TB-Profiler result

Run: SRR25827490
Summary

Run ID: SRR25827490

Sample name:

Date: 21-03-2024 09:21:14

Number of reads: 5945242

Percentage reads mapped: 99.33

Strain: lineage2.2.1

Drug-resistance: 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), rpoB p.Ile480Val (0.74)
Isoniazid R katG p.Ser315Thr (0.99)
Ethambutol R embA c.-16C>T (0.84), embB p.Met306Val (0.97)
Pyrazinamide R pncA p.Tyr41* (0.20), pncA p.Ile5Ser (0.82)
Streptomycin R rpsL p.Lys43Arg (0.99)
Fluoroquinolones R gyrA p.His70Arg (0.78), gyrA p.Ala90Val (0.99)
Moxifloxacin R gyrA p.His70Arg (0.78), gyrA p.Ala90Val (0.99)
Ofloxacin R gyrA p.His70Arg (0.78), gyrA p.Ala90Val (0.99)
Levofloxacin R gyrA p.His70Arg (0.78), gyrA p.Ala90Val (0.99)
Ciprofloxacin R gyrA p.His70Arg (0.78), gyrA p.Ala90Val (0.99)
Aminoglycosides R rrs n.1401A>G (0.19)
Amikacin R rrs n.1401A>G (0.19), eis c.-14C>T (0.84)
Capreomycin R rrs n.1401A>G (0.19), tlyA c.590_591delTG (0.87)
Kanamycin R rrs n.1401A>G (0.19), eis c.-14C>T (0.84)
Cycloserine
Ethionamide R ethA c.80_81delGCinsA (1.00)
Clofazimine
Para-aminosalicylic_acid R thyA p.Thr22Ala (0.78)
Delamanid
Bedaquiline
Linezolid R rrl n.2814G>T (0.90)
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage2 East-Asian Beijing RD105 0.99
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.99
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.99
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 7510 p.His70Arg missense_variant 0.78 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7570 p.Ala90Val missense_variant 0.99 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpoB 761244 p.Ile480Val missense_variant 0.74 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.99 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.19 kanamycin, capreomycin, aminoglycosides, amikacin
rrl 1476471 n.2814G>T non_coding_transcript_exon_variant 0.9 linezolid
tlyA 1918527 c.590_591delTG frameshift_variant 0.87 capreomycin
katG 2155168 p.Ser315Thr missense_variant 0.99 isoniazid
pncA 2289119 p.Tyr41* stop_gained 0.2 pyrazinamide
pncA 2289228 p.Ile5Ser missense_variant 0.82 pyrazinamide
eis 2715346 c.-14C>T upstream_gene_variant 0.84 kanamycin, amikacin
thyA 3074408 p.Thr22Ala missense_variant 0.78 para-aminosalicylic_acid
embA 4243217 c.-16C>T upstream_gene_variant 0.84 ethambutol
embB 4247429 p.Met306Val missense_variant 0.97 ethambutol
ethA 4327393 c.80_81delGCinsA frameshift_variant&stop_gained 1.0 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
gyrB 6737 p.Thr500Ala missense_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 0.99
fgd1 491290 p.Val170Met missense_variant 0.83
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.97
ccsA 620553 c.663T>C synonymous_variant 0.22
ccsA 620625 p.Ile245Met missense_variant 0.99
rpoC 763031 c.-339T>C upstream_gene_variant 0.99
rpoC 764817 p.Val483Ala missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.99
mmpL5 776182 p.Asp767Asn missense_variant 0.99
mmpR5 779124 c.136delT frameshift_variant 0.78
mmpS5 779615 c.-710C>G upstream_gene_variant 0.98
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.99
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475927 n.2270G>T non_coding_transcript_exon_variant 0.8
rpsA 1834177 c.636A>C synonymous_variant 0.99
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.99
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyX 3067949 c.-4C>T upstream_gene_variant 0.75
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449861 c.1360dupC frameshift_variant 0.83
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
embC 4241022 p.Ala387Val missense_variant 0.81
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.98
embB 4247033 p.Ser174Arg missense_variant 0.13
embB 4249757 p.Thr1082Ala missense_variant 0.15
aftB 4267647 p.Asp397Gly missense_variant 0.99
whiB6 4338238 p.Leu95Arg missense_variant 0.83
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.99
gid 4407620 p.Tyr195His missense_variant 0.79
gid 4407927 p.Glu92Asp missense_variant 0.99