TB-Profiler result

Run: ERR11466444
Summary

Run ID: ERR11466444

Sample name:

Date: 2024-10-04T01:07:21.482428

Number of reads: 2027893

Percentage reads mapped: 99.0

Median coverage: 46.0

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 1.0
lineage4 Euro-American None 1.0
lineage4.3.4 Euro-American (LAM) RD174 1.0
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
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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13483 p.Ala26Thr missense_variant 1.0 isoniazid Uncertain significance
rpoB 761189 c.1383T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 761195 c.1389G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 761198 c.1392G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764662 c.1293G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764665 c.1296C>G synonymous_variant 0.14 rifampicin
rpoC 764995 c.1626C>G synonymous_variant 0.98 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 775924 c.2557C>T synonymous_variant 0.16 bedaquiline
clofazimine Not assoc w R - Interim
mmpL5 775937 c.2544G>C synonymous_variant 0.2 bedaquiline
clofazimine
mmpL5 775949 c.2532G>C synonymous_variant 0.17 bedaquiline
clofazimine
mmpL5 775961 c.2520C>G synonymous_variant 0.22 bedaquiline
clofazimine
mmpL5 775975 p.Leu836Met missense_variant 0.15 bedaquiline
clofazimine
mmpL5 775981 p.Leu834Met missense_variant 0.14 bedaquiline
clofazimine
mmpL5 777212 c.1269C>G synonymous_variant 0.14 bedaquiline
clofazimine
mmpL5 777215 c.1266C>G synonymous_variant 0.13 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
sigE 1364434 p.Arg8Trp missense_variant 1.0 pyrazinamide Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472380 n.535G>C non_coding_transcript_exon_variant 0.14 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472489 n.644A>G non_coding_transcript_exon_variant 0.17 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1474753 n.1096A>G non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475202 n.1545G>A non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1475206 n.1549C>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid
rrl 1475209 n.1552G>C non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid
rrl 1475213 n.1556C>T non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.35 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1475989 n.2332T>A non_coding_transcript_exon_variant 0.35 capreomycin
linezolid
rrl 1475997 n.2340A>T non_coding_transcript_exon_variant 0.36 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476032 n.2375C>T non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid
rrl 1476033 n.2376T>C non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid
rrl 1476034 n.2377C>G non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid
rrl 1476045 n.2388G>C non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1476049 n.2392C>T non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476165 n.2508T>A non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1833781 c.240T>G synonymous_variant 0.11 pyrazinamide
rpsA 1833979 c.438T>C synonymous_variant 0.11 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
Rv1979c 2222854 p.Ile104Thr missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
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 1.0 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625747 c.867G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3625755 p.Ala287Thr missense_variant 0.15 rifampicin Uncertain significance
bedaquiline
lpqB 3625762 c.-852A>C upstream_gene_variant 0.14 rifampicin
bedaquiline
mtrB 3625765 p.Ser283Gln missense_variant 0.14 rifampicin
bedaquiline
lpqB 3625795 c.-885G>C upstream_gene_variant 0.17 rifampicin
bedaquiline
clpC1 4038287 c.2418C>T synonymous_variant 1.0 pyrazinamide Not assoc w R
clpC1 4039991 c.714G>A synonymous_variant 1.0 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 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4408156 p.Leu16Arg missense_variant 1.0 streptomycin Not assoc w R