TB-Profiler result

Run: ERR4800671
Summary

Run ID: ERR4800671

Sample name:

Date: 01-04-2023 09:59:09

Number of reads: 3554451

Percentage reads mapped: 99.57

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 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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
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 576108 p.Ala254Gly missense_variant 0.35
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 0.99
rpoC 763031 c.-339T>C upstream_gene_variant 0.99
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.99
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475046 n.1389A>G non_coding_transcript_exon_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
Rv1979c 2221732 p.Pro478Gln missense_variant 0.98
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
ahpC 2726105 c.-88G>A upstream_gene_variant 0.99
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.24
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3841449 c.-30_-29insG upstream_gene_variant 0.98
clpC1 4040062 p.Ile215Val missense_variant 0.96
embC 4242075 p.Arg738Gln missense_variant 0.98
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243218 c.-15C>G upstream_gene_variant 0.98
embA 4244501 c.1269G>A synonymous_variant 0.98
embB 4246584 p.Arg24Pro missense_variant 0.3
embB 4247024 p.Pro171Ala missense_variant 0.15
ethA 4327140 p.Ala112Thr missense_variant 0.97
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338599 c.-78A>C upstream_gene_variant 0.98
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407721 p.Ala161Gly missense_variant 1.0
gid 4408055 p.Leu50Val missense_variant 0.96