TB-Profiler result

Run: ERR4799976

Summary

Run ID: ERR4799976

Sample name:

Date: 20-10-2023 04:03:15

Number of reads: 2823936

Percentage reads mapped: 99.55

Strain: lineage3.1.2

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)
Isoniazid R katG p.Ser315Thr (0.91)
Ethambutol R embA c.-16C>T (0.96), embB p.Met306Ile (0.94)
Pyrazinamide
Streptomycin R rpsL p.Lys43Arg (0.99)
Fluoroquinolones R gyrA p.Ala90Val (0.99)
Moxifloxacin R gyrA p.Ala90Val (0.99)
Ofloxacin R gyrA p.Ala90Val (0.99)
Levofloxacin R gyrA p.Ala90Val (0.99)
Ciprofloxacin R gyrA p.Ala90Val (0.99)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid R thyA c.-4520_*2087del (0.98)
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 0.96
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 0.97
lineage3.1.2 East-African-Indian CAS;CAS2 RD750 0.96
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 7570 p.Ala90Val missense_variant 0.99 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.99 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.91 isoniazid
embA 4243217 c.-16C>T upstream_gene_variant 0.96 ethambutol
embB 4247431 p.Met306Ile missense_variant 0.94 ethambutol
thyA 3071592 c.-4520_*2087del transcript_ablation 0.98 para-aminosalicylic_acid
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
gyrA 9758 c.2457C>T synonymous_variant 0.96
fgd1 491742 c.960T>C synonymous_variant 0.98
rpoB 759746 c.-61C>T upstream_gene_variant 0.99
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 0.97
rpoC 767123 p.Val1252Leu missense_variant 0.91
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.95
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 0.99
tlyA 1918104 c.165G>A synonymous_variant 0.94
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168604 p.Pro670Leu missense_variant 0.93
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288929 p.Gly105Cys missense_variant 0.94
pncA 2289047 c.195C>T synonymous_variant 0.99
pncA 2289365 c.-125delC upstream_gene_variant 0.98
ahpC 2726105 c.-88G>A upstream_gene_variant 0.96
ahpC 2726773 c.583dupG frameshift_variant 0.95
thyX 3067948 c.-3G>T upstream_gene_variant 0.97
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474291 c.285G>A synonymous_variant 0.97
clpC1 4040675 c.30C>G synonymous_variant 0.97
embC 4240256 p.Leu132Ile missense_variant 0.99
embC 4242075 p.Arg738Gln missense_variant 0.99
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247701 p.Met396Ile missense_variant 0.94
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0