TB-Profiler result

Run: SRR25827365
Summary

Run ID: SRR25827365

Sample name:

Date: 01-02-2024 03:30:44

Number of reads: 4909660

Percentage reads mapped: 98.73

Strain: lineage3.1.3;lineage2.2.1

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
Rifampicin R rpoB p.His445Ser (0.64)
Isoniazid R katG p.Ser315Thr (0.67)
Ethambutol R embB p.Met306Leu (0.63)
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
lineage3 East-African-Indian CAS RD750 0.34
lineage2 East-Asian Beijing RD105 0.63
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.65
lineage3.1.3 East-African-Indian CAS RD750 0.35
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.65
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 761139 p.His445Ser missense_variant 0.64 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.67 isoniazid
embB 4247429 p.Met306Leu missense_variant 0.63 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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 0.35
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 0.66
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406613 p.Glu243Ala missense_variant 0.34
Rv1258c 1406760 c.580_581insC frameshift_variant 0.64
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834159 c.618G>A synonymous_variant 0.34
rpsA 1834177 c.636A>C synonymous_variant 0.68
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2222732 c.432delT frameshift_variant 0.39
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 0.36
kasA 2518980 p.Arg289Thr missense_variant 0.68
ahpC 2726105 c.-88G>A upstream_gene_variant 0.31
folC 2747504 p.His32Arg missense_variant 0.59
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.68
fbiB 3640879 c.-656C>T upstream_gene_variant 0.61
embC 4241952 p.Arg697Lys missense_variant 0.38
embC 4242075 p.Arg738Gln missense_variant 0.39
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.64
embB 4247506 c.993C>T synonymous_variant 0.39
embB 4249195 c.2682C>A synonymous_variant 0.34
aftB 4267647 p.Asp397Gly missense_variant 0.7
ethA 4326474 p.Pro334Ala missense_variant 0.63
ethA 4326735 p.Ala247Pro missense_variant 0.65
whiB6 4338293 p.Ala77Ser missense_variant 0.65
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 0.7
gid 4408175 p.Ala10Pro missense_variant 0.35