TB-Profiler result

Run: SRR6824584
Summary

Run ID: SRR6824584

Sample name:

Date: 04-04-2023 16:48:51

Number of reads: 8432079

Percentage reads mapped: 98.6

Strain: lineage2.2.2

Drug-resistance: Pre-XDR-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 0.99
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.99
lineage2.2.2 East-Asian (Beijing) Beijing-RD105/RD207 RD105;RD207 0.99
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
gyrA 7570 p.Ala90Val missense_variant 0.87 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Ala missense_variant 0.11 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.98 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.99 isoniazid, ethionamide
pncA 2288817 p.Thr142Lys missense_variant 1.0 pyrazinamide
embA 4243217 c.-16C>T upstream_gene_variant 0.99 ethambutol
embB 4247429 p.Met306Val missense_variant 0.99 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
gyrA 9308 c.2007C>T synonymous_variant 0.98
fgd1 491742 c.960T>C synonymous_variant 0.99
rpoC 763031 c.-339T>C upstream_gene_variant 0.99
rpoC 766617 p.Arg1083Gln missense_variant 0.99
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.99
mmpS5 779615 c.-710C>G upstream_gene_variant 0.98
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781406 c.-154_-153insC upstream_gene_variant 0.96
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1833909 p.Asp123Ala missense_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.99
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.98
katG 2155217 p.Gly299Ser missense_variant 0.98
katG 2156484 c.-373A>G upstream_gene_variant 0.97
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223277 c.-114_-113insG upstream_gene_variant 0.98
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 0.97
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.97
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.96
aftB 4267647 p.Asp397Gly missense_variant 0.99
ethA 4326632 p.His281Pro missense_variant 0.98
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.99
gid 4407868 p.Val112Asp missense_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 0.99