TB-Profiler result

Run: ERR4812453
Summary

Run ID: ERR4812453

Sample name:

Date: 20-10-2023 05:20:49

Number of reads: 4955266

Percentage reads mapped: 99.71

Strain: lineage4.4.1;lineage4.1.2.1

Drug-resistance: Other

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid
Ethambutol
Pyrazinamide R pncA c.-11A>G (0.11)
Streptomycin R gid p.Gln125* (0.22)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
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
lineage4.1 Euro-American T;X;H None 0.24
lineage4.4 Euro-American S;T None 0.79
lineage4.1.2 Euro-American T;H None 0.25
lineage4.4.1 Euro-American (S-type) S;T None 0.76
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.21
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
pncA 2289252 c.-11A>G upstream_gene_variant 0.11 pyrazinamide
gid 4407830 p.Gln125* stop_gained 0.22 streptomycin
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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 0.26
mshA 575679 p.Asn111Ser missense_variant 0.29
rpoB 760115 c.309C>T synonymous_variant 0.25
rpoC 765150 p.Gly594Glu missense_variant 0.33
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 1475227 n.1572dupA non_coding_transcript_exon_variant 0.75
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 0.76
PPE35 2169840 p.Gly258Asp missense_variant 0.78
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.22
pepQ 2860286 p.Val45Leu missense_variant 0.79
ribD 2986827 c.-12G>A upstream_gene_variant 0.2
Rv2752c 3066389 c.-198C>T upstream_gene_variant 0.76
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 0.78
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.22
whiB6 4338460 p.Met21Thr missense_variant 0.79
whiB6 4338520 c.2T>C start_lost 0.71
whiB6 4338595 c.-75delG upstream_gene_variant 1.0