TB-Profiler result

Run: SRR1019163
Summary

Run ID: SRR1019163

Sample name:

Date: 02-04-2023 16:25:16

Number of reads: 7020545

Percentage reads mapped: 99.25

Strain: lineage4.1.1

Drug-resistance: Pre-XDR-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
lineage4.1.1 Euro-American (X-type) X1;X2;X3 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
gyrA 7581 p.Asp94Tyr missense_variant 0.99 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761109 p.Asp435Tyr missense_variant 1.0 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.99 isoniazid
pncA 2288868 p.Val125Asp missense_variant 0.99 pyrazinamide
folC 2747141 p.Glu153Ala missense_variant 1.0 para-aminosalicylic_acid
ald 3087136 c.317_318insT frameshift_variant 1.0 cycloserine
embA 4243217 c.-16C>T upstream_gene_variant 1.0 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
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 0.99
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2859918 c.501A>C synonymous_variant 0.33
ald 3086772 c.-48A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3641447 p.Thr302Met missense_variant 1.0
alr 3841052 c.369G>T synonymous_variant 0.17
rpoA 3877553 p.Glu319Lys missense_variant 1.0
rpoA 3878559 c.-53_-52insC upstream_gene_variant 0.25
embC 4240897 c.1035C>G synonymous_variant 0.98
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243556 c.324C>T synonymous_variant 0.18
embB 4249408 c.2895G>A synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407781 p.Ala141Glu missense_variant 0.99
gid 4407790 p.Ala138Val missense_variant 0.99