PP_000T5K3.2

USA/PP_000T5K3.2
N. Shashan, J. Makarenko, L. Tallon, L. Sadzewicz, K. Vavikolanu, A. Mehta, J. Aluvathingal, S. Nadendla, T. Myers, Y. Yan & H. Sichtig

US Food and Drug Administration, Center for Devices and Radiological Health

Sample details

Sampling location
USA (MD)
Isolate name
USA-2003

Data use terms

Data use terms
OPEN

Data use terms history

ChangedUserData use terms
2024-12-09 18:48insdc_ingest_userOPEN
Data use terms URL

Clade & Lineage

Clade
IIb
Outbreak
sh2017
Lineage
A

INSDC

INSDC accession
BioProject accession
BioSample accession
NCBI release date
2022-07-30
NCBI update date
2022-07-30
Raw reads accession

Submission details

Submission ID
OK573016.1
Submitting group
Date submitted
2025-02-03 15:01:44 UTC
Date released
2025-02-03 15:02:25 UTC
Earliest release date
2022-07-30

Alignment and QC

Length
6933 (16.1%)
# of SNPs
162
# of inserted bases
19
# of deleted bases
24893
# of frame shifts
11
Frame shifts
OPG151:588-665(nt:130683-130918),OPG151:684-802(nt:130971-131329),OPG151:952-954(nt:131775-131784),OPG153:370-371(nt:136556-136560),OPG156:14-38(nt:139298-139371),OPG156:61-62(nt:139226-139231),OPG156:132-133(nt:139013-139016),OPG156:146-181(nt:138868-138974),OPG156:195-247(nt:138671-138829),OPG156:258-306(nt:138492-138638),OPG157:32-79(nt:139372-139515)

Nucleotide mutations

Mutations called relative to the NC_063383.1 reference

Substitutions

  • G130676A
  • G130677A
  • A130681C
  • C130687T
  • A130688G
  • A130716C
  • A130728C
  • T130729G
  • T130731G
  • G130732C
  • T130733G
  • G130739C
  • A130740C
  • T130742C
  • T130743G
  • A130746G
  • A130747C
  • T130790C
Deletions

130691-130694, 130700-130711, 130718-130725, 130748-130786, 130802-130912, 130919-130935, 130946-130970, 130979-130987, 130996-131016, 131030-131072, 131087-131107, 131115-131147, 131153-131272, 131279-131320, 131330-131468, 131477-131509, 131521-131774, 131785-132049, 132813, 133090-133102, 133177-133186, 136555, 138486-138530, 138540-138617, 138632-138636, 138639, 138640,...
Insertions

ins_130682:CG, ins_132445:TATCAAGAT, ins_136560:CATCATC, ins_139012:G

Amino acid substitutions

Substitutions called relative to the NC_063383.1 reference

Substitutions

OPG151

  • OPG151:V537L
  • OPG151:L564F
  • OPG151:K1159R

OPG153

  • OPG153:M14T
  • OPG153:A292T
  • OPG153:T343A
  • OPG153:I355T
  • OPG153:H408Y

OPG155

  • OPG155:T65I

OPG156

  • OPG156:K134P
  • OPG156:S135L
  • OPG156:S136R
  • OPG156:S183D

OPG158

  • OPG158:F9G
  • OPG158:L10R
  • OPG158:R12W
  • OPG158:L13V
  • OPG158:K15C
Deletions

OPG151

OPG151:423-514, OPG151:565-587, OPG151:666-683, OPG151:803-951, OPG151:955-1043

OPG156

OPG156:39-60, OPG156:63-131, OPG156:138-145, OPG156:182, OPG156:185-194, OPG156:248-257

OPG157

OPG157:12-31
Insertions

OPG153

ins_OPG153:369:DD

OPG157

ins_OPG157:0:ACCLPW

Report an issue with this sequence or metadata

Create GitHub issue