TB-Profiler result

Run: ERR5864917
Summary

Run ID: ERR5864917

Sample name:

Date: 01-04-2023 23:40:56

Number of reads: 954028

Percentage reads mapped: 99.41

Strain: lineage4.1.2.1

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.99
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 761139 p.His445Tyr missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
gid 4407830 p.Gln125* stop_gained 1.0 streptomycin
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
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 761623 p.Gln606Arg missense_variant 0.11
rpoB 762845 p.Phe1013Leu missense_variant 0.12
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 767212 c.3843G>T synonymous_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1407133 p.Gly70Trp missense_variant 0.15
Rv1258c 1407408 c.-68G>A upstream_gene_variant 0.13
embR 1416253 c.1095C>T synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473837 n.180G>T non_coding_transcript_exon_variant 0.15
rrl 1474460 n.803G>T non_coding_transcript_exon_variant 0.12
rpsA 1833630 p.Ile30Ser missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170273 p.Arg114Ser missense_variant 0.12
PPE35 2170360 p.Gln85* stop_gained 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
eis 2715104 p.Leu77Ile missense_variant 0.14
eis 2715148 p.Ala62Glu missense_variant 0.14
folC 2746900 c.699C>A synonymous_variant 0.15
pepQ 2859605 p.Gly272Trp missense_variant 0.12
thyX 3067487 p.Lys153Asn missense_variant 0.12
thyX 3067496 c.450G>T synonymous_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449475 p.Phe324Leu missense_variant 0.14
Rv3083 3449636 p.Leu378Arg missense_variant 0.96
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474009 c.3G>T start_lost 0.12
fbiB 3642278 c.744G>T synonymous_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4244420 c.1188G>T synonymous_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0