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_000P4LA.1

Display Name: Uganda/LOC_000P4LA.1/2018-07-12
S. Balinandi, S. Whitmer, S. Mulei, L. Nyakarahuka, A. Tumusiime, J. Kyondo, L. Mugisha, M. Almberg, J. Lutwama, T. Shoemaker & J. D. Klena

Submission details

Submission ID
MW464979.1.L/MW464980.1.M/MW464981.1.S
Submitting group
Date submitted
2025-07-18 15:35:17 UTC
Date released
2025-07-18 15:39:00 UTC

Data use terms

Data use terms
OPEN

Data Use Terms History

ChangedUserData Use Terms
2025-07-18 15:35insdc_ingest_userOPEN
Data use terms URL

Authors

Author affiliations
CDC, VSPB

Alignment and QC metrics L

Completeness L
99.74%
Length L
12011
Total ambiguous nucs L
0
Total deleted nucs L
81
Total frame shifts L
0
Total inserted nucs L
15
Total SNPs L
1998
Total unknown nucs L
0

Alignment and QC metrics M

Completeness M
91.71%
Frame shifts M
GPC:124-128(nt:461-476),GPC:181-184(nt:632-642),GPC:188-194(nt:654-674),GPC:199-206(nt:687-710),GPC:220-222(nt:750-758),GPC:293-294(nt:968-974)
Length M
4861
Total ambiguous nucs M
0
Total deleted nucs M
148
Total frame shifts M
6
Total inserted nucs M
88
Total SNPs M
1231
Total unknown nucs M
0

Alignment and QC metrics S

Completeness S
96.71%
Length S
1617
Total ambiguous nucs S
0
Total deleted nucs S
1
Total frame shifts S
0
Total inserted nucs S
1
Total SNPs S
274
Total unknown nucs S
0

Sample details

Earliest release date
2021-09-19
Collection country
Uganda
Collection date
2018-07-12
Collection date (lower bound)
2018-07-12
Collection date (upper bound)
2018-07-12
Isolate name
201902740

Host

Host name scientific
Homo sapiens
Host taxon id

INSDC

INSDC accession L
INSDC accession M
INSDC accession S
NCBI release date
2021-09-19

Nucleotide mutations

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

Substitutions

L

  • L:G23T
  • L:A35G
  • L:A42G
  • L:G43T
  • L:C48T
  • L:A53G
  • L:C64T
  • L:G71T
  • L:A72G
  • L:A73G
  • L:C82A
  • L:G93A
  • L:A109G
  • L:T115C
  • L:T131A
  • L:C148T
  • L:T151C
  • L:T154A

    • M

  • M:A432C
  • M:G434A
  • M:A438G
  • M:C472T
  • M:A473C
  • M:G475T
  • M:T491C
  • M:C496A
  • M:C498G
  • M:T501C
  • M:T503A
  • M:C505T
  • M:C507T
  • M:A511C
  • M:G513A
  • M:A514C
  • M:C515T
  • M:C526A

    • S

  • S:A50G
  • S:G54A
  • S:A61G
  • S:C64T
  • S:G67A
  • S:A78C
  • S:A81G
  • S:A85G
  • S:A109G
  • S:A118G
  • S:G122A
  • S:A124C
  • S:A130T
  • S:G136A
  • S:T144A
  • S:C154T
  • S:T157C
  • S:C166T
    • Deletions
    L:57, L:58, L:11939-11948, L:12013-12050, L:12058-12088, M:441-460, M:465-469, M:477-484, M:630, M:631, M:649-653, M:660-665, M:675-678, M:722-724, M:759-774, M:792-797, M:804-815, M:961-967, M:1098-1103, M:5180-5190, M:5209-5215, M:5234, M:5263-5290, M:5333, S:1611
    Insertions
    ins_S:1581:C, ins_M:5220:A, ins_M:5147:TCA, ins_M:974:ACAGGCA, ins_M:1091:CTGACC, ins_M:710:CTATC, ins_M:5158:TTCTGCTGCAGCA, ins_M:5152:A, ins_M:5243:TTTA, ins_M:5320:C, ins_M:686:C, ins_M:5198:CCGCTA, ins_M:642:GGCGGTCATAT, ins_M:5164:GTCC, ins_M:5228:TTC, ins_M:692:AGATCG, ins_M:738:AACAGGTAAAGGAAT, ins_M:749:A, ins_L:65:GCC, ins_L:11930:AATCAACAGCAT

    Amino acid mutations

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

    Substitutions

    GPC

  • GPC:T135K
  • GPC:P136A
  • GPC:S137P
  • GPC:T138I
  • GPC:P139S
  • GPC:Q140P
  • GPC:D141T
  • GPC:P145H
  • GPC:V146S
  • GPC:N148S
  • GPC:V152A
  • GPC:T153G
  • GPC:P155T
  • GPC:G156V
  • GPC:P157A
  • GPC:E159Q
  • GPC:S161T
  • GPC:T162P

    • NP

  • NP:N8T
  • NP:N9S
  • NP:G23S
  • NP:F30Y
  • NP:D116G
  • NP:T124A
  • NP:G125N
  • NP:H195R
  • NP:D199E
  • NP:I246V
  • NP:R270K
  • NP:S275N
  • NP:I277V
  • NP:S301G
  • NP:A307P
  • NP:Y311F
  • NP:T320S
  • NP:Q370E
  • NP:V436I

    • RdRp

  • RdRp:D2E
  • RdRp:S6N
  • RdRp:S19T
  • RdRp:Y60N
  • RdRp:S67E
  • RdRp:R80K
  • RdRp:V82I
  • RdRp:I114V
  • RdRp:I131L
  • RdRp:T163A
  • RdRp:R166K
  • RdRp:A168T
  • RdRp:M172V
  • RdRp:R174K
  • RdRp:S201G
  • RdRp:A202P
  • RdRp:S205P
  • RdRp:N206Y
    • Deletions
    GPC:129-131, GPC:180, GPC:187, GPC:195, GPC:196, GPC:211-217, GPC:223-228, GPC:291, GPC:292
    Insertions
    ins_GPC:186:ST

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