TB-Profiler result

Run: ERR4800007

Summary

Run ID: ERR4800007

Sample name:

Date: 20-10-2023 04:11:07

Number of reads: 1689906

Percentage reads mapped: 99.22

Strain: lineage1.2.2.2

Drug-resistance: Other


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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid
Ethambutol
Pyrazinamide
Streptomycin R gid c.115delC (0.95)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
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
lineage1 Indo-Oceanic EAI RD239 0.96
lineage1.2.2 Indo-Oceanic EAI1 RD239 0.96
lineage1.2.2.2 Indo-Oceanic NA RD239 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
gid 4408087 c.115delC frameshift_variant 0.95 streptomycin
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 0.98
gyrB 6112 p.Met291Ile missense_variant 0.96
gyrA 7268 c.-34C>T upstream_gene_variant 0.94
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8164 p.Ala288Asp missense_variant 0.98
gyrA 8452 p.Ala384Val missense_variant 0.96
gyrA 9143 c.1842T>C synonymous_variant 0.93
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491293 p.Pro171Thr missense_variant 0.93
fgd1 491742 c.960T>C synonymous_variant 1.0
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
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
embR 1417019 p.Cys110Tyr missense_variant 0.96
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1673730 c.-472C>T upstream_gene_variant 0.94
rpsA 1834174 c.633C>T synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103076 c.-34C>T upstream_gene_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168742 p.Gly624Asp missense_variant 0.98
Rv1979c 2222308 p.Asp286Gly missense_variant 0.94
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 0.97
thyA 3074607 c.-136T>C upstream_gene_variant 1.0
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 1.0
fprA 3474597 c.591C>A synonymous_variant 0.96
fprA 3475159 p.Asn385Asp missense_variant 0.98
rpoA 3878065 p.Pro148Leu missense_variant 0.92
clpC1 4038608 c.2097C>T synonymous_variant 0.98
clpC1 4040517 p.Val63Ala missense_variant 0.95
embC 4240671 p.Thr270Ile missense_variant 0.96
embC 4241042 p.Asn394Asp missense_variant 0.98
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 0.95
embB 4247646 p.Glu378Ala missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 0.98
aftB 4269606 c.-770T>C upstream_gene_variant 0.96
ethA 4326148 c.1326G>T synonymous_variant 0.98
ethA 4326439 p.Asn345Lys missense_variant 1.0
whiB6 4338203 p.Arg107Cys missense_variant 0.98
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.98
gid 4407588 c.615A>G synonymous_variant 0.96
gid 4407873 c.330G>T synonymous_variant 0.97