TB-Profiler result

Run: ERR2653184

Summary

Run ID: ERR2653184

Sample name:

Date: 31-03-2023 22:37:55

Number of reads: 2397572

Percentage reads mapped: 97.44

Strain: lineage4.3.4.1

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
lineage4.3 Euro-American (LAM) mainly-LAM None 0.98
lineage4.3.4 Euro-American (LAM) LAM RD174 0.98
lineage4.3.4.1 Euro-American (LAM) LAM1;LAM2 RD174 0.97
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 0.97 rifampicin
rpoC 764363 p.Gly332Arg missense_variant 0.98 rifampicin
rrs 1472751 n.906A>G non_coding_transcript_exon_variant 0.91 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288787 c.454_455insT frameshift_variant 1.0 pyrazinamide
embB 4247730 p.Gly406Ala missense_variant 0.98 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
gyrA 7585 p.Ser95Thr missense_variant 0.99
gyrA 8715 p.Pro472Ser missense_variant 0.97
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576185 p.Pro280Thr missense_variant 0.58
rpoB 759608 c.-199C>T upstream_gene_variant 0.93
rpoC 764995 c.1626C>G synonymous_variant 0.97
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
rrl 1474571 n.914G>A non_coding_transcript_exon_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103149 c.-107G>A upstream_gene_variant 0.26
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726323 p.Pro44Arg missense_variant 0.95
pepQ 2859830 p.Gly197Arg missense_variant 0.95
Rv2752c 3066246 c.-55G>A upstream_gene_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 0.94
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448598 p.Ile32Thr missense_variant 0.98
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 0.96
Rv3236c 3612768 p.Ala117Pro missense_variant 0.95
alr 3841006 p.Asp139His missense_variant 0.95
clpC1 4038287 c.2418C>T synonymous_variant 0.97
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethA 4326137 p.Leu446Pro missense_variant 0.54
ethA 4326515 p.Phe320Ser missense_variant 0.23
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.96