TB-Profiler result

Run: SRR3732591
Summary

Run ID: SRR3732591

Sample name:

Date: 04-04-2023 05:36:26

Number of reads: 1658495

Percentage reads mapped: 99.52

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 0.98
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
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
ethA 4326278 p.Ser399* stop_gained 1.0 ethionamide
gid 4407985 p.Gly73Ala missense_variant 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 575474 p.Asp43Tyr missense_variant 0.12
mshA 575679 p.Asn111Ser missense_variant 1.0
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760563 p.Arg253* stop_gained 0.13
rpoC 763544 p.Glu59* stop_gained 0.12
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766630 c.3261G>T synonymous_variant 0.13
rpoC 766971 p.Ala1201Val missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775847 c.2634G>A synonymous_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473660 n.3G>A non_coding_transcript_exon_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156345 c.-234C>G upstream_gene_variant 0.11
Rv1979c 2222284 p.Ala294Asp missense_variant 0.11
Rv1979c 2222501 p.Ala222Thr missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290124 c.-883C>A upstream_gene_variant 0.22
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518712 p.Gly200* stop_gained 0.12
folC 2746530 p.Ala357Ser missense_variant 0.12
folC 2746904 p.Ala232Val missense_variant 0.12
pepQ 2860084 p.Gly112Asp missense_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087215 c.396G>A synonymous_variant 0.12
ald 3087315 p.Val166Leu missense_variant 0.13
Rv3083 3448587 c.84C>A synonymous_variant 0.13
Rv3083 3448780 p.Gly93Cys missense_variant 0.13
Rv3083 3449216 p.Trp238Leu missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3641771 p.Glu79Asp missense_variant 0.13
ddn 3987003 p.Arg54Ser missense_variant 0.12
panD 4044185 p.Met33Val missense_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4245240 p.Tyr670His missense_variant 0.11
aftB 4267873 p.Gln322Glu missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0