TB-Profiler result

Run: ERR3287746
Summary

Run ID: ERR3287746

Sample name:

Date: 01-04-2023 01:38:05

Number of reads: 3196991

Percentage reads mapped: 99.76

Strain: lineage4.3.4.1

Drug-resistance: HR-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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.1 Euro-American (LAM) LAM1;LAM2 RD174 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
ahpC 2726141 c.-52C>T upstream_gene_variant 1.0 isoniazid
embA 4243217 c.-16C>G upstream_gene_variant 1.0 ethambutol
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
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
gyrB 6028 c.789C>T synonymous_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.99
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 759608 c.-199C>T upstream_gene_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 778973 c.-493T>A upstream_gene_variant 0.29
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801066 c.258G>A synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 0.99
katG 2153911 p.Leu734Arg missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726323 p.Pro44Arg missense_variant 1.0
thyA 3073680 c.791dupG frameshift_variant&stop_lost&splice_region_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448598 p.Ile32Thr missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
rpoA 3878270 p.Leu80Val missense_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4268982 c.-146G>A upstream_gene_variant 1.0
gid 4407929 p.Glu92Lys missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0
whiB6 4338071 c.-2145_*99del transcript_ablation 1.0