TB-Profiler result

Run: ERR4814636
Summary

Run ID: ERR4814636

Sample name:

Date: 01-04-2023 13:24:25

Number of reads: 1141160

Percentage reads mapped: 99.33

Strain: lineage3.1.1

Drug-resistance: Other

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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
lineage3.1.1 East-African-Indian CAS1-Kili 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
gid 4407929 p.Glu92* 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
gyrB 5076 c.-164_-163insT upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7729 p.Arg143Met missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
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 765324 c.1957_1959dupCAC conservative_inframe_insertion 0.12
rpoC 766609 p.Ile1080Met missense_variant 0.11
rpoC 766717 c.3348C>T synonymous_variant 0.11
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
Rv1258c 1406593 c.747delA frameshift_variant 0.13
Rv1258c 1406858 c.483T>C synonymous_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102214 p.Ser277Pro missense_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154840 c.1272G>A synonymous_variant 0.15
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170147 p.Ser156Ala missense_variant 0.17
PPE35 2170461 p.Gly51Glu 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
pncA 2289953 c.-712C>A upstream_gene_variant 0.15
pncA 2290003 c.-762C>T upstream_gene_variant 0.14
kasA 2519169 p.Ala352Gly missense_variant 0.33
eis 2714937 c.396G>A synonymous_variant 0.22
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
pepQ 2859800 p.Pro207Thr missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embC 4240172 p.Val104Met missense_variant 1.0
embC 4241562 p.Arg567His missense_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4268174 c.663G>A synonymous_variant 0.12
aftB 4268776 c.60delG frameshift_variant 0.15
ubiA 4269973 c.-140C>T upstream_gene_variant 0.12
ethA 4328455 c.-982G>A upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0