TB-Profiler result

Run: SRR25827506
Summary

Run ID: SRR25827506

Sample name:

Date: 02-02-2024 06:55:19

Number of reads: 9683261

Percentage reads mapped: 98.61

Strain: lineage4.8;lineage3

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.Ser450Leu (0.54)
Isoniazid R katG p.Ser315Thr (0.55)
Ethambutol R embB p.Met306Val (0.57)
Pyrazinamide R pncA p.Cys14* (0.43)
Streptomycin R rrs n.906A>G (0.39), gid c.351delG (0.54)
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 0.5
lineage4 Euro-American LAM;T;S;X;H None 0.5
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.49
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 761155 p.Ser450Leu missense_variant 0.54 rifampicin
rrs 1472751 n.906A>G non_coding_transcript_exon_variant 0.39 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.55 isoniazid
pncA 2289200 p.Cys14* stop_gained 0.43 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.57 ethambutol
gid 4407851 c.351delG frameshift_variant 0.54 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 0.53
gyrA 9304 p.Gly668Asp missense_variant 0.51
fgd1 491742 c.960T>C synonymous_variant 0.52
rpoB 759746 c.-61C>T upstream_gene_variant 0.53
rpoC 762434 c.-936T>G upstream_gene_variant 0.55
rpoC 763031 c.-339T>C upstream_gene_variant 0.48
rpoC 766488 p.Pro1040Arg missense_variant 0.51
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.5
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 0.58
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.48
PPE35 2167926 p.Leu896Ser missense_variant 0.49
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.5
pncA 2289365 c.-125delC upstream_gene_variant 0.5
ahpC 2726105 c.-88G>A upstream_gene_variant 0.43
ald 3086788 c.-32T>C upstream_gene_variant 0.54
fprA 3473820 c.-187C>A upstream_gene_variant 0.49
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.53
rpoA 3878637 c.-130G>C upstream_gene_variant 0.27
embC 4242075 p.Arg738Gln missense_variant 0.53
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245835 p.Leu868Arg missense_variant 0.16
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.48
gid 4408273 c.-72delG upstream_gene_variant 0.5