TB-Profiler result

Run: ERR4797703
Summary

Run ID: ERR4797703

Sample name:

Date: 01-04-2023 07:50:51

Number of reads: 5155119

Percentage reads mapped: 99.63

Strain: lineage3;lineage2.2.1

Drug-resistance: MDR-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 0.89
lineage2 East-Asian Beijing RD105 0.1
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.11
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.11
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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rplC 801268 p.Cys154Arg missense_variant 0.1 linezolid
fabG1 1673425 c.-15C>T upstream_gene_variant 0.11 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247729 p.Gly406Cys missense_variant 0.89 ethambutol
embB 4248003 p.Gln497Arg missense_variant 0.13 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 490717 c.-66C>T upstream_gene_variant 0.89
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.13
ccsA 620625 p.Ile245Met missense_variant 0.13
rpoB 759746 c.-61C>T upstream_gene_variant 0.89
rpoC 762434 c.-936T>G upstream_gene_variant 0.91
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763555 c.186C>T synonymous_variant 0.92
rpoC 764817 p.Val483Gly missense_variant 0.94
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.12
mmpL5 777371 c.1110C>T synonymous_variant 0.94
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.14
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 0.9
pncA 2289365 c.-125delC upstream_gene_variant 0.93
ahpC 2726105 c.-88G>A upstream_gene_variant 0.89
thyA 3074283 p.Leu63Phe missense_variant 0.84
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473820 c.-187C>A upstream_gene_variant 0.86
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.15
rpoA 3878630 c.-123G>C upstream_gene_variant 0.12
embC 4242075 p.Arg738Gln missense_variant 0.89
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407620 p.Tyr195His missense_variant 0.14
gid 4407927 p.Glu92Asp missense_variant 0.14