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PPD_0039714.1

Display Name: Pakistan/PPD_0039714.1/2022-05-01
Umair, M.; Rehman, Z.; Salman, M.; Ikram, A.; Haider, S. A.; Ammar, M.; Ali, Q.; Hakim, R.; Ansari, S.

Submission details

Submission ID
OP345193.1.L/OP345192.1.M/OP345191.1.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 16:28:16 UTC

Data use terms

Data use terms
OPEN

Data Use Terms History

ChangedUserData Use Terms
2024-11-19 16:17insdc_ingest_userOPEN
Data use terms URL
https://pathoplexus.org/about/terms-of-use/open-data

Authors

Author affiliations
National Institute of Health, Department of Virology

Alignment states and QC metrics L

Completeness L
97.77%
Frame shifts L
RdRp:792-795(nt:2450-2461)
Length L
11838
Total ambiguous nucs L
0
Total deleted nucs L
1
Total frame shifts L
1
Total inserted nucs L
1
Total SNPs L
1542
Total unknown nucs L
0

Alignment states and QC metrics M

Completeness M
95.83%
Frame shifts M
GPC:4-8(nt:100-115),GPC:23-30(nt:159-181),GPC:41-46(nt:211-230),GPC:49(nt:237-238),GPC:56-66(nt:258-290),GPC:87-90(nt:351-362),GPC:96-103(nt:378-400),GPC:111-112(nt:421-428),GPC:115-118(nt:435-446),GPC:127-131(nt:470-485),GPC:181-187(nt:633-651),GPC:189-193(nt:657-669),GPC:207(nt:709-713),GPC:216-217(nt:737-743),GPC:235-238(nt:795-806),GPC:335-337(nt:1093-1103)
Length M
5100
Total ambiguous nucs M
0
Total deleted nucs M
181
Total frame shifts M
16
Total inserted nucs M
139
Total SNPs M
1245
Total unknown nucs M
0

Alignment states and QC metrics S

Completeness S
86.66%
Length S
1449
Total ambiguous nucs S
0
Total deleted nucs S
0
Total frame shifts S
0
Total inserted nucs S
0
Total SNPs S
168
Total unknown nucs S
0

Sample details

Collection country
Pakistan
Collection date
2022-05-01
Isolate name
NIH-03

Host

Host name scientific
Homo sapiens
Host taxon id
9606

INSDC

INSDC accession L
OP345193.1
INSDC accession M
OP345192.1
INSDC accession S
OP345191.1
NCBI release date
2022-10-02

Nucleotide mutations

Substitutions

L

  • L:C85T
  • L:G88A
  • L:G93A
  • L:A109G
  • L:C117A
  • L:A124G
  • L:T131A
  • L:T139C
  • L:C148T
  • L:T151C
  • L:T154C
  • L:T160C
  • L:C208T
  • L:T218C
  • L:T229C
  • L:T250C
  • L:T253C
  • L:T254A

    • M

  • M:T15A
  • M:C18T
  • M:G19T
  • M:A22C
  • M:G24C
  • M:G28A
  • M:A42T
  • M:T45A
  • M:A90T
  • M:G95C
  • M:A97T
  • M:C120T
  • M:T135A
  • M:T140C
  • M:C141A
  • M:T142G
  • M:G143T
  • M:A148T

    • S

  • S:G67A
  • S:T79C
  • S:A81G
  • S:G99A
  • S:A109G
  • S:A118G
  • S:G134A
  • S:C166T
  • S:G169A
  • S:T172C
  • S:C178A
  • S:T182C
  • S:G190A
  • S:G196A
  • S:T199C
  • S:C208T
  • S:C217T
  • S:G229A
    • Deletions
    L:2449, M:29-40, M:48-81, M:99, M:105-113, M:116, M:117, M:125-133, M:182-191, M:207-210, M:216-218, M:272-275, M:297-305, M:333-338, M:346-350, M:363-366, M:385-388, M:401, M:420, M:469, M:576-581, M:588-596, M:610-632, M:708, M:714, M:715, M:735, M:736, M:744-747, M:755-757, M:807, M:808, M:1092, M:5145-5153
    Insertions
    ins_M:428:A, ins_M:158:GGTG, ins_M:698:ACA, ins_M:791:ACACCCTCT, ins_M:1103:A, ins_M:245:ACAAAGACA, ins_M:257:AC, ins_M:236:CCGTCAAC, ins_M:794:ACCAC, ins_M:238:A, ins_M:651:AATGA, ins_M:669:TT, ins_M:290:CG, ins_M:377:ACAGAAGCACCCAC, ins_M:230:CACAACTCCTGCA, ins_M:656:GGGAGTG, ins_M:455:CCT, ins_M:446:GT, ins_M:320:AGCACTGATCCCTCGGTTACCAACAAG, ins_M:485:ACCT, ins_M:86:GATT, ins_M:434:ACCACAC, ins_M:638:CTACTA, ins_L:2461:G

    Amino acid mutations

    Substitutions

    GPC

  • GPC:L14F
  • GPC:C15W
  • GPC:L17S
  • GPC:E19V
  • GPC:H21S
  • GPC:P47A
  • GPC:V48T
  • GPC:A51V
  • GPC:L52S
  • GPC:I54T
  • GPC:A67S
  • GPC:V76S
  • GPC:Y77S
  • GPC:S79D
  • GPC:P81S
  • GPC:I82V
  • GPC:T84N
  • GPC:G85K

    • NP

  • NP:N9S
  • NP:R15K
  • NP:V27M
  • NP:V83A
  • NP:D116E
  • NP:T124S
  • NP:G125N
  • NP:H195R
  • NP:D199E
  • NP:I246V
  • NP:R270K
  • NP:S301G
  • NP:A307V
  • NP:E322D
  • NP:Q405L
  • NP:K428R
  • NP:V436I

    • RdRp

  • RdRp:S6N
  • RdRp:A14D
  • RdRp:S19T
  • RdRp:Y60N
  • RdRp:R63H
  • RdRp:S67V
  • RdRp:R80K
  • RdRp:V82I
  • RdRp:I114V
  • RdRp:T163A
  • RdRp:A168T
  • RdRp:M172V
  • RdRp:R174K
  • RdRp:A202V
  • RdRp:S205P
  • RdRp:N206Y
  • RdRp:I223V
  • RdRp:K275R
    • Deletions
    GPC:9, GPC:31-33, GPC:39, GPC:40, GPC:68-71, GPC:86, GPC:91, GPC:92, GPC:104-107, GPC:110, GPC:174-180, GPC:188, GPC:194-206, GPC:208-215, GPC:218-220, GPC:239, GPC:334
    Insertions
    ins_GPC:173:AG, ins_GPC:85:DTSPT, ins_GPC:122:NSPTL, ins_GPC:92:LETEAP, ins_GPC:158:QTASA, ins_GPC:15:S, ins_GPC:230:GQTXXTTLET, ins_GPC:32:VPTPXXX, ins_GPC:235:TIQGQQTTTPVTTPSITT