TB-Profiler result

Run: ERR117660
Summary

Run ID: ERR117660

Sample name:

Date: 31-03-2023 12:15:55

Number of reads: 4879746

Percentage reads mapped: 99.54

Strain: lineage3;lineage2.2.1

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 0.35
lineage2 East-Asian Beijing RD105 0.66
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.65
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.63
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
fabG1 1673425 c.-15C>T upstream_gene_variant 0.67 isoniazid, ethionamide
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 8056 p.Arg252Leu missense_variant 0.27
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 0.59
rpoB 759746 c.-61C>T upstream_gene_variant 0.34
rpoC 762434 c.-936T>G upstream_gene_variant 0.29
rpoC 763031 c.-339T>C upstream_gene_variant 0.99
rpoC 766047 p.Thr893Ile missense_variant 0.72
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.99
mmpL5 776573 c.1908G>A synonymous_variant 0.34
mmpR5 778463 c.-527T>C upstream_gene_variant 0.4
mmpS5 779615 c.-710C>G upstream_gene_variant 0.62
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.52
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474234 n.577G>A non_coding_transcript_exon_variant 0.4
rpsA 1834177 c.636A>C synonymous_variant 0.69
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 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.3
pncA 2289365 c.-125delC upstream_gene_variant 0.43
eis 2714130 p.Glu401Asp missense_variant 0.34
ahpC 2726105 c.-88G>A upstream_gene_variant 0.39
Rv2752c 3065950 p.His81Arg missense_variant 0.54
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.63
embC 4242075 p.Arg738Gln missense_variant 0.31
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.71
aftB 4267647 p.Asp397Gly missense_variant 0.68
ethA 4326676 p.Ser266Arg missense_variant 0.63
ethA 4328212 c.-740delC upstream_gene_variant 0.26
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407758 p.Ser149Arg missense_variant 0.39
gid 4407927 p.Glu92Asp missense_variant 0.61