TB-Profiler result

Run: ERR2516067
Summary

Run ID: ERR2516067

Sample name:

Date: 20-10-2023 14:19:07

Number of reads: 1051337

Percentage reads mapped: 99.61

Strain: lineage4.1.2;lineage1.2.2.2

Drug-resistance: RR-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 (0.15)
Isoniazid
Ethambutol R embB p.Met306Val (0.23)
Pyrazinamide
Streptomycin
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
lineage4 Euro-American LAM;T;S;X;H None 0.9
lineage1 Indo-Oceanic EAI RD239 0.15
lineage4.1 Euro-American T;X;H None 0.83
lineage1.2.2 Indo-Oceanic EAI1 RD239 0.16
lineage4.1.2 Euro-American T;H None 0.82
lineage1.2.2.2 Indo-Oceanic NA RD239 0.12
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 761155 p.Ser450Leu missense_variant 0.15 rifampicin
embB 4247429 p.Met306Val missense_variant 0.23 ethambutol
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 0.29
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7879 p.Asn193Ser missense_variant 0.15
gyrA 8452 p.Ala384Val missense_variant 0.14
gyrA 9143 c.1842T>C synonymous_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.22
rpoC 763031 c.-339T>C upstream_gene_variant 0.13
rpoC 763552 c.183C>T synonymous_variant 0.25
rpoC 763884 p.Ala172Val missense_variant 0.34
rpoC 763886 c.517C>A synonymous_variant 0.35
rpoC 764333 p.Pro322Ser missense_variant 0.21
rpoC 765150 p.Gly594Glu missense_variant 0.84
rpoC 767123 p.Val1252Leu missense_variant 0.19
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 0.22
embR 1417140 p.Ala70Ser missense_variant 0.84
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673249 c.-191C>T upstream_gene_variant 0.82
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.13
PPE35 2167926 p.Leu896Ser missense_variant 0.2
PPE35 2168742 p.Gly624Asp missense_variant 0.24
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.22
ahpC 2726051 c.-142G>A upstream_gene_variant 0.18
folC 2747022 p.Val193Ile missense_variant 0.83
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.17
Rv3083 3448894 p.Tyr131Asp missense_variant 0.91
Rv3083 3449642 p.Asn380Ser missense_variant 0.93
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.17
fprA 3475159 p.Asn385Asp missense_variant 0.21
fbiA 3641164 p.Ile208Val missense_variant 0.96
clpC1 4040517 p.Val63Ala missense_variant 0.15
clpC1 4040719 c.-15A>G upstream_gene_variant 0.2
embC 4240671 p.Thr270Ile missense_variant 0.18
embC 4241042 p.Asn394Asp missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.84
embB 4246979 p.Gly156Cys missense_variant 0.29
aftB 4268861 c.-25T>C upstream_gene_variant 0.8
ubiA 4269387 p.Glu149Asp missense_variant 0.24
aftB 4269606 c.-770T>C upstream_gene_variant 0.18
ethA 4326148 c.1326G>T synonymous_variant 0.14
ethA 4326439 p.Asn345Lys missense_variant 0.18
whiB6 4338203 p.Arg107Cys missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.26
gid 4407588 c.615A>G synonymous_variant 0.28
gid 4407848 p.Ala119Thr missense_variant 0.13