TB-Profiler result

Run: SRR4033387
Summary

Run ID: SRR4033387

Sample name:

Date: 04-04-2023 06:03:33

Number of reads: 1229219

Percentage reads mapped: 99.52

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 0.99
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
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
rpoC 764822 p.Asp485Asn missense_variant 0.11 rifampicin
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 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 762836 c.-534C>G upstream_gene_variant 0.17
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763207 p.Ser1134Ile missense_variant 0.1
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406232 c.1107_1108dupAC frameshift_variant 0.15
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673874 p.Trp145Cys missense_variant 0.13
rpsA 1834177 c.636A>C synonymous_variant 1.0
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 2289648 c.-407A>G upstream_gene_variant 0.12
kasA 2519093 p.Arg327Cys missense_variant 0.17
thyA 3074183 p.Gln97* stop_gained 0.1
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 1.0
fbiA 3641222 p.Pro227Leu missense_variant 0.17
fbiB 3642523 p.Ala330Val missense_variant 0.11
rpoA 3878238 p.Asp90Glu missense_variant 0.12
panD 4043908 p.Pro125Arg missense_variant 0.12
embC 4240631 p.Met257Val missense_variant 0.11
embC 4242425 p.Arg855Gly missense_variant 0.27
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243792 p.Ala187Val missense_variant 0.15
embB 4247329 c.816C>T synonymous_variant 0.11
embB 4249036 c.2523G>A synonymous_variant 0.17
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268447 c.390G>A synonymous_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407620 p.Tyr195His missense_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0