TB-Profiler result

Run: SRR24035887
Summary

Run ID: SRR24035887

Sample name:

Date: 14-04-2023 01:35:21

Number of reads: 443001

Percentage reads mapped: 99.44

Strain: lineage4.1.2

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 1.0
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 1.0
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766189 c.2822delG frameshift_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777484 p.Gln333* stop_gained 0.15
mmpR5 778994 p.Ser2Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800659 c.-150A>T upstream_gene_variant 0.2
rplC 800956 p.Val50Met missense_variant 0.14
embR 1416352 c.996C>T synonymous_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673519 p.Ile27Asn missense_variant 0.25
inhA 1674359 p.Arg53Gln missense_variant 0.15
rpsA 1833661 c.120A>G synonymous_variant 0.2
rpsA 1833667 c.126C>G synonymous_variant 0.2
rpsA 1833721 c.180A>G synonymous_variant 0.25
rpsA 1833724 c.183C>G synonymous_variant 0.25
rpsA 1833727 c.186G>C synonymous_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102056 c.987G>A synonymous_variant 1.0
ndh 2102337 p.Leu236Met missense_variant 0.14
katG 2156029 p.Tyr28Phe missense_variant 0.14
PPE35 2170607 c.4_5dupCA frameshift_variant 1.0
Rv1979c 2222640 c.525G>C synonymous_variant 1.0
Rv1979c 2222834 p.Ser111Pro missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.25
ribD 2987454 p.Asp206His missense_variant 1.0
ribD 2987506 p.Leu223Arg missense_variant 0.21
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
ddn 3987238 c.397delT frameshift_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4245521 c.-993G>A upstream_gene_variant 0.12
embB 4246529 p.Ser6Arg missense_variant 0.4
embB 4247028 p.Leu172Arg missense_variant 0.29
embB 4248324 p.Ala604Gly missense_variant 0.15
embB 4249588 c.3075C>A synonymous_variant 0.12
aftB 4267981 p.Arg286Trp missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0