TB-Profiler result

Run: ERR234635
Summary

Run ID: ERR234635

Sample name:

Date: 21-10-2023 13:09:01

Number of reads: 4726734

Percentage reads mapped: 99.36

Strain: lineage4.1;lineage1.1.1.1

Drug-resistance: HR-TB

Download CSV Download TXT Download PDF Download JSON
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid R fabG1 c.-8T>G (0.15), katG p.Ser315Thr (0.19)
Ethambutol
Pyrazinamide
Streptomycin R rpsL p.Lys88Arg (0.18)
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 0.18
lineage1 Indo-Oceanic EAI RD239 0.77
lineage4.1 Euro-American T;X;H None 0.15
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.76
lineage1.1.1 Indo-Oceanic EAI4;EAI5 RD239 0.78
lineage1.1.1.1 Indo-Oceanic EAI4;ZERO RD239 0.74
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
rpsL 781822 p.Lys88Arg missense_variant 0.18 streptomycin
fabG1 1673432 c.-8T>G upstream_gene_variant 0.15 isoniazid
katG 2155168 p.Ser315Thr missense_variant 0.19 isoniazid
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 5949 p.Ala237Val missense_variant 0.79
gyrB 6112 p.Met291Ile missense_variant 0.75
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7634 c.333C>T synonymous_variant 0.73
gyrA 8452 p.Ala384Val missense_variant 0.75
gyrA 9143 c.1842T>C synonymous_variant 0.76
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490972 p.Arg64Ser missense_variant 0.77
fgd1 491742 c.960T>C synonymous_variant 0.8
rpoC 763031 c.-339T>C upstream_gene_variant 0.73
rpoC 763884 p.Ala172Val missense_variant 0.75
rpoC 763886 c.517C>A synonymous_variant 0.73
rpoC 765171 p.Pro601Leu missense_variant 0.84
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.84
mmpL5 777027 p.Thr485Asn missense_variant 0.79
mmpL5 777310 p.Gly391Ser missense_variant 0.14
mmpL5 777581 p.Tyr300* stop_gained 0.77
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 0.78
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474709 n.1052G>T non_coding_transcript_exon_variant 0.72
rpsA 1834319 p.Val260Ile missense_variant 0.75
rpsA 1834772 p.Arg411Ser missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.84
katG 2156389 c.-278G>C upstream_gene_variant 0.78
PPE35 2167926 p.Leu896Ser missense_variant 0.82
PPE35 2167983 p.Gly877Asp missense_variant 0.78
PPE35 2168435 c.2178C>T synonymous_variant 0.17
PPE35 2168703 p.Gly637Asp missense_variant 0.84
Rv1979c 2222308 p.Asp286Gly missense_variant 0.81
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.69
ahpC 2726051 c.-142G>A upstream_gene_variant 0.71
Rv2752c 3064632 c.1560C>T synonymous_variant 0.77
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.73
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.82
fprA 3474774 c.768G>C synonymous_variant 0.2
fprA 3475159 p.Asn385Asp missense_variant 0.77
alr 3841505 c.-85C>T upstream_gene_variant 0.19
rpoA 3878630 c.-124delC upstream_gene_variant 0.64
clpC1 4040517 p.Val63Ala missense_variant 0.78
embC 4240671 p.Thr270Ile missense_variant 0.75
embC 4241042 p.Asn394Asp missense_variant 0.81
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.2
embA 4243848 p.Val206Met missense_variant 0.73
embA 4244096 c.864C>T synonymous_variant 0.84
embA 4245969 p.Pro913Ser missense_variant 0.79
embB 4247646 p.Glu378Ala missense_variant 0.82
embB 4247825 p.Ala438Thr missense_variant 0.78
embB 4249408 c.2895G>A synonymous_variant 0.22
ubiA 4269387 p.Glu149Asp missense_variant 0.78
aftB 4269606 c.-770T>C upstream_gene_variant 0.74
ethA 4326446 p.Gly343Ala missense_variant 0.14
ethR 4328005 p.Ile153Val missense_variant 0.82
ethA 4328299 c.-826A>G upstream_gene_variant 0.1
whiB6 4338242 p.Gln94Glu missense_variant 0.84
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.74
gid 4407588 c.615A>G synonymous_variant 0.86
gid 4407873 c.330G>T synonymous_variant 0.79