TB-Profiler result

Run: ERR2515738
Summary

Run ID: ERR2515738

Sample name:

Date: 31-03-2023 21:05:26

Number of reads: 358577

Percentage reads mapped: 99.71

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 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
rpoB 761139 p.His445Asp missense_variant 1.0 rifampicin
pncA 2289085 p.Asp53Asn missense_variant 0.12 pyrazinamide
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 9238 p.Gly646Asp missense_variant 0.11
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
ccsA 620855 p.Gly322Ala missense_variant 0.13
rpoB 759711 c.-95_-88delGCCGAAAC upstream_gene_variant 0.13
rpoB 759723 c.-84C>T upstream_gene_variant 0.13
rpoB 759726 c.-81A>T upstream_gene_variant 0.13
rpoB 759727 c.-80A>T upstream_gene_variant 0.14
rpoB 759730 c.-77A>G upstream_gene_variant 0.13
rpoC 762980 c.-390T>A upstream_gene_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766500 p.Ala1044Val missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775971 p.Ala837Val missense_variant 0.11
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 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407482 c.-142G>A upstream_gene_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475242 n.1585G>C non_coding_transcript_exon_variant 0.1
rpsA 1833749 p.Ile70Leu missense_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918537 p.Asp200Tyr missense_variant 0.11
ndh 2102295 p.Thr250Ala missense_variant 0.15
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169573 p.Phe347Tyr missense_variant 0.12
PPE35 2170412 c.201G>A synonymous_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289661 c.-420C>G upstream_gene_variant 0.29
kasA 2518512 c.403delC frameshift_variant 0.12
eis 2714526 c.805_806delAC frameshift_variant 1.0
Rv2752c 3065711 p.Gly161Ser missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339333 c.216G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
rpoA 3878630 c.-124delC upstream_gene_variant 1.0
panD 4044235 p.Thr16Ser missense_variant 0.12
embC 4241859 p.Leu666Pro missense_variant 0.14
embC 4241877 p.Val672Ala missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4246159 p.Pro976Leu missense_variant 0.13
embB 4247253 p.Ser247Leu missense_variant 0.15
embB 4247751 c.1240delG frameshift_variant 0.12
embB 4248434 c.1928_1930delCCA disruptive_inframe_deletion 0.11
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268374 p.Met155Val missense_variant 0.12
ethA 4328231 c.-758G>C upstream_gene_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0