TB-Profiler result

Run: ERR4799589
Summary

Run ID: ERR4799589

Sample name:

Date: 20-10-2023 03:51:46

Number of reads: 2677501

Percentage reads mapped: 99.3

Strain: lineage1.2.2.2

Drug-resistance: MDR-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.Leu452Pro (0.98)
Isoniazid R fabG1 c.-8T>A (0.95), inhA p.Ile21Thr (0.98), katG p.Ala110Val (0.96)
Ethambutol R embA c.-16C>T (0.98)
Pyrazinamide R pncA p.Gly162Asp (0.90)
Streptomycin R rrs n.514A>C (0.97)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R inhA p.Ile21Thr (0.98), ethA c.864delC (0.95), ethA c.864delC (0.95)
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
lineage1.2.2 Indo-Oceanic EAI1 RD239 0.97
lineage1.2.2.2 Indo-Oceanic NA 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
rpoB 761161 p.Leu452Pro missense_variant 0.98 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.97 streptomycin
fabG1 1673432 c.-8T>A upstream_gene_variant 0.95 isoniazid
inhA 1674263 p.Ile21Thr missense_variant 0.98 isoniazid, ethionamide
katG 2155783 p.Ala110Val missense_variant 0.96 isoniazid
pncA 2288757 p.Gly162Asp missense_variant 0.9 pyrazinamide
embA 4243217 c.-16C>T upstream_gene_variant 0.98 ethambutol
ethA 4326609 c.864delC frameshift_variant 0.95 ethionamide, 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 5075 c.-165C>T upstream_gene_variant 0.95
gyrB 6112 p.Met291Ile missense_variant 0.98
gyrA 7268 c.-34C>T upstream_gene_variant 0.95
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.98
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 761330 c.1524G>A synonymous_variant 0.98
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.97
rpoC 763886 c.517C>A synonymous_variant 0.97
rpoC 765877 c.2508C>T synonymous_variant 0.95
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpR5 779236 p.Leu83Phe missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475687 n.2030C>A non_coding_transcript_exon_variant 0.96
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102240 p.Arg268His missense_variant 0.98
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168742 p.Gly624Asp missense_variant 0.99
Rv1979c 2222308 p.Asp286Gly missense_variant 0.98
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 0.96
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.97
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 0.94
embB 4247702 p.Pro397Ser missense_variant 0.97
aftB 4268545 p.Leu98Phe missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 0.97
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326148 c.1326G>T synonymous_variant 0.97
ethA 4326330 p.Tyr382Asn missense_variant 0.99
ethA 4326439 p.Asn345Lys missense_variant 0.95
whiB6 4338203 p.Arg107Cys missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.99
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407848 p.Ala119Thr missense_variant 0.95
gid 4407873 c.330G>T synonymous_variant 0.98