TB-Profiler result

Run: ERR11243545
Summary

Run ID: ERR11243545

Sample name:

Date: 21-04-2023 21:28:06

Number of reads: 636934

Percentage reads mapped: 99.59

Strain: 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), rpoB p.Glu761Asp (1.00)
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol R embB p.Asp354Ala (1.00)
Pyrazinamide R pncA p.Tyr103His (1.00)
Streptomycin R rrs n.517C>T (1.00)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin R tlyA c.661_662insCTTG (0.13), tlyA c.675_678delCAAG (0.13)
Kanamycin R eis c.-37G>T (1.00)
Cycloserine
Ethionamide R ethA c.-7T>C (1.00)
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 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.99
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 1.0
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
rpoB 762089 p.Glu761Asp missense_variant 1.0 rifampicin
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 1.0 streptomycin
tlyA 1918600 c.661_662insCTTG frameshift_variant&stop_gained 0.13 capreomycin
tlyA 1918613 c.675_678delCAAG frameshift_variant 0.13 capreomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288935 p.Tyr103His missense_variant 1.0 pyrazinamide
eis 2715369 c.-37G>T upstream_gene_variant 1.0 kanamycin
embB 4247574 p.Asp354Ala missense_variant 1.0 ethambutol
ethA 4327480 c.-7T>C upstream_gene_variant 1.0 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
gyrA 9750 p.Arg817Cys missense_variant 0.14
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575565 p.Leu73Pro missense_variant 0.11
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761711 c.1905C>T synonymous_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766645 p.Glu1092Asp missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777923 c.558C>T synonymous_variant 0.12
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781842 p.Tyr95His missense_variant 0.1
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474970 n.1313G>T non_coding_transcript_exon_variant 0.12
inhA 1674908 p.Thr236Met missense_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918603 p.Ser222Ala missense_variant 0.13
tlyA 1918607 p.Val223Asp missense_variant 0.13
tlyA 1918610 p.Gly224Ala missense_variant 0.13
ndh 2102054 p.Pro330Leu missense_variant 0.13
katG 2154577 p.Gly512Val missense_variant 0.15
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155090 p.Trp341* stop_gained 0.22
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2860318 p.Ser34* stop_gained 0.14
Rv2752c 3065804 p.Glu130* stop_gained 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086793 c.-27A>G upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612098 p.Ile340Asn missense_variant 0.15
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3613024 c.93G>A synonymous_variant 0.15
fbiB 3642730 p.Gly399Asp missense_variant 0.12
clpC1 4038495 p.Arg737Leu missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243192 c.-41A>C upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243825 p.Thr198Met missense_variant 0.11
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267846 p.Gly331Ser missense_variant 0.17
aftB 4268847 c.-11C>T upstream_gene_variant 0.11
whiB6 4338563 c.-42G>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0