TB-Profiler result

Run: ERR2516477
Summary

Run ID: ERR2516477

Sample name:

Date: 31-03-2023 21:33:33

Number of reads: 3372903

Percentage reads mapped: 99.55

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 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 761139 p.His445Asp missense_variant 0.26 rifampicin
katG 2154793 c.1314_1318delGCAGG frameshift_variant 0.2 isoniazid
katG 2155411 p.Gly234Glu missense_variant 0.48 isoniazid
katG 2156089 c.22dupA frameshift_variant 0.16 isoniazid, 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 1.0
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 762836 c.-534C>G 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
fbiC 1304839 p.Glu637Lys missense_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1674076 p.Thr213Pro missense_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.28
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 0.14
thyA 3073806 c.666C>G synonymous_variant 0.29
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038857 c.1848C>A synonymous_variant 0.38
embC 4239842 c.-21C>A upstream_gene_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.27
whiB6 4338595 c.-75delG upstream_gene_variant 1.0