TB-Profiler result

Run: SRR2101633
Summary

Run ID: SRR2101633

Sample name:

Date: 03-04-2023 23:49:54

Number of reads: 616802

Percentage reads mapped: 99.59

Strain: lineage2.2.1

Drug-resistance: Sensitive

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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
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
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576478 c.1131G>T synonymous_variant 0.2
mshA 576539 c.1195delG frameshift_variant 0.15
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
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 779524 c.-619C>A upstream_gene_variant 0.11
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
Rv1258c 1407457 c.-117A>T upstream_gene_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
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
katG 2155437 p.Met225Ile missense_variant 0.11
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168251 p.Gln788* stop_gained 0.12
PPE35 2170479 p.Phe45Tyr missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290110 c.-869C>T upstream_gene_variant 1.0
kasA 2518444 c.330T>C synonymous_variant 0.12
pepQ 2859702 p.Leu239Phe missense_variant 0.14
thyX 3068088 c.-143A>G upstream_gene_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339213 c.96G>A synonymous_variant 0.12
Rv3083 3448559 p.Thr19Lys missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612465 c.652T>C synonymous_variant 0.2
Rv3236c 3612808 c.309C>A synonymous_variant 0.15
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
alr 3840194 c.1227A>G stop_lost&splice_region_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4246567 c.54G>T synonymous_variant 1.0
embB 4247880 p.Val456Ala missense_variant 0.12
embB 4249170 p.Asn886Ser missense_variant 0.11
aftB 4267586 c.1251C>A synonymous_variant 0.15
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.97
gid 4407927 p.Glu92Asp missense_variant 1.0