TB-Profiler result

Run: ERR4829831
Summary

Run ID: ERR4829831

Sample name:

Date: 20-10-2023 06:33:37

Number of reads: 2997088

Percentage reads mapped: 99.62

Strain: lineage4.2.1;lineage2.2.1

Drug-resistance: MDR-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.Ser450Leu (1.00)
Isoniazid R inhA c.-154G>A (0.12), katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Ile (0.87), embB p.Gln497Lys (0.23)
Pyrazinamide R pncA p.Thr76Pro (0.13), pncA p.Asp49Glu (0.82)
Streptomycin R rpsL p.Lys43Arg (0.83), rpsL p.Lys88Arg (0.18)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R inhA c.-154G>A (0.12), ethA c.884delT (0.82), ethA c.884delT (0.82)
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage2 East-Asian Beijing RD105 0.84
lineage4 Euro-American LAM;T;S;X;H None 0.14
lineage4.2 Euro-American H;T;LAM None 0.17
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.82
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.84
lineage4.2.1 Euro-American (TUR) H3;H4 None 0.18
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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.83 streptomycin
rpsL 781822 p.Lys88Arg missense_variant 0.18 streptomycin
inhA 1674048 c.-154G>A upstream_gene_variant 0.12 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289016 p.Thr76Pro missense_variant 0.13 pyrazinamide
pncA 2289095 p.Asp49Glu missense_variant 0.82 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 0.87 ethambutol
embB 4248002 p.Gln497Lys missense_variant 0.23 ethambutol
ethA 4326589 c.884delT frameshift_variant 0.82 ethionamide, ethionamide
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 491247 c.465C>T synonymous_variant 0.13
fgd1 491742 c.960T>C synonymous_variant 0.85
mshA 575907 p.Ala187Val missense_variant 0.81
ccsA 619969 p.Val27Ile missense_variant 0.16
ccsA 620625 p.Ile245Met missense_variant 0.83
rpoB 761293 p.Val496Ala missense_variant 0.86
rpoC 763031 c.-339T>C upstream_gene_variant 0.87
rpoC 766488 p.Pro1040Arg missense_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.89
mmpL5 776182 p.Asp767Asn missense_variant 0.84
mmpS5 779615 c.-710C>G upstream_gene_variant 0.9
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.86
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.85
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.85
PPE35 2167926 p.Leu896Ser missense_variant 0.86
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ribD 2986827 c.-12G>A upstream_gene_variant 0.14
ald 3086731 c.-89A>G upstream_gene_variant 0.84
ald 3086742 c.-78A>C upstream_gene_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.83
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243346 c.114A>G synonymous_variant 0.83
embA 4243460 c.228C>T synonymous_variant 0.82
embB 4249594 c.3081G>A synonymous_variant 0.24
aftB 4267647 p.Asp397Gly missense_variant 0.9
ubiA 4269391 p.Val148Ala missense_variant 0.12
ethA 4328376 c.-903G>C upstream_gene_variant 0.17
whiB6 4338371 p.Thr51Pro missense_variant 0.88
whiB6 4338591 c.-70G>C upstream_gene_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.84
gid 4407927 p.Glu92Asp missense_variant 0.81