TB-Profiler result

Run: ERR6052025
Summary

Run ID: ERR6052025

Sample name:

Date: 02-04-2023 01:39:21

Number of reads: 1716557

Percentage reads mapped: 99.7

Strain: lineage4.1.1.3

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 1.0
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 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 761095 p.Leu430Pro missense_variant 1.0 rifampicin
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 0.96
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 762473 c.-897C>T upstream_gene_variant 0.12
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 1.0
rrs 1472309 n.464C>A non_coding_transcript_exon_variant 0.25
rrl 1474091 n.434C>A non_coding_transcript_exon_variant 0.33
rrl 1475200 n.1543T>C non_coding_transcript_exon_variant 0.25
rrl 1476136 n.2479A>G non_coding_transcript_exon_variant 1.0
fabG1 1673380 c.-60C>G upstream_gene_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168274 p.Thr780Met missense_variant 0.25
PPE35 2169792 p.Asn274Ser missense_variant 0.11
PPE35 2170048 p.Leu189Val missense_variant 0.36
PPE35 2170053 p.Thr187Ser missense_variant 0.37
Rv1979c 2223293 c.-129A>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
ddn 3986827 c.-17T>C upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4249408 c.2895G>A synonymous_variant 1.0
ethA 4326256 p.Leu406Phe missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
embR 1413438 c.1165_*2742del stop_lost&conservative_inframe_deletion&splice_region_variant 1.0