TB-Profiler result

Run: ERR2516725
Summary

Run ID: ERR2516725

Sample name:

Date: 31-03-2023 21:42:06

Number of reads: 2878816

Percentage reads mapped: 99.5

Strain: 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 1.0
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.99
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 761095 p.Leu430Arg missense_variant 1.0 rifampicin
rpoB 761109 p.Asp435Tyr missense_variant 1.0 rifampicin
pncA 2289100 c.141dupC frameshift_variant 1.0 pyrazinamide
ahpC 2726112 c.-81C>T upstream_gene_variant 0.99 isoniazid
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 0.98
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 762836 c.-534C>G upstream_gene_variant 0.24
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
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155561 p.Gly184Asp missense_variant 1.0
PPE35 2168975 c.1638C>T synonymous_variant 1.0
PPE35 2168981 c.1632A>G synonymous_variant 1.0
PPE35 2168985 p.Thr543Met missense_variant 1.0
PPE35 2168987 p.Thr542Ala missense_variant 1.0
PPE35 2168990 c.1623T>G synonymous_variant 1.0
PPE35 2169031 p.Asp528Asn missense_variant 1.0
PPE35 2169041 c.1572G>A synonymous_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.23
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
ribD 2987307 p.Ala157Pro missense_variant 0.17
thyA 3073806 c.666C>G synonymous_variant 0.24
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.99
clpC1 4038857 c.1848C>A synonymous_variant 0.21
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
whiB6 4338472 p.Arg17Met missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407824 p.Gln127Glu missense_variant 1.0
gid 4407966 p.Leu79Phe missense_variant 0.11
gid 4407977 p.Gly76Arg missense_variant 0.29