TB-Profiler result

Run: ERR4872201
Summary

Run ID: ERR4872201

Sample name:

Date: 01-04-2023 21:26:49

Number of reads: 315800

Percentage reads mapped: 99.5

Strain: lineage4.1

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 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
pncA 2289105 p.Ala46Glu missense_variant 1.0 pyrazinamide
ahpC 2726145 c.-48G>A upstream_gene_variant 1.0 isoniazid
embA 4243222 c.-11C>A upstream_gene_variant 1.0 ethambutol
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
ethA 4326452 p.Ala341Val missense_variant 1.0 ethionamide
gid 4407851 c.351delG 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 760115 c.309C>T synonymous_variant 1.0
rpoB 761211 p.Val469Met missense_variant 0.29
rpoC 763521 p.Ile51Thr missense_variant 0.4
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765506 p.Val713Ile missense_variant 0.29
rpoC 765570 p.Ala734Val missense_variant 1.0
rpoC 766337 p.Asp990Asn missense_variant 0.4
rpoC 766812 p.Ser1148Leu missense_variant 0.4
rpoC 767086 c.3717C>T synonymous_variant 0.29
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303261 p.Pro111Ser missense_variant 0.5
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1833908 p.Asp123Asn missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102949 p.Lys32Glu missense_variant 1.0
ndh 2103166 c.-124C>T upstream_gene_variant 0.4
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289293 c.-52C>T upstream_gene_variant 0.29
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
ahpC 2725923 c.-270A>T upstream_gene_variant 0.33
folC 2747742 c.-145delA upstream_gene_variant 0.4
ribD 2987526 p.Gly230* stop_gained 0.4
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087111 p.Ala98Thr missense_variant 0.4
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568763 c.-84C>T upstream_gene_variant 0.5
fbiB 3642692 c.1158C>T synonymous_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4242868 c.-365C>T upstream_gene_variant 0.22
embA 4244435 c.1203G>A synonymous_variant 0.29
embA 4245469 p.Asn746Ser missense_variant 0.33
embA 4245834 p.Leu868Met missense_variant 0.67
embB 4248098 p.Ile529Val missense_variant 0.25
embB 4248144 p.Leu544Ser missense_variant 0.22
embB 4248589 c.2076C>A synonymous_variant 0.25
ubiA 4269353 p.Ala161Pro missense_variant 0.67
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407628 p.Gly192Asp missense_variant 0.5