TB-Profiler result

Run: ERR4817617
Summary

Run ID: ERR4817617

Sample name:

Date: 01-04-2023 15:05:48

Number of reads: 195251

Percentage reads mapped: 97.49

Strain: lineage4

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
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
ethA 4326312 c.1161delC frameshift_variant 0.33 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 5165 c.-75C>G upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7841 c.540C>A synonymous_variant 0.33
gyrA 9111 p.Pro604Ser missense_variant 0.5
rpoB 760023 p.Asp73Tyr missense_variant 0.33
rpoB 760394 c.588C>A synonymous_variant 0.67
rpoC 765387 p.Phe673Ser missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 779292 c.-812C>T upstream_gene_variant 0.4
rpsL 781883 c.326delA frameshift_variant 0.33
fbiC 1305045 c.2115A>G synonymous_variant 1.0
fbiC 1305050 p.Thr707Met missense_variant 1.0
fbiC 1305240 c.2310T>C synonymous_variant 0.4
Rv1258c 1406366 p.Tyr325* stop_gained 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472536 n.691G>A non_coding_transcript_exon_variant 0.67
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 1.0
rrs 1472986 n.1141_1142insA non_coding_transcript_exon_variant 1.0
rrs 1472989 n.1145delA non_coding_transcript_exon_variant 1.0
rrs 1472996 n.1151T>C non_coding_transcript_exon_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474466 n.809G>A non_coding_transcript_exon_variant 0.67
rrl 1474488 n.831G>T non_coding_transcript_exon_variant 0.67
rrl 1474498 n.841G>T non_coding_transcript_exon_variant 0.67
rrl 1474505 n.848C>G non_coding_transcript_exon_variant 0.67
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 1.0
rrl 1474529 n.872A>C non_coding_transcript_exon_variant 1.0
rrl 1474530 n.873G>A non_coding_transcript_exon_variant 1.0
rpsA 1834130 p.Glu197* stop_gained 0.29
tlyA 1918125 p.Trp62Cys missense_variant 0.13
ndh 2101813 p.Lys410Asn missense_variant 0.67
katG 2156003 p.Asp37Asn missense_variant 0.5
PPE35 2167662 p.Ser984Ile missense_variant 1.0
PPE35 2168394 p.Ser740Asn missense_variant 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518204 p.Glu30Asp missense_variant 0.5
ahpC 2725988 c.-205T>C upstream_gene_variant 0.2
ahpC 2726131 c.-62C>T upstream_gene_variant 0.4
folC 2747378 p.Gly74Val missense_variant 0.29
Rv2752c 3065745 c.447C>A synonymous_variant 0.25
Rv2752c 3066090 c.101delT frameshift_variant 0.67
Rv2752c 3066204 c.-13G>T upstream_gene_variant 0.5
thyX 3068025 c.-80G>T upstream_gene_variant 0.5
ald 3086650 c.-170C>A upstream_gene_variant 0.67
ald 3086695 c.-125C>A upstream_gene_variant 0.67
fprA 3475022 p.Gly339Glu missense_variant 0.33
fprA 3475302 c.1296C>T synonymous_variant 1.0
Rv3236c 3612150 c.965_966delGG frameshift_variant 0.4
fbiA 3641292 p.Lys250Asn missense_variant 0.25
embA 4242325 c.-908C>T upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242830 p.Ala990Thr missense_variant 0.5
embA 4244605 p.Val458Ala missense_variant 1.0
embA 4244812 p.Cys527Ser missense_variant 0.33
embB 4248378 p.Ser622* stop_gained 0.5
embB 4249022 c.2510delT frameshift_variant 1.0
aftB 4267569 p.Pro423Leu missense_variant 0.22
ubiA 4269984 c.-151G>A upstream_gene_variant 0.15
whiB6 4338552 c.-31A>G upstream_gene_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407683 p.His174Tyr missense_variant 0.33
gid 4408284 c.-82G>A upstream_gene_variant 0.5
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0