TB-Profiler result

Run: ERR5866345

Summary

Run ID: ERR5866345

Sample name:

Date: 02-04-2023 00:38:16

Number of reads: 1000183

Percentage reads mapped: 97.62

Strain: lineage2.2.1

Drug-resistance: MDR-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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289057 p.Pro62Leu missense_variant 1.0 pyrazinamide
eis 2715369 c.-37G>T upstream_gene_variant 1.0 kanamycin
embB 4247730 p.Gly406Asp missense_variant 1.0 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 9034 p.Arg578Gln missense_variant 0.95
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
mshA 576227 p.Arg294Cys missense_variant 0.13
ccsA 620625 p.Ile245Met missense_variant 1.0
ccsA 620759 p.Arg290His missense_variant 0.14
rpoB 761280 p.Gly492Cys missense_variant 0.15
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765765 p.Ile799Asn missense_variant 0.11
rpoC 766645 p.Glu1092Asp missense_variant 1.0
rpoC 767001 p.Thr1211Lys missense_variant 0.2
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
fbiC 1303990 c.1064delG frameshift_variant 0.12
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1673463 c.-739G>T upstream_gene_variant 0.1
inhA 1674726 c.525G>T synonymous_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
PPE35 2170048 p.Leu189Val missense_variant 0.14
PPE35 2170053 p.Thr187Ser missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290228 c.-988delT upstream_gene_variant 0.12
kasA 2519153 p.Ile347Val missense_variant 0.11
folC 2746686 p.Ala305Ser missense_variant 0.14
Rv2752c 3066301 c.-111delC upstream_gene_variant 0.15
thyX 3067212 p.Pro245Gln missense_variant 0.14
thyX 3067412 c.534C>A synonymous_variant 0.1
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086890 p.Ala24Val missense_variant 0.11
ald 3086915 p.Glu32Asp missense_variant 0.11
fbiD 3339322 p.Ala69Thr missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
rpoA 3878639 c.-132C>G upstream_gene_variant 1.0
clpC1 4038696 p.Thr670Asn missense_variant 0.15
clpC1 4039149 p.Ile519Asn missense_variant 0.13
clpC1 4039729 p.Asp326Asn missense_variant 0.1
clpC1 4040092 p.Ser205Thr missense_variant 0.13
embC 4240890 p.Trp343* stop_gained 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244184 p.Ser318Leu missense_variant 0.14
embA 4244397 p.Val389Met missense_variant 1.0
embB 4245545 c.-969C>A upstream_gene_variant 0.15
embB 4245929 c.-585C>A upstream_gene_variant 0.12
embB 4246548 p.Pro12Gln missense_variant 0.18
embB 4246555 c.42G>C synonymous_variant 0.19
embB 4246556 p.Ala15Pro missense_variant 0.19
embB 4246563 p.Leu17Trp missense_variant 0.18
embB 4246567 c.54G>T synonymous_variant 0.19
embB 4246990 c.477C>A synonymous_variant 0.12
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267671 p.Ala389Val missense_variant 0.14
aftB 4268599 p.Glu80Lys missense_variant 0.15
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