TB-Profiler result

Run: ERR4831734
Summary

Run ID: ERR4831734

Sample name:

Date: 20-10-2023 12:58:58

Number of reads: 2692422

Percentage reads mapped: 99.53

Strain: lineage2.2.1;lineage1.1.1.1

Drug-resistance: HR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid R inhA c.-154G>A (0.83), katG p.Ser315Gly (0.89)
Ethambutol R embB p.Met306Val (0.86)
Pyrazinamide
Streptomycin R rpsL p.Lys43Arg (0.91)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R inhA c.-154G>A (0.83)
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage2 East-Asian Beijing RD105 0.87
lineage1 Indo-Oceanic EAI RD239 0.17
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.15
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.86
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.85
lineage1.1.1 Indo-Oceanic EAI4;EAI5 RD239 0.15
lineage1.1.1.1 Indo-Oceanic EAI4;ZERO RD239 0.14
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 781687 p.Lys43Arg missense_variant 0.91 streptomycin
inhA 1674048 c.-154G>A upstream_gene_variant 0.83 isoniazid, ethionamide
katG 2155169 p.Ser315Gly missense_variant 0.89 isoniazid
embB 4247429 p.Met306Val missense_variant 0.86 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 6112 p.Met291Ile missense_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.17
gyrA 9143 c.1842T>C synonymous_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 0.88
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763272 c.-98C>T upstream_gene_variant 0.14
rpoC 763884 p.Ala172Val missense_variant 0.12
rpoC 763886 c.517C>A synonymous_variant 0.12
rpoC 765171 p.Pro601Leu missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 0.82
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.87
embR 1417019 p.Cys110Tyr missense_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474709 n.1052G>T non_coding_transcript_exon_variant 0.12
rrl 1476584 n.2927C>G non_coding_transcript_exon_variant 0.2
inhA 1674687 c.486G>A synonymous_variant 0.16
rpsA 1834177 c.636A>C synonymous_variant 0.82
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 0.16
PPE35 2170177 p.Leu146Val missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 0.19
Rv2752c 3064632 c.1560C>T synonymous_variant 0.17
Rv2752c 3065129 c.1063C>T synonymous_variant 0.83
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474286 p.Ser94Ala missense_variant 0.24
fprA 3474597 c.591C>A synonymous_variant 0.22
fprA 3475159 p.Asn385Asp missense_variant 0.11
Rv3236c 3612037 p.Phe360Leu missense_variant 0.8
Rv3236c 3612813 p.Thr102Ala missense_variant 0.82
clpC1 4039869 p.Arg279Leu missense_variant 0.22
clpC1 4040517 p.Val63Ala missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.86
embA 4245969 p.Pro913Ser missense_variant 0.19
embB 4247646 p.Glu378Ala missense_variant 0.16
aftB 4267647 p.Asp397Gly missense_variant 0.93
ubiA 4269387 p.Glu149Asp missense_variant 0.16
aftB 4269606 c.-770T>C upstream_gene_variant 0.11
ethA 4326676 p.Ser266Arg missense_variant 0.92
whiB6 4338242 p.Gln94Glu missense_variant 0.13
whiB6 4338579 c.-58C>T upstream_gene_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.12
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 0.14
gid 4407927 p.Glu92Asp missense_variant 0.91