TB-Profiler result

Run: ERR11050763
Summary

Run ID: ERR11050763

Sample name:

Date: 03-04-2023 20:01:03

Number of reads: 2449190

Percentage reads mapped: 99.61

Strain: lineage3

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
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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
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 491742 c.960T>C synonymous_variant 1.0
mshA 576616 c.1269G>C synonymous_variant 0.11
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 761498 c.1692C>T synonymous_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673553 p.Asp38Glu missense_variant 0.19
fabG1 1673558 p.His40Pro missense_variant 0.11
rpsA 1834328 p.Leu263Phe missense_variant 1.0
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
PPE35 2170065 p.Ala183Gly missense_variant 0.27
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 0.22
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
folC 2747256 p.Ile115Val missense_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.28
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087816 p.Cys333Gly missense_variant 0.2
fbiD 3339734 p.Ala206Gly missense_variant 0.7
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3841473 c.-53G>A upstream_gene_variant 1.0
rpoA 3878613 c.-106A>C upstream_gene_variant 0.25
rpoA 3878618 c.-111A>C upstream_gene_variant 0.38
rpoA 3878641 c.-134C>G upstream_gene_variant 0.44
embC 4240409 p.Pro183Ala missense_variant 0.24
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246527 p.Ala5Gly missense_variant 0.24
embB 4246529 p.Ser6Gly missense_variant 0.17
embB 4246584 p.Arg24Pro missense_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407656 c.540_546delATCGGGC frameshift_variant 1.0