TB-Profiler result

Run: ERR2679267

Summary

Run ID: ERR2679267

Sample name:

Date: 31-03-2023 23:00:42

Number of reads: 305831

Percentage reads mapped: 99.5

Strain: lineage4

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
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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpoC 765609 p.Asp747Ala missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embA 4243221 c.-12C>T upstream_gene_variant 1.0 ethambutol
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
gid 4407796 p.Ser136* stop_gained 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
mshA 575562 p.Met72Thr missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801105 c.297A>G synonymous_variant 0.12
fbiC 1304064 c.1134G>A synonymous_variant 0.12
embR 1417401 c.-54C>A upstream_gene_variant 0.12
embR 1417518 c.-171A>G upstream_gene_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154777 c.1335C>T synonymous_variant 0.13
katG 2154980 c.1132C>T synonymous_variant 1.0
PPE35 2168629 p.Ile662Val missense_variant 0.11
PPE35 2170596 p.Leu6Ser missense_variant 1.0
PPE35 2170811 c.-199C>T upstream_gene_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518127 p.Ser5Pro missense_variant 0.1
folC 2746991 p.Asp203Val missense_variant 0.17
folC 2747591 p.Ser3Trp missense_variant 0.12
Rv2752c 3065567 p.Pro209Ser missense_variant 0.14
Rv2752c 3066033 c.159C>T synonymous_variant 0.17
Rv3083 3449145 c.642G>A synonymous_variant 1.0
rpoA 3878417 p.Gly31Arg missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4268076 p.Met254Ala missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0