TB-Profiler result

Run: ERR5863794
Summary

Run ID: ERR5863794

Sample name:

Date: 01-04-2023 22:55:12

Number of reads: 398539

Percentage reads mapped: 99.56

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.Ser450Phe missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288820 p.Gln141Pro missense_variant 1.0 pyrazinamide
eis 2715369 c.-37G>T upstream_gene_variant 1.0 kanamycin
embB 4247429 p.Met306Val 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
gyrB 5675 p.Trp146Arg missense_variant 0.2
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 490988 p.Leu69Pro missense_variant 0.17
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576663 p.Ala439Asp missense_variant 0.22
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761615 c.1809A>G synonymous_variant 0.15
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765807 p.Gln813Arg missense_variant 0.13
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 1304236 p.Gln436Lys missense_variant 0.25
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673781 c.346delG frameshift_variant 0.18
inhA 1674434 p.Val78Ala missense_variant 0.33
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 2221761 p.Tyr468* stop_gained 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2715058 p.Arg92Leu missense_variant 0.11
folC 2747342 p.Val86Ala missense_variant 0.14
folC 2747544 p.Pro19Ser missense_variant 0.15
folC 2747566 c.33G>T synonymous_variant 0.15
pepQ 2860125 c.294G>A synonymous_variant 0.1
Rv2752c 3064670 p.Val508Met missense_variant 0.14
Rv2752c 3065150 c.1041_1042insA frameshift_variant 1.0
Rv2752c 3067187 c.-997_-996insG upstream_gene_variant 1.0
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448690 p.Gly63Cys missense_variant 0.22
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
alr 3841364 c.56delG frameshift_variant 0.13
panD 4043993 p.Arg97Trp missense_variant 0.25
panD 4044179 p.Ala35Thr missense_variant 0.2
embC 4241162 c.1300T>C synonymous_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243346 c.114A>G synonymous_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4246379 p.Asp1049Glu missense_variant 0.11
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267763 c.1074C>T synonymous_variant 0.25
whiB6 4338371 p.Thr51Pro 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