TB-Profiler result

Run: SRR25827351

Summary

Run ID: SRR25827351

Sample name:

Date: 01-02-2024 02:32:07

Number of reads: 3960404

Percentage reads mapped: 49.85

Strain: lineage4.1.1.3;lineage2.2.1

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 (1.00), rpoC p.Ile491Thr (0.26)
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol R embA c.-16C>T (0.29)
Pyrazinamide R pncA p.Ile5Ser (0.28)
Streptomycin R rpsL p.Lys43Arg (0.29)
Fluoroquinolones R gyrA p.Asp94Gly (1.00)
Moxifloxacin R gyrA p.Asp94Gly (1.00)
Ofloxacin R gyrA p.Asp94Gly (1.00)
Levofloxacin R gyrA p.Asp94Gly (1.00)
Ciprofloxacin R gyrA p.Asp94Gly (1.00)
Aminoglycosides R rrs n.1401A>G (0.73)
Amikacin R rrs n.1401A>G (0.73)
Capreomycin R rrs n.1401A>G (0.73)
Kanamycin R rrs n.1401A>G (0.73), eis c.-12C>T (0.32)
Cycloserine
Ethionamide R ethA c.1290delC (0.20), ethA c.1290delC (0.20)
Clofazimine
Para-aminosalicylic_acid R thyA p.Thr22Ala (0.30)
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage2 East-Asian Beijing RD105 0.27
lineage4 Euro-American LAM;T;S;X;H None 0.72
lineage4.1 Euro-American T;X;H None 0.7
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.29
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.29
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 0.7
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 0.74
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 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpoC 764841 p.Ile491Thr missense_variant 0.26 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.29 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.73 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289228 p.Ile5Ser missense_variant 0.28 pyrazinamide
eis 2715344 c.-12C>T upstream_gene_variant 0.32 kanamycin
thyA 3074408 p.Thr22Ala missense_variant 0.3 para-aminosalicylic_acid
embA 4243217 c.-16C>T upstream_gene_variant 0.29 ethambutol
ethA 4326183 c.1290delC frameshift_variant 0.2 ethionamide, ethionamide
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 491290 p.Val170Met missense_variant 0.3
fgd1 491742 c.960T>C synonymous_variant 0.26
mshA 575907 p.Ala187Val missense_variant 0.27
ccsA 620625 p.Ile245Met missense_variant 0.27
rpoC 763031 c.-339T>C upstream_gene_variant 0.31
rpoC 765150 p.Gly594Glu missense_variant 0.75
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.34
mmpL5 776182 p.Asp767Asn missense_variant 0.28
mmpS5 779615 c.-710C>G upstream_gene_variant 0.29
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.26
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.33
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918478 p.Leu180Arg missense_variant 0.29
katG 2154724 p.Arg463Leu missense_variant 0.3
PPE35 2167926 p.Leu896Ser missense_variant 0.24
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyX 3067949 c.-4C>T upstream_gene_variant 0.29
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 0.23
alr 3840423 p.Arg333Lys missense_variant 0.71
embC 4241022 p.Ala387Val missense_variant 0.26
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.71
embA 4243460 c.228C>T synonymous_variant 0.31
embB 4247028 p.Leu172Arg missense_variant 0.28
embB 4247847 p.Gln445Arg missense_variant 0.23
embB 4249408 c.2895G>A synonymous_variant 0.75
aftB 4267647 p.Asp397Gly missense_variant 0.22
whiB6 4338292 p.Ala77Val missense_variant 0.27
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.24
gid 4407620 p.Tyr195His missense_variant 0.24
gid 4407927 p.Glu92Asp missense_variant 0.32