TB-Profiler result

Run: SRR1723783
Summary

Run ID: SRR1723783

Sample name:

Date: 18-08-2022 08:20:54

Number of reads: 1823207

Percentage reads mapped: 99.33

Strain: lineage2.2.1

Drug-resistance: RR-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 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.99
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
pncA 2288718 p.Met175Thr missense_variant 1.0 pyrazinamide
embA 4243221 c.-12C>T upstream_gene_variant 0.89 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
mshA 575907 p.Ala187Val missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 0.88
rpoC 767314 p.Tyr1315* stop_gained 0.29
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673246 c.-194G>T upstream_gene_variant 0.15
rpsA 1834177 c.636A>C synonymous_variant 0.96
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
thyA 3074465 p.Pro3Ala missense_variant 0.21
ald 3086788 c.-32T>C upstream_gene_variant 1.0
alr 3840349 p.Ala358Thr missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
ubiA 4269292 p.Ala181Val missense_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0