TB-Profiler result

Run: ERR4815378
Summary

Run ID: ERR4815378

Sample name:

Date: 01-04-2023 13:49:49

Number of reads: 400656

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 2155783 p.Ala110Val 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
gyrB 6639 p.Ala467Val missense_variant 0.29
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9516 p.Glu739* stop_gained 0.13
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 619807 c.-84G>A upstream_gene_variant 0.17
ccsA 620531 p.Gly214Asp missense_variant 0.2
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
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777550 p.Leu311Val missense_variant 0.15
mmpL5 777599 c.882C>T synonymous_variant 0.22
mmpL5 777978 p.Ala168Val missense_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800765 c.-44G>A upstream_gene_variant 0.67
fbiC 1303209 c.279G>T synonymous_variant 0.25
fbiC 1305343 p.Asn805Asp missense_variant 0.25
Rv1258c 1406675 c.666G>A synonymous_variant 0.29
atpE 1460858 c.-187C>A upstream_gene_variant 0.5
fabG1 1673936 p.Ser166* stop_gained 0.29
inhA 1674426 c.225C>A synonymous_variant 0.22
inhA 1675002 c.801A>G synonymous_variant 0.1
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155045 p.Lys356Arg missense_variant 0.18
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170797 c.-185A>G upstream_gene_variant 0.22
Rv1979c 2222663 p.Val168Ile missense_variant 0.33
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
eis 2714814 c.519C>A synonymous_variant 0.2
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726121 c.-72C>T upstream_gene_variant 1.0
folC 2747506 c.93G>A synonymous_variant 0.14
folC 2747512 p.Gln29His missense_variant 0.15
folC 2747766 c.-168A>T upstream_gene_variant 0.12
pepQ 2859620 p.Gly267Ser missense_variant 0.15
ribD 2986760 c.-79C>T upstream_gene_variant 0.18
Rv2752c 3065998 p.Arg65His missense_variant 0.5
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087315 p.Val166Ile missense_variant 0.15
fbiD 3339168 c.51G>A synonymous_variant 0.17
Rv3083 3449461 p.Gln320Lys missense_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038426 p.Ala760Gly missense_variant 0.29
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245978 p.Ile916Phe missense_variant 0.33
embB 4247115 p.Ala201Val missense_variant 0.2
embB 4247484 p.Gly324Asp missense_variant 0.25
aftB 4268075 p.Met254Ile missense_variant 0.29
aftB 4268113 p.Ala242Ser missense_variant 0.18
ethA 4326341 p.Pro378Arg missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0