TB-Profiler result

Run: ERR4800202

Summary

Run ID: ERR4800202

Sample name:

Date: 20-10-2023 03:57:57

Number of reads: 4596454

Percentage reads mapped: 99.55

Strain: lineage3.1.2.1

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.His445Tyr (0.92)
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Ile (0.97)
Pyrazinamide
Streptomycin R rrs n.517C>T (0.96)
Fluoroquinolones R gyrA p.Asp94Gly (0.76)
Moxifloxacin R gyrA p.Asp94Gly (0.76)
Ofloxacin R gyrA p.Asp94Gly (0.76)
Levofloxacin R gyrA p.Asp94Gly (0.76)
Ciprofloxacin R gyrA p.Asp94Gly (0.76)
Aminoglycosides
Amikacin R eis c.-14C>T (0.99)
Capreomycin R tlyA p.Leu74Pro (0.28)
Kanamycin R eis c.-14C>T (0.99)
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 0.98
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 0.98
lineage3.1.2 East-African-Indian CAS;CAS2 RD750 0.97
lineage3.1.2.1 East-African-Indian CAS2 RD750 0.97
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 0.76 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761139 p.His445Tyr missense_variant 0.92 rifampicin
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.96 streptomycin
tlyA 1918160 p.Leu74Pro missense_variant 0.28 capreomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
eis 2715346 c.-14C>T upstream_gene_variant 0.99 kanamycin, amikacin
embB 4247431 p.Met306Ile missense_variant 0.97 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 0.99
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 0.96
rpoC 763031 c.-339T>C upstream_gene_variant 0.99
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.99
mmpS5 778941 c.-36A>G upstream_gene_variant 0.97
mmpR5 779045 p.Phe19Ser missense_variant 0.8
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474706 n.1049G>T non_coding_transcript_exon_variant 0.97
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168604 p.Pro670Leu missense_variant 0.98
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.97
pncA 2289365 c.-125delC upstream_gene_variant 0.97
ahpC 2726105 c.-88G>A upstream_gene_variant 0.98
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 0.97
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.99
gid 4407989 p.Ala72Thr missense_variant 0.97