TB-Profiler result

Run: ERR4423584
Summary

Run ID: ERR4423584

Sample name:

Date: 01-04-2023 05:54:15

Number of reads: 678126

Percentage reads mapped: 99.49

Strain: lineage4.1.3

Drug-resistance: MDR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.3 Euro-American T;X;H None 1.0
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
rpoB 761110 p.Asp435Val missense_variant 1.0 rifampicin
fabG1 1673432 c.-8T>C upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
gid 4407967 p.Leu79Ser missense_variant 1.0 streptomycin
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9557 c.2256G>C synonymous_variant 1.0
mshA 576578 p.Gly411Arg missense_variant 0.22
rpoB 761889 p.Val695Met missense_variant 0.13
rpoC 764240 p.Arg291Gly missense_variant 0.18
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781421 c.-139C>A upstream_gene_variant 1.0
fbiC 1304610 c.1680C>T synonymous_variant 1.0
embR 1416774 c.573delC frameshift_variant 0.3
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475192 n.1535C>G non_coding_transcript_exon_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.56
PPE35 2170053 p.Thr187Ser missense_variant 0.55
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519223 p.Thr370Asn missense_variant 0.22
kasA 2519226 p.Leu371Pro missense_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339454 p.Leu113Met missense_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4039273 p.Glu478* stop_gained 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4244184 p.Ser318Arg missense_variant 0.18
aftB 4267761 p.Asp359Gly missense_variant 0.15
ubiA 4269313 p.Lys174Thr missense_variant 0.17