TB-Profiler result

Run: ERR4796969
Summary

Run ID: ERR4796969

Sample name:

Date: 01-04-2023 07:15:02

Number of reads: 5786978

Percentage reads mapped: 98.76

Strain: lineage4.8

Drug-resistance: Pre-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 1.0
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
gyrB 6735 p.Asn499Thr missense_variant 0.99 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761139 p.His445Cys missense_variant 0.99 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.98 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289252 c.-11A>G upstream_gene_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.99 ethambutol
ethA 4326972 c.501delG frameshift_variant 1.0 ethionamide, ethionamide
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 5332 c.93C>T synonymous_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8168 p.Glu289Asp missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.26
mshA 576113 p.Arg256Gly missense_variant 0.22
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 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2170065 p.Ala183Gly missense_variant 0.21
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2747470 p.Ile43Ala missense_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.15
fbiD 3339734 p.Ala206Gly missense_variant 0.52
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
whiB7 3568428 c.252A>G synonymous_variant 0.22
clpC1 4039729 p.Asp326Asn missense_variant 0.98
embC 4240409 p.Pro183Ala missense_variant 0.21
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245417 p.Gly729Arg missense_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.24
embB 4248324 p.Ala604Gly missense_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0