TB-Profiler result

Run: ERR4800344
Summary

Run ID: ERR4800344

Sample name:

Date: 20-10-2023 04:18:54

Number of reads: 2994824

Percentage reads mapped: 99.57

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 (0.97)
Ethambutol R embB p.Met306Val (1.00)
Pyrazinamide R pncA c.-11A>G (0.97)
Streptomycin R rpsL p.Lys43Arg (1.00)
Fluoroquinolones R gyrB p.Thr500Asn (0.12), gyrA p.Ser91Pro (0.99)
Moxifloxacin R gyrB p.Thr500Asn (0.12), gyrA p.Ser91Pro (0.99)
Ofloxacin R gyrB p.Thr500Asn (0.12), gyrA p.Ser91Pro (0.99)
Levofloxacin R gyrB p.Thr500Asn (0.12), gyrA p.Ser91Pro (0.99)
Ciprofloxacin R gyrB p.Thr500Asn (0.12), gyrA p.Ser91Pro (0.99)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R ethA c.1047delT (0.11), ethA c.1047delT (0.11), ethA c.181dupA (0.17), ethA p.His22Pro (0.57)
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 0.99
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 0.98
lineage3.1.2 East-African-Indian CAS;CAS2 RD750 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
gyrB 6738 p.Thr500Asn missense_variant 0.12 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7572 p.Ser91Pro missense_variant 0.99 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.97 isoniazid
pncA 2289252 c.-11A>G upstream_gene_variant 0.97 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4326426 c.1047delT frameshift_variant 0.11 ethionamide, ethionamide
ethA 4327292 c.181dupA frameshift_variant 0.17 ethionamide
ethA 4327409 p.His22Pro missense_variant 0.57 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
gyrA 9758 c.2457C>T synonymous_variant 0.99
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575688 c.345delG frameshift_variant 0.16
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 0.99
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
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 1.0
tlyA 1918104 c.165G>A synonymous_variant 0.99
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 0.99
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 0.98
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
thyA 3074247 p.His75Gln missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449677 p.Asn392Asp missense_variant 0.21
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474291 c.285G>A synonymous_variant 1.0
clpC1 4040675 c.30C>G synonymous_variant 0.98
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4267442 p.Met465Ile missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0