TB-Profiler result

Run: ERR2516555
Summary

Run ID: ERR2516555

Sample name:

Date: 31-03-2023 21:36:21

Number of reads: 3750782

Percentage reads mapped: 99.5

Strain: lineage4.1

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
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.Asp435Gly missense_variant 0.99 rifampicin
rpoB 761149 p.Arg448Gln missense_variant 1.0 rifampicin
katG 2154109 c.2002dupT frameshift_variant 0.99 isoniazid, isoniazid
ahpC 2726141 c.-52C>T upstream_gene_variant 1.0 isoniazid
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
ethA 4326452 p.Ala341Val missense_variant 1.0 ethionamide
pncA 2288063 c.14_*617del frameshift_variant&stop_lost&splice_region_variant 1.0 pyrazinamide
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 8694 c.1393C>T synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 764613 p.Gln415Arg missense_variant 1.0
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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473306 n.1461A>G non_coding_transcript_exon_variant 1.0
rpsA 1834348 c.807T>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154676 p.Ala479Gly missense_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ribD 2987307 p.Ala157Pro missense_variant 0.3
thyA 3073806 c.666C>G synonymous_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449738 p.His412Arg missense_variant 0.96
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475346 p.Leu447Arg missense_variant 1.0
Rv3236c 3612515 p.Arg201His missense_variant 1.0
clpC1 4038857 c.1848C>A synonymous_variant 0.29
embC 4239842 c.-21C>A upstream_gene_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.18
embB 4249408 c.2895G>A synonymous_variant 1.0
whiB6 4338250 p.Ala91Gly missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408031 p.Leu58Phe missense_variant 1.0
whiB6 4337987 c.271_*183del stop_lost&conservative_inframe_deletion&splice_region_variant 1.0