TB-Profiler result

Run: ERR11082848
Summary

Run ID: ERR11082848

Sample name:

Date: 11-04-2023 08:46:43

Number of reads: 554232

Percentage reads mapped: 99.55

Strain: lineage4.1.2.1

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
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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
gyrB 6470 p.Val411Met missense_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7367 p.Gln22His missense_variant 0.11
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9146 c.1845C>T synonymous_variant 0.16
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 576221 p.Gly292Arg missense_variant 1.0
mshA 576282 p.Leu312Pro missense_variant 0.13
rpoB 759749 c.-58T>A upstream_gene_variant 0.13
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 762856 p.Val1017Ala missense_variant 0.11
rpoB 762910 p.Ile1035Thr missense_variant 0.13
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765930 p.His854Leu missense_variant 0.11
rpoC 766759 c.3390G>A synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777469 p.Pro338Ser missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416995 p.Glu118Gly missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155028 p.Gly362Ser missense_variant 0.14
PPE35 2169428 c.1185C>T synonymous_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290057 c.-816G>A upstream_gene_variant 0.12
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
eis 2714650 c.682delG frameshift_variant 0.14
eis 2715546 c.-214C>T upstream_gene_variant 0.17
Rv2752c 3064823 p.Val457Leu missense_variant 0.29
Rv2752c 3066199 c.-8G>A upstream_gene_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087659 c.840G>A synonymous_variant 0.12
ald 3087818 p.Cys333Trp missense_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3640357 c.-186G>A upstream_gene_variant 0.11
rpoA 3878641 c.-134C>G upstream_gene_variant 0.29
clpC1 4038951 p.Phe585Tyr missense_variant 0.2
embC 4239722 c.-141C>T upstream_gene_variant 0.11
embC 4240409 p.Pro183Ala missense_variant 0.22
embC 4242153 p.Gly764Val missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242788 p.Gly976Cys missense_variant 0.11
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4246077 p.Ser949Arg missense_variant 0.18
embB 4246781 p.Ala90Thr missense_variant 0.12
embB 4247218 c.705G>T synonymous_variant 0.25
embB 4249077 p.Gln855Arg missense_variant 0.1
ethA 4328448 c.-975A>G upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0