TB-Profiler result

Run: ERR4830092
Summary

Run ID: ERR4830092

Sample name:

Date: 20-10-2023 01:37:51

Number of reads: 2607502

Percentage reads mapped: 99.66

Strain: lineage4.3.3;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 (0.29)
Isoniazid R katG p.Ser315Thr (0.28)
Ethambutol R embB p.Met306Ile (0.24)
Pyrazinamide R pncA c.122delA (0.19)
Streptomycin R rpsL p.Lys43Arg (0.11)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid R thyX c.-16C>T (0.20), thyA p.Arg222Gly (0.22)
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 0.19
lineage4 Euro-American LAM;T;S;X;H None 0.8
lineage4.3 Euro-American (LAM) mainly-LAM None 0.82
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.21
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.22
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.77
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 0.29 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.11 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.28 isoniazid
pncA 2289119 c.122delA frameshift_variant 0.19 pyrazinamide
thyX 3067961 c.-16C>T upstream_gene_variant 0.2 para-aminosalicylic_acid
thyA 3073808 p.Arg222Gly missense_variant 0.22 para-aminosalicylic_acid
embB 4247431 p.Met306Ile missense_variant 0.24 ethambutol
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 6142 c.903G>C synonymous_variant 0.76
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 0.76
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9752 c.2451C>G synonymous_variant 0.78
mshA 575907 p.Ala187Val missense_variant 0.19
ccsA 620625 p.Ile245Met missense_variant 0.21
rpoB 761268 p.Ile488Val missense_variant 0.16
rpoC 763031 c.-339T>C upstream_gene_variant 0.22
rpoC 764995 c.1626C>G synonymous_variant 0.77
rpoC 766645 p.Glu1092Asp missense_variant 0.24
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.2
mmpL5 776182 p.Asp767Asn missense_variant 0.14
mmpS5 779615 c.-710C>G upstream_gene_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476729 n.3072A>G non_coding_transcript_exon_variant 0.78
rpsA 1834177 c.636A>C synonymous_variant 0.13
rpsA 1834836 p.Met432Thr missense_variant 0.76
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.23
katG 2156196 c.-85C>T upstream_gene_variant 0.76
PPE35 2167926 p.Leu896Ser missense_variant 0.21
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 0.76
folC 2746340 p.Ala420Val missense_variant 0.8
thyA 3073868 p.Thr202Ala missense_variant 0.74
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 0.14
fbiB 3641810 c.276G>C synonymous_variant 0.28
clpC1 4038287 c.2418C>T synonymous_variant 0.8
clpC1 4038968 c.1737G>A synonymous_variant 0.85
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 0.21
ethA 4326339 p.Asn379Asp missense_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 0.17
gid 4408156 p.Leu16Arg missense_variant 0.78