TB-Profiler result

Run: SRR6982490
Summary

Run ID: SRR6982490

Sample name:

Date: 04-04-2023 18:39:04

Number of reads: 298377

Percentage reads mapped: 99.62

Strain: lineage2.2.1

Drug-resistance: Other

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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
tlyA 1918734 c.797_798delAG frameshift_variant 0.15 capreomycin
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
gyrB 5405 p.Glu56* stop_gained 0.14
gyrB 5603 p.Gly122Cys missense_variant 0.15
gyrB 5937 p.Ala233Glu missense_variant 0.2
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8282 c.981G>T synonymous_variant 0.11
gyrA 9199 p.Lys633Arg missense_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491064 c.282A>G synonymous_variant 0.15
fgd1 491083 p.Val101Phe missense_variant 0.22
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 620748 c.858T>G synonymous_variant 0.17
rpoC 762398 c.-972T>C upstream_gene_variant 0.22
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764174 p.Asp269Asn missense_variant 0.18
rpoC 765164 p.Tyr599Asn missense_variant 0.11
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
rplC 801287 p.Val160Gly missense_variant 0.2
fbiC 1305201 c.2271G>A synonymous_variant 0.14
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1406835 p.Gly169Val missense_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673346 c.-94C>G upstream_gene_variant 0.14
fabG1 1673349 c.-91G>C upstream_gene_variant 0.18
fabG1 1673357 c.-83G>A upstream_gene_variant 0.2
fabG1 1673359 c.-81T>C upstream_gene_variant 0.2
fabG1 1673361 c.-79C>G upstream_gene_variant 0.2
fabG1 1673380 c.-60C>G upstream_gene_variant 0.2
fabG1 1673770 p.Ala111Thr missense_variant 0.5
fabG1 1674040 p.Gly201Trp missense_variant 0.12
rpsA 1833601 p.Glu20Asp missense_variant 0.11
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834503 p.Val321Ala missense_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154988 p.Pro375Arg missense_variant 0.17
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168544 p.Gly690Val missense_variant 0.17
Rv1979c 2222997 c.168T>C synonymous_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289034 p.Pro70Thr missense_variant 0.14
pncA 2289339 c.-98C>T upstream_gene_variant 0.25
kasA 2518400 p.Glu96* stop_gained 0.29
eis 2714249 c.1083delT frameshift_variant 0.15
ahpC 2726051 c.-142G>T upstream_gene_variant 0.13
Rv2752c 3065605 p.Val196Ala missense_variant 0.18
Rv2752c 3066085 p.His36Arg missense_variant 0.1
thyA 3073749 p.Tyr241* stop_gained 0.11
ald 3086712 c.-108C>A upstream_gene_variant 0.5
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475166 p.Gly387Asp missense_variant 0.15
whiB7 3568526 p.Cys52Arg missense_variant 0.17
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3641711 c.177G>A synonymous_variant 0.25
alr 3841159 p.Glu88* stop_gained 0.12
clpC1 4038655 p.Gly684Ser missense_variant 0.13
clpC1 4039783 p.Leu308Met missense_variant 0.17
clpC1 4040011 p.Ala232Thr missense_variant 0.1
panD 4044476 c.-195G>T upstream_gene_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4246181 c.-333C>T upstream_gene_variant 0.17
embB 4248356 c.1847dupC frameshift_variant 0.15
aftB 4267647 p.Asp397Gly missense_variant 1.0
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
gid 4408282 c.-80G>T upstream_gene_variant 0.18