TB-Profiler result

Run: ERR11081873
Summary

Run ID: ERR11081873

Sample name:

Date: 09-04-2023 13:59:38

Number of reads: 5334534

Percentage reads mapped: 99.52

Strain: lineage4.2.1;lineage4.1.2.1

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
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 1.0
lineage4.1 Euro-American T;X;H None 0.82
lineage4.2 Euro-American H;T;LAM None 0.18
lineage4.1.2 Euro-American T;H None 0.82
lineage4.2.1 Euro-American (TUR) H3;H4 None 0.17
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.81
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 0.99 rifampicin
rpoC 764822 p.Asp485Asn missense_variant 0.23 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.81 streptomycin
rpsL 781822 p.Lys88Arg missense_variant 0.18 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.19 kanamycin, capreomycin, aminoglycosides, amikacin
inhA 1674048 c.-154G>A upstream_gene_variant 0.19 isoniazid, ethionamide
katG 2155167 p.Ser315Thr missense_variant 0.8 isoniazid
pncA 2289040 p.Trp68Gly missense_variant 0.81 pyrazinamide
pncA 2289252 c.-11A>G upstream_gene_variant 0.16 pyrazinamide
eis 2715344 c.-12C>T upstream_gene_variant 0.83 kanamycin
embB 4247429 p.Met306Val missense_variant 0.85 ethambutol
embB 4248003 p.Gln497Arg missense_variant 0.17 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 491247 c.465C>T synonymous_variant 0.13
fgd1 491591 p.Lys270Met missense_variant 0.84
mshA 575679 p.Asn111Ser missense_variant 0.85
mshA 576108 p.Ala254Gly missense_variant 0.22
ccsA 619969 p.Val27Ile missense_variant 0.18
rpoB 760106 c.300G>A synonymous_variant 0.84
rpoB 760115 c.309C>T synonymous_variant 0.84
rpoB 761292 p.Val496Leu missense_variant 0.87
rpoC 765150 p.Gly594Glu missense_variant 0.8
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304253 c.1323G>T synonymous_variant 0.21
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169879 p.Phe245Cys missense_variant 0.21
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.77
ribD 2986827 c.-12G>A upstream_gene_variant 0.17
ald 3086742 c.-78A>C upstream_gene_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878630 c.-123G>C upstream_gene_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.74
embB 4246584 p.Arg24Pro missense_variant 0.2
embB 4249594 c.3081G>A synonymous_variant 0.17
ethA 4326314 p.Thr387Ile missense_variant 0.19
ethA 4327298 p.Met59Arg missense_variant 0.87
ethA 4328376 c.-903G>C upstream_gene_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0