TB-Profiler result

Run: ERR2513498
Summary

Run ID: ERR2513498

Sample name:

Date: 20-10-2023 10:51:19

Number of reads: 4284721

Percentage reads mapped: 99.5

Strain: lineage5.1.2;lineage4.1.1.3

Drug-resistance: Pre-XDR-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.Asp435Tyr (0.64)
Isoniazid
Ethambutol
Pyrazinamide
Streptomycin
Fluoroquinolones R gyrA p.Ala90Val (0.15)
Moxifloxacin R gyrA p.Ala90Val (0.15)
Ofloxacin R gyrA p.Ala90Val (0.15)
Levofloxacin R gyrA p.Ala90Val (0.15)
Ciprofloxacin R gyrA p.Ala90Val (0.15)
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 0.84
lineage5 West-Africa 1 AFRI_2;AFRI_3 RD711 0.16
lineage4.1 Euro-American T;X;H None 0.83
lineage5.1.2 West-Africa 1 AFRI_2;AFRI_3 RD711 0.14
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 0.82
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 0.85
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
gyrA 7570 p.Ala90Val missense_variant 0.15 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761109 p.Asp435Tyr missense_variant 0.64 rifampicin
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 9143 c.1842T>C synonymous_variant 0.1
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9566 c.2265C>T synonymous_variant 0.12
fgd1 491035 p.Val85Ile missense_variant 0.12
fgd1 491216 p.Gly145Ala missense_variant 0.12
fgd1 491742 c.960T>C synonymous_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 0.15
rpoC 765150 p.Gly594Glu missense_variant 0.82
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 0.17
Rv1258c 1406382 p.Val320Ala missense_variant 0.15
Rv1258c 1407273 p.Asp23Val missense_variant 0.16
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1673338 c.-864G>A upstream_gene_variant 0.12
rpsA 1834957 c.1416C>T synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 0.11
PPE35 2170265 c.347delG frameshift_variant 0.15
Rv1979c 2223170 c.-6G>A upstream_gene_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 0.84
ald 3087084 c.266delA frameshift_variant 0.15
Rv3083 3449644 p.Ala381Thr missense_variant 0.21
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 0.18
alr 3840932 c.489C>T synonymous_variant 0.16
rpoA 3878493 c.15G>A synonymous_variant 0.12
ddn 3986987 c.144G>T synonymous_variant 0.25
ddn 3987180 p.Asp113Asn missense_variant 0.15
embC 4239843 c.-20A>C upstream_gene_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.88
embA 4244635 p.Val468Ala missense_variant 0.17
embA 4245147 p.Pro639Ser missense_variant 0.14
embB 4247646 p.Glu378Ala missense_variant 0.1
embB 4249408 c.2895G>A synonymous_variant 0.91
ubiA 4269387 p.Glu149Asp missense_variant 0.12
ethR 4326928 c.-621G>A upstream_gene_variant 0.14
ethR 4326976 c.-573G>A upstream_gene_variant 0.18
ethA 4327103 p.Gly124Asp missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407798 c.405G>T synonymous_variant 0.87