This is a demonstration environment. It may contain non-accurate test data and should not be used for real-world applications. Data will be deleted regularly.

LOC_000NKQP.1

Display Name: India/LOC_000NKQP.1/2016
Yadav, P. D.

Submission details

Submission ID
MH396667.1.L/MH396668.1.M/MH396669.1.S
Submitting group
Automated Ingest from INSDC/NCBI Virus by Loculus
Date submitted
2025-04-03 11:38:38 UTC
Date released
2025-04-03 11:41:22 UTC

Data use terms

Data use terms
OPEN

Data Use Terms History

ChangedUserData Use Terms
2025-04-03 11:38insdc_ingest_userOPEN
Data use terms URL
https://#TODO-MVP/open

Authors

Author affiliations
National Institute of Virology, Maximum Containment Laboratory

Alignment and QC metrics L

Completeness L
99.88%
Frame shifts L
RdRp:792-795(nt:2450-2461)
Length L
12162
Total ambiguous nucs L
0
Total deleted nucs L
13
Total frame shifts L
1
Total inserted nucs L
81
Total SNPs L
1617
Total unknown nucs L
0

Alignment and QC metrics M

Completeness M
99.16%
Length M
5322
Total ambiguous nucs M
0
Total deleted nucs M
6
Total frame shifts M
0
Total inserted nucs M
7
Total SNPs M
648
Total unknown nucs M
0

Alignment and QC metrics S

Completeness S
98.80%
Length S
1653
Total ambiguous nucs S
0
Total deleted nucs S
6
Total frame shifts S
0
Total inserted nucs S
7
Total SNPs S
223
Total unknown nucs S
0

Sample details

Earliest release date
2020-03-22
Collection subdivision level 1
Gujarat State
Collection country
India
Collection date
2016
Collection date (lower bound)
2016-01-01
Collection date (upper bound)
2016-12-31

Host

Host name scientific
Homo sapiens
Host taxon id
9606

INSDC

INSDC accession L
MH396667.1
INSDC accession M
MH396668.1
INSDC accession S
MH396669.1
NCBI release date
2020-03-22

Nucleotide mutations

Mutations called relative to the NC_005301.3, NC_005300.2 & NC_005302.1 references

Substitutions

L

  • L:G23T
  • L:A35G
  • L:G43T
  • L:T49C
  • L:T67G
  • L:G69C
  • L:G71C
  • L:C76T
  • L:C85T
  • L:G88A
  • L:G93A
  • L:A109G
  • L:C117A
  • L:A124G
  • L:T131A
  • L:T139A
  • L:T151C
  • L:T154C

    • M

  • M:C85T
  • M:T86C
  • M:T100C
  • M:A104T
  • M:A107G
  • M:G110A
  • M:C115T
  • M:A117G
  • M:C119T
  • M:T122C
  • M:C126T
  • M:A128G
  • M:G138A
  • M:G143A
  • M:A146G
  • M:G147A
  • M:G149A
  • M:T155C

    • S

  • S:T48C
  • S:G54A
  • S:A61G
  • S:C64T
  • S:G67A
  • S:T79C
  • S:A85G
  • S:G99A
  • S:A118G
  • S:C142T
  • S:T157C
  • S:C166T
  • S:C178A
  • S:T182C
  • S:G190A
  • S:G196A
  • S:C214T
  • S:C217T
    • Deletions
    L:59-61, L:2449, L:11920-11924, L:11981, L:11982, L:12076, L:12083, M:5166-5171, S:1575-1580
    Insertions
    ins_S:1585:ACCAACC, ins_M:5164:GGGGGGG, ins_L:11973:A, ins_L:11977:A, ins_L:12054:TACAATTTT, ins_L:12064:GGTTAACCT, ins_L:11917:CATTATC, ins_L:12101:CG, ins_L:12108:TCGGAAGAGACACGTCT, ins_L:12096:GTTC, ins_L:69:CTCA, ins_L:2461:G, ins_L:12104:TATTATTTCTGGGGTGTGGGGGGAAC

    Amino acid mutations

    Mutations called relative to the NC_005301.3, NC_005300.2 & NC_005302.1 references

    Substitutions

    GPC

  • GPC:I3T
  • GPC:M6I
  • GPC:A8V
  • GPC:I9V
  • GPC:G16S
  • GPC:E19K
  • GPC:E26G
  • GPC:R28E
  • GPC:T34V
  • GPC:P42Q
  • GPC:S44P
  • GPC:P47L
  • GPC:S53P
  • GPC:I54V
  • GPC:L56P
  • GPC:T65A
  • GPC:P80S
  • GPC:P81S

    • NP

  • NP:R15K
  • NP:D116E
  • NP:T124A
  • NP:G125N
  • NP:N150H
  • NP:E168D
  • NP:H195R
  • NP:D199E
  • NP:I246V
  • NP:R270K
  • NP:S275N
  • NP:S301G
  • NP:K354R
  • NP:V436I

    • RdRp

  • RdRp:S6N
  • RdRp:A14D
  • RdRp:S19T
  • RdRp:Y60N
  • RdRp:R63H
  • RdRp:E66G
  • RdRp:S67V
  • RdRp:R80K
  • RdRp:V82I
  • RdRp:K91T
  • RdRp:I114V
  • RdRp:A122T
  • RdRp:A168T
  • RdRp:M172V
  • RdRp:R174K
  • RdRp:S205P
  • RdRp:N206Y
  • RdRp:I223V
    • Deletions
    None
    Insertions
    None

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