TB-Profiler result

Run: SRR25827525

Summary

Run ID: SRR25827525

Sample name:

Date: 15-02-2024 05:21:10

Number of reads: 8366857

Percentage reads mapped: 98.95

Strain: lineage4.8;lineage3

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
Rifampicin R rpoB p.Asn437Asp (0.27), rpoB p.Leu452Pro (0.30)
Isoniazid R katG p.Ser315Thr (0.26)
Ethambutol R embB p.Met306Leu (0.27)
Pyrazinamide R pncA p.Pro54Leu (0.23)
Streptomycin R rpsL p.Lys43Arg (0.29)
Fluoroquinolones R gyrA p.Ala90Val (0.26)
Moxifloxacin R gyrA p.Ala90Val (0.26)
Ofloxacin R gyrA p.Ala90Val (0.26)
Levofloxacin R gyrA p.Ala90Val (0.26)
Ciprofloxacin R gyrA p.Ala90Val (0.26)
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 0.73
lineage4 Euro-American LAM;T;S;X;H None 0.27
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.25
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 0.26 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761115 p.Asn437Asp missense_variant 0.27 rifampicin
rpoB 761161 p.Leu452Pro missense_variant 0.3 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.29 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.26 isoniazid
pncA 2289081 p.Pro54Leu missense_variant 0.23 pyrazinamide
embB 4247429 p.Met306Leu missense_variant 0.27 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 0.73
gyrA 9304 p.Gly668Asp missense_variant 0.67
fgd1 491742 c.960T>C synonymous_variant 0.76
rpoB 759746 c.-61C>T upstream_gene_variant 0.75
rpoC 762434 c.-936T>G upstream_gene_variant 0.72
rpoC 763031 c.-339T>C upstream_gene_variant 0.75
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.74
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917884 c.-56G>A upstream_gene_variant 0.73
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.78
PPE35 2167926 p.Leu896Ser missense_variant 0.75
PPE35 2168149 p.Pro822Ser missense_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.78
pncA 2289365 c.-125delC upstream_gene_variant 0.73
ahpC 2726105 c.-88G>A upstream_gene_variant 0.73
ald 3086788 c.-32T>C upstream_gene_variant 0.81
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.7
clpC1 4039729 p.Asp326Asn missense_variant 0.21
embC 4242075 p.Arg738Gln missense_variant 0.69
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244738 c.1506C>T synonymous_variant 0.7
embB 4247015 p.Ser168Ala missense_variant 0.23
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.8