TB-Profiler result

Run: ERR4799055
Summary

Run ID: ERR4799055

Sample name:

Date: 20-10-2023 03:09:28

Number of reads: 2510073

Percentage reads mapped: 99.21

Strain: lineage4.8;lineage1.2.2.2

Drug-resistance: Sensitive

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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
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 0.13
lineage1 Indo-Oceanic EAI RD239 0.73
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.11
lineage1.2.2 Indo-Oceanic EAI1 RD239 0.76
lineage3.1.2 East-African-Indian CAS;CAS2 RD750 0.05
lineage1.2.2.2 Indo-Oceanic NA RD239 0.77
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
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 0.58
gyrB 6112 p.Met291Ile missense_variant 0.84
gyrA 7268 c.-34C>T upstream_gene_variant 0.72
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.83
gyrA 8452 p.Ala384Val missense_variant 0.82
gyrA 9143 c.1842T>C synonymous_variant 0.86
gyrA 9304 p.Gly668Asp missense_variant 0.94
fgd1 491742 c.960T>C synonymous_variant 0.9
rpoB 759746 c.-61C>T upstream_gene_variant 0.19
rpoC 763031 c.-339T>C upstream_gene_variant 0.9
rpoC 763884 p.Ala172Val missense_variant 0.76
rpoC 763886 c.517C>A synonymous_variant 0.75
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.91
mmpL5 778426 p.Ala19Pro missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305438 c.2508C>T synonymous_variant 0.16
embR 1416778 c.570G>C synonymous_variant 0.7
embR 1417019 p.Cys110Tyr missense_variant 0.77
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 0.74
PPE35 2167926 p.Leu896Ser missense_variant 0.91
PPE35 2168742 p.Gly624Asp missense_variant 0.82
Rv1979c 2222308 p.Asp286Gly missense_variant 0.84
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 0.12
kasA 2518132 c.18C>T synonymous_variant 0.74
ahpC 2726051 c.-142G>A upstream_gene_variant 0.78
ald 3086788 c.-32T>C upstream_gene_variant 0.85
Rv3083 3448714 p.Asp71His missense_variant 0.93
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.79
fprA 3474597 c.591C>A synonymous_variant 0.79
fprA 3475159 p.Asn385Asp missense_variant 0.85
fbiA 3641432 p.Glu297Ala missense_variant 0.71
clpC1 4039385 c.1320C>T synonymous_variant 0.68
clpC1 4040517 p.Val63Ala missense_variant 0.75
embC 4240671 p.Thr270Ile missense_variant 0.69
embC 4241042 p.Asn394Asp missense_variant 0.78
embC 4242075 p.Arg738Gln missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 0.98
embA 4245969 p.Pro913Ser missense_variant 0.84
embB 4247646 p.Glu378Ala missense_variant 0.86
ubiA 4269387 p.Glu149Asp missense_variant 0.82
aftB 4269606 c.-770T>C upstream_gene_variant 0.82
ethA 4326148 c.1326G>T synonymous_variant 0.77
ethA 4326439 p.Asn345Lys missense_variant 0.74
whiB6 4338203 p.Arg107Cys missense_variant 0.8
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.87
gid 4407588 c.615A>G synonymous_variant 0.94
gid 4407848 p.Ala119Thr missense_variant 0.78
gid 4407873 c.330G>T synonymous_variant 0.76