TB-Profiler result

Run: ERR4796895
Summary

Run ID: ERR4796895

Sample name:

Date: 01-04-2023 07:11:23

Number of reads: 4038998

Percentage reads mapped: 99.64

Strain: lineage3

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
lineage3 East-African-Indian CAS RD750 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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289225 p.Ile6Thr missense_variant 1.0 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
ethA 4327356 c.117delA frameshift_variant 0.12 ethionamide, ethionamide
gid 4408087 c.115delC frameshift_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
gyrB 6153 p.Ala305Val missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7599 c.301delC frameshift_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490756 c.-27T>G upstream_gene_variant 0.19
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576113 p.Arg256Gly missense_variant 0.4
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765223 c.1854G>T synonymous_variant 1.0
rpoC 766487 p.Pro1040Ser missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 778614 p.Ser98Pro missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416974 p.Ala125Gly missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473526 n.-132A>C upstream_gene_variant 0.2
rrl 1475778 n.2121G>T non_coding_transcript_exon_variant 0.4
fabG1 1673553 p.Asp38Glu missense_variant 0.2
fabG1 1673575 p.His46Tyr missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2222873 p.His98Tyr missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
kasA 2519071 p.Asp319Glu missense_variant 0.23
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.46
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.5
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474212 p.Lys69Thr missense_variant 0.18
fprA 3474224 c.223delC frameshift_variant 0.11
embC 4240409 p.Pro183Ala missense_variant 0.31
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247028 p.Leu172Pro missense_variant 0.15
embB 4247346 p.Leu278Arg missense_variant 0.15
embB 4249778 p.Trp1089Arg missense_variant 1.0
aftB 4267337 c.1500C>T synonymous_variant 1.0
aftB 4267676 c.1161G>A synonymous_variant 0.12
ethR 4328041 p.Thr165Pro missense_variant 0.23
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0