TB-Profiler result

Run: ERR4799443
Summary

Run ID: ERR4799443

Sample name:

Date: 20-10-2023 03:49:34

Number of reads: 3760801

Percentage reads mapped: 99.33

Strain: lineage1.1.2

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 c.1312_1314delAAC (0.96)
Isoniazid R katG p.Ser315Thr (0.99)
Ethambutol
Pyrazinamide R pncA c.391dupG (0.94), pncA c.391dupG (0.94)
Streptomycin
Fluoroquinolones R gyrB p.Asp461Asn (0.94), gyrA p.Ala90Val (0.98)
Moxifloxacin R gyrB p.Asp461Asn (0.94), gyrA p.Ala90Val (0.98)
Ofloxacin R gyrB p.Asp461Asn (0.94), gyrA p.Ala90Val (0.98)
Levofloxacin R gyrB p.Asp461Asn (0.94), gyrA p.Ala90Val (0.98)
Ciprofloxacin R gyrB p.Asp461Asn (0.94), gyrA p.Ala90Val (0.98)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine R ald c.436_437dupGC (0.96)
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
lineage1 Indo-Oceanic EAI RD239 0.98
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.96
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 0.98
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 6620 p.Asp461Asn missense_variant 0.94 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7570 p.Ala90Val missense_variant 0.98 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761114 c.1312_1314delAAC conservative_inframe_deletion 0.96 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.99 isoniazid
pncA 2288850 c.391dupG frameshift_variant 0.94 pyrazinamide, pyrazinamide
ald 3087252 c.436_437dupGC frameshift_variant 0.96 cycloserine
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 6112 p.Met291Ile missense_variant 0.95
gyrB 6124 c.885C>T synonymous_variant 0.94
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.96
gyrA 9143 c.1842T>C synonymous_variant 0.96
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 760490 c.684C>T synonymous_variant 0.97
rpoC 763031 c.-339T>C upstream_gene_variant 0.99
rpoC 763884 p.Ala172Val missense_variant 0.95
rpoC 763886 c.517C>A synonymous_variant 0.95
rpoC 765171 p.Pro601Leu missense_variant 0.95
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776395 p.Phe696Leu missense_variant 0.92
mmpR5 779474 p.Gly162Glu missense_variant 0.97
rpsL 781395 c.-165T>C upstream_gene_variant 0.99
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
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 2167983 p.Gly877Asp missense_variant 0.98
Rv1979c 2222308 p.Asp286Gly missense_variant 0.99
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.96
ahpC 2726051 c.-142G>A upstream_gene_variant 0.98
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3065065 p.Ala376Gly missense_variant 0.95
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.99
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 0.96
rpoA 3877872 c.636C>T synonymous_variant 0.96
rpoA 3878268 c.240C>T synonymous_variant 0.99
clpC1 4040517 p.Val63Ala missense_variant 0.97
embC 4240671 p.Thr270Ile missense_variant 0.97
embC 4241042 p.Asn394Asp missense_variant 0.97
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 0.97
embA 4245969 p.Pro913Ser missense_variant 0.99
embB 4247413 p.Asp300Glu missense_variant 0.97
embB 4247646 p.Glu378Ala missense_variant 0.97
ubiA 4269387 p.Glu149Asp missense_variant 0.94
aftB 4269606 c.-770T>C upstream_gene_variant 0.96
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.97
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 0.98
gid 4407977 p.Gly76Cys missense_variant 0.98