TB-Profiler result

Run: ERR4828955
Summary

Run ID: ERR4828955

Sample name:

Date: 01-04-2023 19:11:32

Number of reads: 992476

Percentage reads mapped: 99.74

Strain: lineage4.8

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
lineage4.8 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
katG 2155532 c.579delC frameshift_variant 0.14 isoniazid
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 5084 c.-156G>A upstream_gene_variant 1.0
gyrB 5855 p.Ile206Val missense_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7879 p.Asn193Ser missense_variant 0.11
gyrA 8477 c.1176C>A synonymous_variant 1.0
gyrA 8824 p.Glu508Ala missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpS5 778622 p.Thr95Met missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406492 c.849C>A synonymous_variant 0.2
embR 1417130 p.His73Pro missense_variant 0.14
embR 1417461 c.-114C>A upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474885 n.1228G>T non_coding_transcript_exon_variant 0.13
rrl 1474962 n.1305T>G non_coding_transcript_exon_variant 0.13
rrl 1475532 n.1875A>G non_coding_transcript_exon_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167745 p.Thr956Arg missense_variant 0.33
PPE35 2169488 c.1125G>C synonymous_variant 0.14
PPE35 2169491 c.1122T>C synonymous_variant 0.17
PPE35 2169902 p.Leu237Phe missense_variant 0.21
PPE35 2169910 p.Asn235Tyr missense_variant 0.2
PPE35 2170048 p.Leu189Val missense_variant 0.15
Rv1979c 2222988 c.177T>C synonymous_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3064910 p.Ser428Cys missense_variant 0.13
Rv2752c 3065431 p.Ala254Val missense_variant 0.11
thyA 3074106 p.Asp122Glu missense_variant 0.12
thyA 3074414 p.Asp20Asn missense_variant 0.12
ald 3086982 p.Ala55Pro missense_variant 1.0
ald 3086987 p.Gln56His missense_variant 1.0
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
alr 3840764 c.657G>C synonymous_variant 1.0
embC 4240996 c.1134G>A synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244755 p.Glu508Gly missense_variant 0.12
embB 4247028 p.Leu172Arg missense_variant 0.2
ethA 4328357 c.-884A>G upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0