TB-Profiler result

Run: ERR11081430

Summary

Run ID: ERR11081430

Sample name:

Date: 08-04-2023 21:04:20

Number of reads: 695298

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 0.99
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.97
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
embB 4247431 p.Met306Ile missense_variant 0.38 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 8475 p.Arg392Cys missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575401 c.54G>A synonymous_variant 0.12
mshA 575582 c.235C>T synonymous_variant 0.11
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 619775 c.-116G>A upstream_gene_variant 0.11
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766645 p.Glu1092Asp missense_variant 1.0
mmpL5 775616 c.2865G>A synonymous_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777980 c.501A>G synonymous_variant 0.12
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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472782 n.937G>C non_coding_transcript_exon_variant 0.4
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102285 p.Asp253Ala missense_variant 0.12
katG 2154625 p.Arg496His missense_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155994 p.Pro40Ser missense_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289866 c.-626delG upstream_gene_variant 0.18
pncA 2290189 c.-948G>C upstream_gene_variant 0.17
kasA 2518737 c.624_625delGG frameshift_variant 0.12
kasA 2518805 p.Asp231Asn missense_variant 0.15
folC 2747670 c.-72C>G upstream_gene_variant 0.17
pepQ 2859750 c.669C>A synonymous_variant 0.2
ribD 2986872 c.38delC frameshift_variant 0.13
thyA 3074356 p.Ser39Leu missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448314 c.-190C>T upstream_gene_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3642236 c.702G>A synonymous_variant 0.18
alr 3841158 p.Glu88Gly missense_variant 0.1
alr 3841347 p.Met25Thr missense_variant 0.17
alr 3841425 c.-6delT upstream_gene_variant 0.11
clpC1 4039972 c.732delC frameshift_variant 0.12
clpC1 4040425 p.Glu94* stop_gained 0.12
panD 4044034 c.247dupG frameshift_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243216 c.-17G>A upstream_gene_variant 0.14
embA 4243217 c.-16C>A upstream_gene_variant 0.33
embA 4243460 c.228C>T synonymous_variant 0.94
embB 4246726 c.213G>A synonymous_variant 0.12
embB 4247028 p.Leu172Gln missense_variant 0.25
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267654 p.Met395Leu missense_variant 0.17
ubiA 4268938 p.Val299Gly missense_variant 0.14
ethA 4326133 c.1341C>T synonymous_variant 0.11
ethA 4326450 p.Thr342Ala missense_variant 0.44
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