:1577:A, ins_S:0:GACCA, ins_S:1629:CTATCTTTCA, ins_S:29:TCC, ins_M:335:ACA, ins_M:5366:GTGGAGGTCGCTAGATGGTC, ins_M:5171:T, ins_M:0:CA, ins_M:14:ACC, ins_L:57:AT, ins_L:12092:CTATTCATACCAGTTTTATTATTTGAAGGGTATGGGGGG, ins_L:12108:AATGCAGAGCAGCTAGCTCGTTTGAGAGCTTTGATGCTGGCAACTACTATGGTATAGACTGTCTCGTTTGCCCTTGGGACATTGAAAGACAGTGGAGGTCGCTAGATGG, ins_L:11928:CG, ins_L:11973:ATACCATAA, ins_L:25:T, ins_L:0:GACCATCTAGCGACCTCCACTTCAGTCACTGGCTGCAACAGTCCAAATGATTATTGTAATGCCCATTTCTTTGGCTAGCATGGATG

    Amino acid mutations

    Substitutions

    GPC

  • GPC:I3T
  • GPC:S4L
  • GPC:M6V
  • GPC:Y7C
  • GPC:A8F
  • GPC:C11Y
  • GPC:C15L
  • GPC:E19G
  • GPC:T20A
  • GPC:S23Q
  • GPC:H24P
  • GPC:E26A
  • GPC:R28E
  • GPC:K31G
  • GPC:T32A
  • GPC:D33N
  • GPC:M35T
  • GPC:T37A

    • 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:S301G
  • NP:A307P
  • NP:Y311F

    • RdRp

  • RdRp:S6N
  • RdRp:S19T
  • RdRp:D55A
  • RdRp:Y60N
  • RdRp:R63H
  • RdRp:S67L
  • RdRp:I131M
  • RdRp:M172V
  • RdRp:R174K
  • RdRp:I176M
  • RdRp:A202V
  • RdRp:S205P
  • RdRp:N206Y
  • RdRp:K218R
  • RdRp:K275R
  • RdRp:I279V
  • RdRp:V352I
  • RdRp:N390S
    • Deletions
    GPC:77, GPC:105
    Insertions
    ins_GPC:114:T