TB-Profiler result

Run: ERR12544072
Summary

Run ID: ERR12544072

Sample name:

Date: 22-02-2024 19:14:05

Number of reads: 2670602

Percentage reads mapped: 99.55

Strain: lineage6.2.3;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 0.47
lineage6 West-Africa 2 AFRI_1 RD702 0.54
lineage6.2 West-Africa 2 AFRI_1 RD702 0.49
lineage4.1 Euro-American T;X;H None 0.45
lineage4.1.2 Euro-American T;H None 0.46
lineage6.2.3 West-Africa 2 AFRI_1 RD702 0.52
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.45
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 5072 c.-168G>T upstream_gene_variant 0.65
gyrB 6153 p.Ala305Val missense_variant 0.72
gyrB 6446 p.Ala403Ser missense_variant 0.59
gyrB 7121 p.Pro628Ser missense_variant 0.69
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7965 p.Arg222Trp missense_variant 0.38
gyrA 8493 p.Leu398Phe missense_variant 0.65
gyrA 9143 c.1842T>C synonymous_variant 0.46
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 0.46
fgd1 491668 p.Lys296Glu missense_variant 0.53
fgd1 491742 c.960T>C synonymous_variant 0.57
mshA 575679 p.Asn111Ser missense_variant 0.41
mshA 575759 p.Arg138Cys missense_variant 0.54
rpoB 759989 c.183G>A synonymous_variant 0.58
rpoB 760115 c.309C>T synonymous_variant 0.3
rpoB 760969 p.Ser388Leu missense_variant 0.7
rpoB 761723 p.Glu639Asp missense_variant 0.61
rpoC 763031 c.-339T>C upstream_gene_variant 0.5
rpoC 765150 p.Gly594Glu missense_variant 0.47
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.53
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 0.6
Rv1258c 1406685 p.Val219Ala missense_variant 0.64
atpE 1461251 c.207G>T synonymous_variant 0.64
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674434 p.Val78Ala missense_variant 0.6
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.5
katG 2155503 c.609C>T synonymous_variant 0.61
PPE35 2167926 p.Leu896Ser missense_variant 0.66
PPE35 2169269 c.1340_1344delGCCAAinsT frameshift_variant&missense_variant 0.6
Rv1979c 2222308 p.Asp286Gly missense_variant 0.68
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.34
kasA 2518132 c.18C>T synonymous_variant 0.72
ribD 2987354 c.516G>A synonymous_variant 0.52
Rv2752c 3064905 c.1287C>T synonymous_variant 0.86
ald 3086728 c.-92C>T upstream_gene_variant 0.6
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087084 c.266delA frameshift_variant 0.45
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 0.59
Rv3236c 3612800 p.Val106Ala missense_variant 0.64
alr 3840559 p.Arg288Ser missense_variant 0.56
alr 3840618 p.Asp268Gly missense_variant 0.56
embC 4240671 p.Thr270Ile missense_variant 0.43
embC 4241843 p.Leu661Ile missense_variant 0.56
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.49
embC 4242910 p.Phe1016Leu missense_variant 0.45
embA 4243541 c.309C>T synonymous_variant 0.56
embA 4244220 c.988C>T synonymous_variant 0.54
embA 4244379 p.Pro383Ser missense_variant 0.55
embB 4246864 c.351C>T synonymous_variant 0.44
embB 4247646 p.Glu378Ala missense_variant 0.45
aftB 4268052 p.Arg262Gln missense_variant 0.57
aftB 4269351 c.-515C>T upstream_gene_variant 0.49
ubiA 4269387 p.Glu149Asp missense_variant 0.56
aftB 4269522 c.-686C>T upstream_gene_variant 0.55
aftB 4269606 c.-770T>C upstream_gene_variant 0.48
ethA 4326465 p.Ile337Val missense_variant 0.52
ethR 4328030 p.Ala161Gly missense_variant 0.3
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.57