TB-Profiler result

Run: ERR2513919
Summary

Run ID: ERR2513919

Sample name:

Date: 31-03-2023 19:59:38

Number of reads: 2295883

Percentage reads mapped: 99.04

Strain: lineage4.6.2.2

Drug-resistance: HR-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
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, 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 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.11
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.12
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.19
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.24
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.19
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.13
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.27
rrs 1472487 n.643dupT non_coding_transcript_exon_variant 1.0
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.2
rrs 1472954 n.1109T>C non_coding_transcript_exon_variant 0.25
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.25
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.25
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.2
rrs 1472988 n.1143T>C non_coding_transcript_exon_variant 0.15
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.31
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.15
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.17
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.41
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.27
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.33
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.33
rrl 1474734 n.1077G>T non_coding_transcript_exon_variant 0.57
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.75
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.75
rrl 1475751 n.2094C>A non_coding_transcript_exon_variant 1.0
rrl 1475754 n.2097G>A non_coding_transcript_exon_variant 1.0
rrl 1475756 n.2099T>C non_coding_transcript_exon_variant 1.0
rrl 1475762 n.2105G>C non_coding_transcript_exon_variant 1.0
rrl 1475774 n.2117C>T non_coding_transcript_exon_variant 1.0
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 1.0
rrl 1476373 n.2716A>G non_coding_transcript_exon_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155389 c.723C>G synonymous_variant 1.0
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 0.97
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyX 3067474 p.Pro158Ala missense_variant 1.0
Rv3083 3448567 p.His22Asp missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612571 c.546C>T synonymous_variant 1.0
Rv3236c 3612910 p.Leu69Phe missense_variant 1.0
embA 4242550 c.-683C>G upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4267272 p.Lys522Arg missense_variant 1.0
aftB 4268622 p.Trp72Leu missense_variant 0.16
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