TB-Profiler result

Run: SRR1062906
Summary

Run ID: SRR1062906

Sample name:

Date: 02-04-2023 18:39:46

Number of reads: 2963613

Percentage reads mapped: 99.62

Strain: lineage4.6.1.2

Drug-resistance: MDR-TB

Download CSV Download TXT Download PDF Download JSON
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
lineage4.6 Euro-American T;LAM None 1.0
lineage4.6.1 Euro-American (Uganda) T2 RD724 1.0
lineage4.6.1.2 Euro-American T2 RD724 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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.98 isoniazid
pncA 2289207 p.Asp12Ala missense_variant 1.0 pyrazinamide
embA 4243221 c.-12C>T upstream_gene_variant 1.0 ethambutol
embB 4247730 p.Gly406Asp missense_variant 1.0 ethambutol
ethA 4327147 p.Trp109* stop_gained 1.0 ethionamide
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 7539 p.Thr80Ala missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416410 p.Leu313Arg missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474616 n.959G>C non_coding_transcript_exon_variant 0.11
rrl 1474634 n.977T>C non_coding_transcript_exon_variant 0.12
rrl 1475235 n.1582delA non_coding_transcript_exon_variant 0.12
inhA 1674465 c.264C>T synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168474 c.2139C>A synonymous_variant 0.12
PPE35 2168490 p.Ala708Gly missense_variant 0.1
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726287 p.Gly32Asp missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3613029 c.88T>C synonymous_variant 0.97
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243709 c.477C>T synonymous_variant 1.0
embA 4245055 p.Thr608Asn missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338635 c.-114A>C upstream_gene_variant 1.0
gid 4408115 p.Gly30Arg missense_variant 1.0