TB-Profiler result

Run: ERR3077944
Summary

Run ID: ERR3077944

Sample name:

Date: 01-04-2023 00:12:00

Number of reads: 681649

Percentage reads mapped: 99.7

Strain: lineage4.8

Drug-resistance: MDR-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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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 761110 p.Asp435Val missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4248003 p.Gln497Arg missense_variant 1.0 ethambutol
ethA 4327397 c.76delC frameshift_variant 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
gyrB 6247 c.1008G>A synonymous_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
fgd1 491724 c.942A>C synonymous_variant 0.13
ccsA 620757 p.Asp289Glu missense_variant 0.12
rpoB 759615 c.-192A>C upstream_gene_variant 0.33
rpoB 761930 c.2124G>T synonymous_variant 0.12
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
rrl 1473688 n.31C>A non_coding_transcript_exon_variant 0.12
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rpsA 1834640 p.Glu367* stop_gained 0.15
tlyA 1917839 c.-101A>G upstream_gene_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102039 p.Gly335Val missense_variant 0.12
PPE35 2168149 p.Pro822Ser missense_variant 1.0
Rv1979c 2222859 c.306G>A synonymous_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519173 c.1059C>T synonymous_variant 0.12
Rv2752c 3065565 c.627C>A synonymous_variant 0.12
thyX 3067477 p.Gln157Lys missense_variant 0.11
thyA 3074173 p.Ser100* stop_gained 0.12
thyA 3074521 c.-50G>T upstream_gene_variant 0.13
ald 3086848 p.Lys10Thr missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethR 4327974 p.Met142Ile missense_variant 1.0
ethR 4327975 p.Gln143Lys missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
pncA 2289037 c.-512_204del start_lost&conservative_inframe_deletion 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0