TB-Profiler result

Run: ERR1035319

Summary

Run ID: ERR1035319

Sample name:

Date: 31-03-2023 10:10:40

Number of reads: 7098518

Percentage reads mapped: 99.6

Strain: lineage4.6.4;lineage4.3.3

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 0.15
lineage4.6 Euro-American T;LAM None 0.86
lineage4.6.4 Euro-American T;LAM None 0.86
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.16
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
rpsL 781822 p.Lys88Met missense_variant 0.16 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289016 p.Thr76Pro missense_variant 0.97 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.85 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 1.0
gyrA 8040 p.Gly247Ser missense_variant 0.15
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 762715 p.Val970Ala missense_variant 0.82
mmpL5 775639 p.Ile948Val missense_variant 0.99
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474750 n.1093C>T non_coding_transcript_exon_variant 0.91
inhA 1674685 p.Thr162Ala missense_variant 0.91
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2222795 p.Asp124Asn missense_variant 0.87
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288792 c.450C>T synonymous_variant 0.92
kasA 2518919 p.Gly269Ser missense_variant 0.15
eis 2714393 p.Val314Leu missense_variant 0.83
thyA 3073806 c.666C>G synonymous_variant 0.23
thyA 3073868 p.Thr202Ala missense_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3641176 p.Ala212Pro missense_variant 0.14
clpC1 4038287 c.2418C>T synonymous_variant 0.16
embC 4242182 p.Ala774Ser missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4248437 p.Thr642Ala missense_variant 0.1
aftB 4268040 p.Leu266Pro missense_variant 0.2
ethA 4326693 p.Arg261Trp missense_variant 0.85
ethA 4327229 p.Leu82Pro missense_variant 0.1
whiB6 4338546 c.-25G>C upstream_gene_variant 0.85
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407946 p.Leu86Pro missense_variant 0.92
gid 4408156 p.Leu16Arg missense_variant 0.16