TB-Profiler result

Run: SRR6982467
Summary

Run ID: SRR6982467

Sample name:

Date: 04-04-2023 18:38:24

Number of reads: 435997

Percentage reads mapped: 98.84

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 0.99
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
ethR 4327831 p.Ala95Thr missense_variant 1.0 ethionamide
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 8365 p.Thr355Met missense_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9724 c.2426delG frameshift_variant 0.15
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620330 c.442delC frameshift_variant 0.13
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 760000 p.Arg65His missense_variant 0.1
rpoC 763031 c.-339T>C upstream_gene_variant 0.94
rpoC 766556 p.Lys1063Glu missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.92
mmpL5 776182 p.Asp767Asn missense_variant 0.8
mmpL5 777052 p.Gly477Arg missense_variant 1.0
mmpL5 777242 c.1239C>A synonymous_variant 0.22
mmpL5 777994 p.Asn163Asp missense_variant 0.15
mmpS5 778979 c.-74G>T upstream_gene_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781833 p.Gly92Ser missense_variant 0.14
fbiC 1303016 p.Val29Gly missense_variant 0.44
fbiC 1305241 p.Ala771Ser missense_variant 0.13
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834456 c.915T>C synonymous_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101827 p.Gly406Trp missense_variant 0.25
katG 2153971 p.Asp714Ala missense_variant 0.22
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167859 c.2754T>G synonymous_variant 0.22
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170685 c.-73C>T upstream_gene_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289598 c.-357T>C upstream_gene_variant 0.2
ahpC 2726341 p.Val50Gly missense_variant 0.17
Rv2752c 3065951 p.His81Asn missense_variant 0.14
thyA 3074252 p.Glu74Lys missense_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3612835 c.282T>G synonymous_variant 0.22
alr 3840520 p.Ala301Ser missense_variant 0.13
ddn 3986911 p.Arg23Gln missense_variant 0.13
clpC1 4038831 p.Asp625Val missense_variant 0.11
clpC1 4039347 p.Arg453Leu missense_variant 0.11
clpC1 4039484 c.1221T>G synonymous_variant 0.25
embC 4239783 c.-80C>A upstream_gene_variant 0.12
embC 4240648 c.786C>T synonymous_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
aftB 4267030 p.Asp603His missense_variant 0.15
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268934 c.-98C>A upstream_gene_variant 0.33
ethA 4327546 c.-73T>G upstream_gene_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