TB-Profiler result

Run: SRR23862167
Summary

Run ID: SRR23862167

Sample name:

Date: 12-04-2023 21:52:03

Number of reads: 3930942

Percentage reads mapped: 99.68

Strain: lineage4.8

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
Streptomycin R rpsL p.Lys43Arg (1.00)
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
lineage4.8 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
rpsL 781687 p.Lys43Arg missense_variant 1.0 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
mshA 576100 c.753T>C synonymous_variant 0.17
mshA 576113 p.Arg256Gly missense_variant 0.32
mshA 576613 c.1266A>C synonymous_variant 0.22
mshA 576618 p.His424Pro missense_variant 0.21
mshA 576626 p.Thr427Pro missense_variant 0.27
mshA 576631 p.Phe428Leu missense_variant 0.25
mshA 576651 p.Asp435Ala missense_variant 0.22
mshA 576657 p.Leu437Arg missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 778107 p.Ser125Cys 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 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 2170098 p.Leu172Arg missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
whiB7 3568425 c.255T>G synonymous_variant 0.28
whiB7 3568437 c.243T>C synonymous_variant 0.21
whiB7 3568441 p.Lys80Thr missense_variant 0.17
rpoA 3878580 c.-73A>C upstream_gene_variant 0.21
rpoA 3878591 c.-84C>G upstream_gene_variant 0.18
rpoA 3878597 c.-90G>C upstream_gene_variant 0.36
rpoA 3878608 c.-101C>G upstream_gene_variant 0.5
rpoA 3878609 c.-102T>G upstream_gene_variant 0.33
rpoA 3878613 c.-106A>C upstream_gene_variant 0.71
rpoA 3878618 c.-111A>C upstream_gene_variant 0.43
rpoA 3878639 c.-133_-132insG upstream_gene_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247007 p.Lys165Thr missense_variant 0.18
embB 4247015 p.Ser168Ala missense_variant 0.28
embB 4247028 p.Leu172Arg missense_variant 0.24
ethA 4328378 c.-905G>C upstream_gene_variant 0.99
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0