PP_000RF4U.2

Display Name: North_Macedonia/PP_000RF4U.2/2023-01-01
Jakimovski, D.; Spasovska, K.; Grozdanovski, K.; Rangelov, G.; Cvetanovska, M.; Cana, F.; Banovic, P.; Simin, V.; Bogdan, I.; Mijatovic, D.; Cvetkovikj, A.; Djadjovski, I.; Christova, I.; Meletis, E.; Kostoulas, P.; Zana, B.; Lanszki, Z.; Gorfol, T.; Tauber, Z.; Kemenesi, G.; Urban, P.

Submission details

Submission ID
PP729066.1.L/PP729065.1.M/PP729064.1.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
University of Pecs, Szentagothai Research Center

Alignment states and QC metrics L

Completeness L
99.91%
Length L
12141
Total ambiguous nucs L
0
Total deleted nucs L
9
Total frame shifts L
0
Total inserted nucs L
53
Total SNPs L
1286
Total unknown nucs L
0

Alignment states and QC metrics M

Completeness M
99.57%
Length M
5341
Total ambiguous nucs M
0
Total deleted nucs M
6
Total frame shifts M
0
Total inserted nucs M
4
Total SNPs M
1045
Total unknown nucs M
0

Alignment states and QC metrics S

Completeness S
98.56%
Length S
1649
Total ambiguous nucs S
0
Total deleted nucs S
16
Total frame shifts S
0
Total inserted nucs S
17
Total SNPs S
231
Total unknown nucs S
0

Sample details

Collection country
North Macedonia
Collection date
2023-01-01
Isolate name
Kuchica/North Macedonia-1/2023

Host

Host name scientific
Homo sapiens
Host taxon id
9606

INSDC

INSDC accession L
PP729066.1
INSDC accession M
PP729065.1
INSDC accession S
PP729064.1
NCBI release date
2024-05-05

Nucleotide mutations

Substitutions

L

  • 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
  • L:C148T

    • 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:11982-11990, M:318-323, S:1542-1547, S:1610-1619
    Insertions
    ins_S:1563:TATG, ins_S:1566:AT, ins_S:1577:A, ins_S:1629:CTATCTTTCA, ins_M:335:ACA, ins_M:5171:T, ins_L:57:AT, ins_L:12092:CTATTCATACCAGTTTTATTATTTGAAGGGTATGGGGGG, ins_L:11928:CG, ins_L:11973:ATACCATAA, ins_L:25:T

    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