TB-Profiler result

Run: ERR4797182
Summary

Run ID: ERR4797182

Sample name:

Date: 20-10-2023 02:14:03

Number of reads: 3228677

Percentage reads mapped: 99.3

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.Ser450Leu (0.99)
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Ile (0.20), embB p.Gln497Arg (0.86)
Pyrazinamide R pncA c.397_412dupATTGCCACCGATCATT (0.54)
Streptomycin R rpsL p.Lys43Arg (0.87)
Fluoroquinolones R gyrA p.Asp94Gly (0.78)
Moxifloxacin R gyrA p.Asp94Gly (0.78)
Ofloxacin R gyrA p.Asp94Gly (0.78)
Levofloxacin R gyrA p.Asp94Gly (0.78)
Ciprofloxacin R gyrA p.Asp94Gly (0.78)
Aminoglycosides R rrs n.1401A>G (0.76)
Amikacin R rrs n.1401A>G (0.76)
Capreomycin R rrs n.1401A>G (0.76)
Kanamycin R rrs n.1401A>G (0.76)
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 0.16
lineage4 Euro-American LAM;T;S;X;H None 0.86
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.82
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 7582 p.Asp94Gly missense_variant 0.78 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.99 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.87 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.76 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288829 c.397_412dupATTGCCACCGATCATT frameshift_variant 0.54 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 0.2 ethambutol
embB 4248003 p.Gln497Arg missense_variant 0.86 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 0.22
gyrA 9304 p.Gly668Asp missense_variant 0.17
fgd1 491310 c.528C>T synonymous_variant 0.15
fgd1 491742 c.960T>C synonymous_variant 0.18
ccsA 620854 p.Gly322Ser missense_variant 0.18
rpoB 759746 c.-61C>T upstream_gene_variant 0.1
rpoC 762434 c.-936T>G upstream_gene_variant 0.16
rpoC 763031 c.-339T>C upstream_gene_variant 0.14
rpoC 764817 p.Val483Ala missense_variant 0.21
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.26
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 0.78
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.22
PPE35 2167926 p.Leu896Ser missense_variant 0.27
PPE35 2168149 p.Pro822Ser missense_variant 0.87
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 0.17
ahpC 2726105 c.-88G>A upstream_gene_variant 0.24
ald 3086788 c.-32T>C upstream_gene_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.21
Rv3236c 3612659 p.Ser153Leu missense_variant 0.17
clpC1 4039729 p.Asp326Asn missense_variant 0.71
embC 4242075 p.Arg738Gln missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246277 c.-237G>C upstream_gene_variant 0.28
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.17
gid 4407980 p.Pro75Ser missense_variant 0.19