PPD_0039DMR.1

Display Name: North_Macedonia/PPD_0039DMR.1/2023-01-01

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

2024-11-19 16:17:00 UTC

Date released

2024-11-19 16:30:17 UTC

Data use terms

Changed	User	Data Use Terms
2024-11-19 16:17	insdc_ingest_user	OPEN

OPEN

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

Total deleted nucs L

Total frame shifts L

Total inserted nucs L

248

Total SNPs L

1287

Total unknown nucs L

Alignment states and QC metrics M

Completeness M

100.00%

Length M

5388

Total ambiguous nucs M

Total deleted nucs M

Total frame shifts M

Total inserted nucs M

Total SNPs M

1056

Total unknown nucs M

Alignment states and QC metrics S

Completeness S

100.00%

Length S

1814

Total ambiguous nucs S

Total deleted nucs S

Total frame shifts S

Total inserted nucs S

160

Total SNPs S

243

Total unknown nucs S

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:1566:AT, ins_S:1672:ATGGACTTGGTATGTCCAGATCCCTGAGCAGCGTCATCAGGATTGGCAACAGGGATTGTTCCAAAGCAGACACCCATTTCACTGATTCTACCGGCTGTCAACACAGCAGGGTGCATGTAGATCCTGTTCTGCTGG, ins_S:1563:TATG, 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