TB-Profiler result

Run: SRR3732686

Summary

Run ID: SRR3732686

Sample name:

Date: 04-04-2023 05:37:41

Number of reads: 4249408

Percentage reads mapped: 99.64

Strain: lineage4;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
lineage2 East-Asian Beijing RD105 0.21
lineage4 Euro-American LAM;T;S;X;H None 0.8
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.22
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.19
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 1673423 c.-17G>T upstream_gene_variant 0.89 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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.16
mshA 575907 p.Ala187Val missense_variant 0.21
ccsA 620625 p.Ile245Met missense_variant 0.18
rpoB 761889 p.Val695Leu missense_variant 0.74
rpoC 763031 c.-339T>C upstream_gene_variant 0.33
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 0.18
mmpS5 779630 c.-725T>C upstream_gene_variant 0.19
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801009 c.201A>G synonymous_variant 0.74
Rv1258c 1406760 c.580_581insC frameshift_variant 0.24
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 0.18
Rv1979c 2223214 c.-50A>C upstream_gene_variant 0.87
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3065517 c.675C>T synonymous_variant 0.87
Rv2752c 3067039 c.-848T>C upstream_gene_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 0.31
ald 3087755 c.936G>T synonymous_variant 0.28
Rv3083 3448439 c.-64delA upstream_gene_variant 0.72
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.19
fprA 3474299 p.Asp98Gly missense_variant 0.77
Rv3236c 3612536 p.Gly194Val missense_variant 0.12
Rv3236c 3612813 p.Thr102Ala missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.18
ethA 4328317 c.-844C>T upstream_gene_variant 0.71
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.16
gid 4407927 p.Glu92Asp missense_variant 0.25