TB-Profiler result

Run: ERR4831519
Summary

Run ID: ERR4831519

Sample name:

Date: 20-10-2023 07:07:27

Number of reads: 3853697

Percentage reads mapped: 99.52

Strain: lineage3;lineage2.2.1.1

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.Ser450Leu (0.90)
Isoniazid R katG p.Ser315Thr (0.76)
Ethambutol R embB p.Gln497Arg (0.86)
Pyrazinamide R pncA p.Arg154Met (0.80)
Streptomycin R rpsL p.Lys43Arg (0.82)
Fluoroquinolones R gyrA p.Asp94Gly (0.85)
Moxifloxacin R gyrA p.Asp94Gly (0.85)
Ofloxacin R gyrA p.Asp94Gly (0.85)
Levofloxacin R gyrA p.Asp94Gly (0.85)
Ciprofloxacin R gyrA p.Asp94Gly (0.85)
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
lineage3 East-African-Indian CAS RD750 0.83
lineage2 East-Asian Beijing RD105 0.21
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.19
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.16
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 0.17
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 7582 p.Asp94Gly missense_variant 0.85 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.9 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.82 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.76 isoniazid
pncA 2288781 p.Arg154Met missense_variant 0.8 pyrazinamide
embB 4248003 p.Gln497Arg missense_variant 0.86 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
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 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.12
ccsA 620625 p.Ile245Met missense_variant 0.18
rpoB 759746 c.-61C>T upstream_gene_variant 0.83
rpoC 762434 c.-936T>G upstream_gene_variant 0.86
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764820 p.Trp484Ser missense_variant 0.82
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.2
mmpS5 779615 c.-710C>G upstream_gene_variant 0.21
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471826 n.-20_-19insTCCAAAGGGA upstream_gene_variant 0.5
rpsA 1834177 c.636A>C synonymous_variant 0.24
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223014 p.Tyr51Asn missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.8
pncA 2289365 c.-125delC upstream_gene_variant 0.85
eis 2714846 p.Val163Ile missense_variant 0.17
ahpC 2726105 c.-88G>A upstream_gene_variant 0.77
ahpC 2726116 c.-77T>A upstream_gene_variant 0.76
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
Rv3236c 3613004 p.Leu38Ser missense_variant 0.83
embC 4242075 p.Arg738Gln missense_variant 0.8
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4248115 c.1602C>T synonymous_variant 0.14
aftB 4267647 p.Asp397Gly missense_variant 0.21
ubiA 4269302 p.Leu178Val missense_variant 0.84
whiB6 4338596 c.-76_-75delAGinsT upstream_gene_variant 0.78
whiB6 4338596 c.-75delG upstream_gene_variant 0.22
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 0.14