TB-Profiler result

Run: ERR2516422
Summary

Run ID: ERR2516422

Sample name:

Date: 31-03-2023 21:31:40

Number of reads: 2115218

Percentage reads mapped: 99.72

Strain: lineage4.7

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
lineage4.7 Euro-American (mainly T) T1;T5 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
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 1.0 streptomycin
katG 2154912 c.1199dupA frameshift_variant 1.0 isoniazid
pncA 2289252 c.-11A>G upstream_gene_variant 1.0 pyrazinamide
ahpC 2726141 c.-52C>T upstream_gene_variant 1.0 isoniazid
embA 4243221 c.-12C>T upstream_gene_variant 1.0 ethambutol
embB 4247730 p.Gly406Ala 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
rpoC 764724 p.Phe452Cys missense_variant 0.98
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775715 c.2766G>A synonymous_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304233 p.Trp435Gly missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.21
Rv1979c 2222562 c.603C>T synonymous_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518617 p.Val168Gly missense_variant 1.0
ahpC 2726338 p.Val49Gly missense_variant 0.33
ribD 2987307 p.Ala157Pro missense_variant 0.12
Rv2752c 3065201 c.990delT frameshift_variant 1.0
thyA 3073806 c.666C>G synonymous_variant 0.18
alr 3841071 p.Gly117Asp missense_variant 1.0
clpC1 4038857 c.1848C>A synonymous_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243977 p.Ala249Thr missense_variant 1.0
embB 4248549 p.Ala679Val missense_variant 1.0
embB 4249732 c.3219C>G synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 0.97
gid 4407590 p.Ala205Thr missense_variant 1.0
gid 4407602 p.Thr201Pro missense_variant 1.0