TB-Profiler result

Run: SRR25827551
Summary

Run ID: SRR25827551

Sample name:

Date: 21-03-2024 12:33:13

Number of reads: 8607400

Percentage reads mapped: 99.04

Strain: lineage4.8;lineage3.1.2

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 (0.22), rpoC p.Leu527Val (0.20)
Isoniazid R katG p.Ser315Thr (0.51)
Ethambutol R embB p.Met306Ile (0.20)
Pyrazinamide
Streptomycin R gid c.102delG (0.38)
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 0.51
lineage4 Euro-American LAM;T;S;X;H None 0.44
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.46
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 0.31
lineage3.1.2 East-African-Indian CAS;CAS2 RD750 0.29
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 0.22 rifampicin
rpoC 764948 p.Leu527Val missense_variant 0.2 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.51 isoniazid
embB 4247431 p.Met306Ile missense_variant 0.2 ethambutol
gid 4408100 c.102delG frameshift_variant 0.38 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 0.51
gyrA 9304 p.Gly668Asp missense_variant 0.47
fgd1 491742 c.960T>C synonymous_variant 0.55
ccsA 620241 c.351C>G synonymous_variant 0.37
rpoB 759746 c.-61C>T upstream_gene_variant 0.6
rpoC 762434 c.-936T>G upstream_gene_variant 0.49
rpoC 763031 c.-339T>C upstream_gene_variant 0.54
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.57
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 0.52
PPE35 2167926 p.Leu896Ser missense_variant 0.57
PPE35 2168604 p.Pro670Leu missense_variant 0.35
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.55
pncA 2289365 c.-125delC upstream_gene_variant 0.51
ahpC 2726105 c.-88G>A upstream_gene_variant 0.55
ald 3086788 c.-32T>C upstream_gene_variant 0.49
ald 3087862 p.Gly348Glu missense_variant 0.23
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.51
embC 4242075 p.Arg738Gln missense_variant 0.58
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245131 c.1899G>A synonymous_variant 0.16
whiB6 4338194 p.Arg110Trp missense_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.55
gid 4407742 p.Arg154Pro missense_variant 0.21
gid 4408273 c.-72delG upstream_gene_variant 0.51