TB-Profiler result

Run: ERR4829163
Summary

Run ID: ERR4829163

Sample name:

Date: 01-04-2023 19:19:18

Number of reads: 2185395

Percentage reads mapped: 99.54

Strain: lineage4.6.2.2

Drug-resistance: RR-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
lineage4.6 Euro-American T;LAM None 1.0
lineage4.6.2 Euro-American T;LAM RD726 1.0
lineage4.6.2.2 Euro-American (Cameroon) LAM10-CAM RD726 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.His445Tyr missense_variant 1.0 rifampicin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.11 kanamycin, capreomycin, aminoglycosides, amikacin
ethA 4326452 p.Ala341Val missense_variant 0.26 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 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 778298 c.-692C>T upstream_gene_variant 0.99
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474173 n.516T>C non_coding_transcript_exon_variant 0.12
rrl 1474457 n.800C>A non_coding_transcript_exon_variant 0.12
rrl 1474925 n.1268G>T non_coding_transcript_exon_variant 0.13
rrl 1475796 n.2139A>T non_coding_transcript_exon_variant 0.13
rrl 1475881 n.2224T>A non_coding_transcript_exon_variant 0.11
rrl 1476352 n.2695T>A non_coding_transcript_exon_variant 0.22
inhA 1673393 c.-809G>C upstream_gene_variant 1.0
rpsA 1834983 c.1444delT frameshift_variant&stop_lost&splice_region_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 0.99
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv3083 3448567 p.His22Asp missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
ddn 3987011 c.168C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246555 c.42G>C synonymous_variant 0.29
embB 4246556 p.Ala15Pro missense_variant 0.29
embB 4246563 p.Leu17Trp missense_variant 0.25
embB 4246584 p.Arg24Pro missense_variant 0.31
aftB 4267272 p.Lys522Arg missense_variant 1.0
ethR 4326739 c.-810G>C upstream_gene_variant 1.0
ethA 4328004 c.-531C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407917 p.Arg96Ser missense_variant 1.0