TB-Profiler result

Run: ERR9992903
Summary

Run ID: ERR9992903

Sample name:

Date: 02-04-2023 13:55:01

Number of reads: 5300791

Percentage reads mapped: 99.65

Strain: lineage4.3.2.1

Drug-resistance: XDR-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 0.92
lineage4.3 Euro-American (LAM) mainly-LAM None 0.94
lineage4.3.2 Euro-American (LAM) LAM3 None 0.86
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 0.85
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
gyrA 7570 p.Ala90Val missense_variant 0.93 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.92 rifampicin
mmpR5 779181 c.198dupG frameshift_variant 0.56 clofazimine, bedaquiline
embB 4247429 p.Met306Val missense_variant 0.12 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 5520 p.Pro94Leu missense_variant 0.83
gyrA 7222 c.-80C>T upstream_gene_variant 0.8
gyrA 7268 c.-34C>T upstream_gene_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.13
mshA 576108 p.Ala254Gly missense_variant 0.31
rpoC 764995 c.1626C>G synonymous_variant 0.93
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 779364 c.377_382delGCGACG disruptive_inframe_deletion 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471666 n.-180A>C upstream_gene_variant 0.88
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 0.86
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726293 p.Tyr34Cys missense_variant 0.88
thyA 3073868 p.Thr202Ala missense_variant 0.91
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 0.93
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.92