TB-Profiler result

Run: ERR11465579
Summary

Run ID: ERR11465579

Sample name:

Date: 2024-04-15T20:35:23.092330

Number of reads: 1589868

Percentage reads mapped: 99.41

Median coverage: 36.0

Strain: lineage4.3.4.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 1.0
lineage4.3.4.1 Euro-American (LAM) RD174 0.99
lineage4 Euro-American None 1.0
lineage4.3.4 Euro-American (LAM) RD174 0.99
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence Comment
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence
dnaA 876 c.876C>G synonymous_variant 0.13 isoniazid
dnaA 877 c.877T>C synonymous_variant 0.13 isoniazid
gyrA 6724 c.-578G>C upstream_gene_variant 0.15 levofloxacin
moxifloxacin
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8129 c.828T>C synonymous_variant 0.12 levofloxacin
moxifloxacin
gyrA 8903 c.1602T>C synonymous_variant 0.11 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13483 p.Ala26Thr missense_variant 0.97 isoniazid Uncertain significance
rpoB 761015 c.1209G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 763100 c.-270G>A upstream_gene_variant 0.15 rifampicin
rpoC 764405 c.1036_1038delAGGinsCC frameshift_variant&missense_variant 0.13 rifampicin
rpoC 764923 c.1554A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764995 c.1626C>G synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 765478 c.2109T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 775937 c.2544G>C synonymous_variant 0.17 clofazimine
bedaquiline
mmpL5 775946 c.2535C>G synonymous_variant 0.21 clofazimine
bedaquiline
mmpL5 775951 c.2530C>T synonymous_variant 0.26 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781793 c.234G>C synonymous_variant 0.13 streptomycin
rpsL 781796 p.Met79Ile missense_variant 0.12 streptomycin
sigE 1364434 p.Arg8Trp missense_variant 1.0 pyrazinamide Not assoc w R
Rv1258c 1406209 p.Ala378Thr missense_variant 1.0 streptomycin
isoniazid
pyrazinamide
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473062 n.1217T>G non_coding_transcript_exon_variant 0.19 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473201 n.1356A>T non_coding_transcript_exon_variant 0.2 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473202 n.1357C>T non_coding_transcript_exon_variant 0.18 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.3 streptomycin Uncertain significance
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
rrl 1474676 n.1019T>C non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474677 n.1020A>G non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474688 n.1031G>C non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474690 n.1033C>T non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475480 n.1823A>G non_coding_transcript_exon_variant 0.21 capreomycin
linezolid
rrl 1475483 n.1826C>T non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475508 n.1851A>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476015 n.2358G>C non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rrl 1476251 n.2594T>G non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid
rrl 1476256 n.2599A>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1834639 c.1098T>C synonymous_variant 0.13 pyrazinamide
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
PPE35 2167745 p.Thr956Arg missense_variant 0.16 pyrazinamide
Rv1979c 2222854 p.Ile104Thr missense_variant 0.94 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518864 c.750G>C synonymous_variant 0.14 isoniazid
thyA 3073868 p.Thr202Ala missense_variant 1.0 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 0.96 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
rpoA 3877926 c.582G>C synonymous_variant 0.2 rifampicin
clpC1 4038287 c.2418C>T synonymous_variant 1.0 pyrazinamide Not assoc w R
clpC1 4039898 c.807C>G synonymous_variant 0.24 pyrazinamide
clpC1 4039991 c.714G>A synonymous_variant 0.98 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
whiB6 4338840 c.-319T>G upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4408156 p.Leu16Arg missense_variant 1.0 streptomycin Not assoc w R