This is a demo instance. You can upload any data you like, including test data to try things out. You can find test data to upload in the example data repository. This instance should not be used for analysis.

PPD_0047WDU.1

Display Name: USA/PPD_0047WDU.1/2024-10-22
Kath, C.; Haw, M.; Espinosa, A.; Hacker, J.

Submission details

Submission ID
PQ781665.1
Submitting group
Automated Ingest from INSDC/NCBI Virus by Loculus
Date submitted
2024-12-25 03:48:18 UTC
Date released
2024-12-25 03:48:49 UTC

Data use terms

Data use terms
OPEN

Data Use Terms History

ChangedUserData Use Terms
2024-12-25 03:48insdc_ingest_userOPEN
Data use terms URL
https://pathoplexus.org/about/terms-of-use/open-data

Authors

Author affiliations
CDPH, VRDL

INSDC

Bioproject accession
PRJNA884422
INSDC accession
PQ781665.1
NCBI release date
2024-12-24
NCBI update date
2024-12-24

Clade & Lineage

Clade
IIb
Lineage
F.1
Outbreak
hMPXV-1

Alignment and QC metrics

Completeness
95.41%
Length
195815
Total ambiguous nucs
0
Total deleted nucs
109
Total frame shifts
0
Total inserted nucs
58
Total SNPs
87
Total stop codons
0
Total unknown nucs
7712

Sample details

Earliest release date
2024-12-24
Collection country
USA
Collection date
2024-10-22
Collection date (lower bound)
2024-10-22
Collection date (upper bound)
2024-10-22
Isolate name
hMpxV/USA/CA-CDPH-1M1000698/2024

Host

Host name scientific
Homo sapiens
Host taxon id
9606

Nucleotide mutations

Mutations called relative to the NC_063383.1 reference

Substitutions

  • G1262A
  • G2591A
  • G3111A
  • G3522A
  • C3818T
  • C7771T
  • G11668A
  • G14000T
  • G15428A
  • G16748A
  • G16767A
  • A18769G
  • C20453T
  • G21723A
  • C23353T
  • C23564T
  • G23565A
  • G25661A
    • Deletions
    133177-133186, 179145-179243
    Insertions
    ins_6464:TATTATCAT, ins_133122:NNN, ins_174076:NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

    Amino acid mutations

    Mutations called relative to the NC_063383.1 reference

    Substitutions

    OPG001

  • OPG001:S105L

    • OPG002

  • OPG002:S54F

    • OPG003

  • OPG003:D264N

    • OPG025

  • OPG025:A423D

    • OPG029

  • OPG029:R108C

    • OPG039

  • OPG039:S185L
  • OPG039:D256N

    • OPG047

  • OPG047:R48C

    • OPG053

  • OPG053:P78S

    • OPG056

  • OPG056:E125K

    • OPG057

  • OPG057:E353K

    • OPG071

  • OPG071:L108F

    • OPG072

  • OPG072:D56N

    • OPG092

  • OPG092:D196N

    • OPG093

  • OPG093:S30L
  • OPG093:D88N

    • OPG094

  • OPG094:M142I

    • OPG098

  • OPG098:E162K

    • OPG105

  • OPG105:S734L

    • OPG109

  • OPG109:H740Y

    • OPG117

  • OPG117:S297L

    • OPG118

  • OPG118:K606E

    • OPG136

  • OPG136:D98N

    • OPG139

  • OPG139:A17T

    • OPG145

  • OPG145:E62K
  • OPG145:R243Q
  • OPG145:E435K

    • OPG150

  • OPG150:S307L

    • OPG154

  • OPG154:S21F

    • OPG176

  • OPG176:H221Y

    • OPG193

  • OPG193:L263F

    • OPG210

  • OPG210:D209N
  • OPG210:P722S
  • OPG210:D1668N
  • OPG210:M1741I
    • Deletions
    None
    Insertions
    None

    Report an issue with this sequence or metadata

    Create GitHub issue