TB-Profiler result

Run: ERR4972578
Summary

Run ID: ERR4972578

Sample name:

Date: 01-04-2023 21:47:38

Number of reads: 215997

Percentage reads mapped: 99.36

Strain:

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
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 1.0
lineage4.1.2.1.1 Euro-American (Haarlem) T1;H1 RD182 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
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289213 p.Gln10Pro missense_variant 1.0 pyrazinamide
embB 4247730 p.Gly406Ala missense_variant 1.0 ethambutol
gid 4407872 c.329_330delTG frameshift_variant 1.0 streptomycin
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 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
rpoB 759961 p.Thr52Asn missense_variant 0.18
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 761254 p.Pro483His missense_variant 0.33
rpoC 763292 c.-78C>T upstream_gene_variant 0.13
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475725 n.2068T>C non_coding_transcript_exon_variant 0.33
rrl 1475797 n.2140C>T non_coding_transcript_exon_variant 0.22
fabG1 1673324 c.-116G>A upstream_gene_variant 0.4
rpsA 1834316 p.Thr259Ala missense_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169751 p.Gly288* stop_gained 1.0
PPE35 2170691 c.-79C>T upstream_gene_variant 0.12
Rv1979c 2221875 c.1289delT frameshift_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518859 p.Glu249* stop_gained 0.67
eis 2714399 p.His312Tyr missense_variant 0.13
ahpC 2726700 p.Ser170Thr missense_variant 0.2
Rv2752c 3065305 p.Ala296Glu missense_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3877702 c.805delG frameshift_variant 0.67
clpC1 4038171 p.Pro845Arg missense_variant 0.5
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244031 c.800delT frameshift_variant 0.2
embA 4244633 c.1401C>T synonymous_variant 0.22
embB 4246544 p.Thr11Pro missense_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.67
embB 4248324 p.Ala604Gly missense_variant 0.27
embB 4248582 p.Pro690His missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407609 c.594G>T synonymous_variant 0.4