PP_000RFKX.2

Display Name: North_Macedonia/PP_000RFKX.2/2023-01-01
Bosevska, G.; Emmerich, P.; von Possel, R.; Toth, E. G.; Osmani, D.; Cadar, D.

Submission details

Submission ID
PP963971.1.L/PP963972.1.M/PP963973.1.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
68.06%
Length L
11902
Total ambiguous nucs L
0
Total deleted nucs L
19
Total frame shifts L
0
Total inserted nucs L
2
Total SNPs L
863
Total unknown nucs L
3678

Alignment states and QC metrics M

Completeness M
82.30%
Length M
5204
Total ambiguous nucs M
0
Total deleted nucs M
62
Total frame shifts M
0
Total inserted nucs M
3
Total SNPs M
875
Total unknown nucs M
847

Alignment states and QC metrics S

Completeness S
58.55%
Length S
1480
Total ambiguous nucs S
0
Total deleted nucs S
0
Total frame shifts S
0
Total inserted nucs S
0
Total SNPs S
136
Total unknown nucs S
501

Sample details

Collection country
North Macedonia
Collection date
2023-01-01
Isolate name
Skopje-2795

Host

Host name scientific
Homo sapiens
Host taxon id
9606

INSDC

INSDC accession L
PP963971.1
INSDC accession M
PP963972.1
INSDC accession S
PP963973.1
NCBI release date
2024-07-06

Nucleotide mutations

Substitutions

L

  • L:A91G
  • L:G93A
  • L:C100T
  • L:A109G
  • L:T131A
  • L:C148T
  • L:T151C
  • L:T154C
  • L:T160C
  • L:T163C
  • L:T202C
  • L:T229C
  • L:A240C
  • L:T253C
  • L:T254A
  • L:G264A
  • L:C265T
  • L:A268G

    • M

  • 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
  • M:C92T
  • M:T100C
  • M:T102C
  • M:C103T
  • M:A108G

    • S

  • S:T49C
  • S:A50T
  • S:G54A
  • S:T79C
  • S:A81G
  • S:G99A
  • S:G100A
  • S:A109G
  • S:C115T
  • S:A121G
  • S:G134A
  • S:C142T
  • S:T157C
  • S:G171A
  • S:T175A
  • S:C178A
  • S:T182C
  • S:C187T
    • Deletions
    L:50-53, L:59-73, M:318-323, M:5147-5155, M:5199-5215, M:5220, M:5223, M:5224, M:5232-5235, M:5239-5255, M:5281-5286
    Insertions
    ins_M:335:ACA, ins_L:11928:CG

    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:D33N
  • GPC:M35T
  • GPC:T37A
  • GPC:D40T
  • GPC:N41S
  • GPC:P42Q

    • NP

  • NP:N9S
  • NP:R15K
  • NP:V27M
  • NP:S39N
  • NP:R45K
  • NP:A100S
  • NP:S109N
  • NP:T111A
  • NP:T124A
  • NP:G125N
  • NP:I246V
  • NP:R270K
  • NP:S301G
  • NP:A307P
  • NP:Y311F
  • NP:V327I
  • NP:G335W
  • NP:V436I

    • 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:S232F
  • RdRp:K275R
  • RdRp:I279V
  • RdRp:V352I
    • Deletions
    GPC:77, GPC:105
    Insertions
    ins_GPC:114:T