TB-Profiler result

Run: ERR5864126
Summary

Run ID: ERR5864126

Sample name:

Date: 01-04-2023 23:08:20

Number of reads: 1065055

Percentage reads mapped: 99.09

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 2288971 p.Glu91* stop_gained 0.11 pyrazinamide
pncA 2289072 p.His57Arg missense_variant 1.0 pyrazinamide
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9604 p.Val768Ala missense_variant 0.12
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620128 p.Gly80Arg missense_variant 0.4
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 762344 c.2542delT frameshift_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765113 p.Val582Leu missense_variant 0.91
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775796 p.Phe895Leu missense_variant 0.2
mmpL5 776100 p.Thr794Ile missense_variant 0.91
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 776343 p.Gly713Val missense_variant 0.12
mmpL5 776564 c.1917C>A synonymous_variant 0.13
mmpL5 776969 p.Gln504His missense_variant 0.1
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303219 c.289T>C synonymous_variant 0.15
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407180 p.Pro54Gln missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674395 p.Val65Ala missense_variant 0.12
rpsA 1833584 p.Asp15Asn missense_variant 0.12
rpsA 1833765 c.228delC frameshift_variant 0.12
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918572 c.633C>A synonymous_variant 0.18
katG 2153894 p.Arg740Cys missense_variant 0.14
katG 2154688 p.Thr475Ile missense_variant 0.2
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155390 p.Pro241Leu missense_variant 0.11
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168406 p.Leu736Pro missense_variant 0.12
PPE35 2168463 p.Pro717His missense_variant 0.11
PPE35 2170438 p.Gly59Cys missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289585 c.-345delT upstream_gene_variant 0.14
pncA 2289666 c.-425C>T upstream_gene_variant 0.11
pncA 2289698 c.-457C>T upstream_gene_variant 0.12
pncA 2290120 c.-879T>C upstream_gene_variant 0.18
kasA 2518512 c.403delC frameshift_variant 0.12
ahpC 2726345 c.157delT frameshift_variant 0.13
pepQ 2859761 p.Ile220Phe missense_variant 0.17
ribD 2986725 c.-114A>G upstream_gene_variant 0.13
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086814 c.-6G>A upstream_gene_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474208 c.206delA frameshift_variant 0.18
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3613286 c.-170C>G upstream_gene_variant 0.12
fbiA 3641267 p.Gly242Val missense_variant 0.13
rpoA 3877958 p.Glu184Lys missense_variant 0.15
ddn 3987099 p.Pro86Thr missense_variant 0.12
clpC1 4038961 p.Met582Leu missense_variant 0.13
clpC1 4040038 p.Thr223Ser missense_variant 0.29
clpC1 4040088 p.Arg206Gln missense_variant 0.22
embC 4240002 p.Thr47Asn missense_variant 0.14
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 4245026 c.1794T>C synonymous_variant 0.12
embA 4245365 p.Phe711Leu missense_variant 0.12
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4269192 c.-356C>A upstream_gene_variant 0.11
ubiA 4269339 c.494delG frameshift_variant 0.2
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