TB-Profiler result

Run: SRR25340863
Summary

Run ID: SRR25340863

Sample name:

Date: 29-01-2024 03:47:51

Number of reads: 11638031

Percentage reads mapped: 99.66

Strain: lineage4.8;lineage1.1.2

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.Ser428Arg (0.15)
Isoniazid
Ethambutol
Pyrazinamide
Streptomycin R rrs n.905C>A (0.91)
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 0.87
lineage1 Indo-Oceanic EAI RD239 0.1
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.1
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.88
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 0.11
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 761090 p.Ser428Arg missense_variant 0.15 rifampicin
rrs 1472750 n.905C>A non_coding_transcript_exon_variant 0.91 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.17
gyrA 9143 c.1842T>C synonymous_variant 0.13
fgd1 491742 c.960T>C synonymous_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 0.12
rpoC 763884 p.Ala172Val missense_variant 0.14
rpoC 763886 c.517C>A synonymous_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776395 p.Phe696Leu missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.84
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156563 c.-452G>A upstream_gene_variant 0.91
PPE35 2167983 p.Gly877Asp missense_variant 0.15
Rv1979c 2222308 p.Asp286Gly missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.14
ahpC 2726051 c.-142G>A upstream_gene_variant 0.19
Rv2752c 3064632 c.1560C>T synonymous_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 0.15
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 0.11
alr 3840713 c.708C>T synonymous_variant 0.13
ddn 3987057 p.Arg72Trp missense_variant 0.12
embC 4240671 p.Thr270Ile missense_variant 0.15
embC 4241042 p.Asn394Asp missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 0.16
embB 4247646 p.Glu378Ala missense_variant 0.14
ubiA 4269387 p.Glu149Asp missense_variant 0.15
aftB 4269606 c.-770T>C upstream_gene_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.14