TB-Profiler result

Run: SRR12882141
Summary

Run ID: SRR12882141

Sample name:

Date: 03-04-2023 07:12:33

Number of reads: 1247551

Percentage reads mapped: 98.97

Strain: lineage3.1.1

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
lineage3 East-African-Indian CAS RD750 0.99
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 1.0
lineage3.1.1 East-African-Indian CAS1-Kili RD750 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
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 759757 c.-50G>A upstream_gene_variant 0.18
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoB 762445 p.Ala880Val missense_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 0.94
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406385 p.Ala319Val missense_variant 0.13
Rv1258c 1407083 c.258G>C synonymous_variant 0.12
Rv1258c 1407088 p.Ala85Thr missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674455 p.Gly85Val missense_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102515 c.528C>A synonymous_variant 0.14
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154890 p.Phe408Ile missense_variant 0.11
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.25
PPE35 2170053 p.Thr187Ser missense_variant 0.22
PPE35 2170461 p.Gly51Glu missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
kasA 2518763 p.Ser217Thr missense_variant 0.15
eis 2714732 p.Leu201Val missense_variant 0.12
eis 2715510 c.-178G>T upstream_gene_variant 0.12
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474877 p.Arg291Ser missense_variant 1.0
fprA 3475103 p.Gly366Val missense_variant 0.2
fbiB 3642563 p.Asp343Glu missense_variant 0.12
clpC1 4038691 p.Asp672His missense_variant 0.12
clpC1 4038756 p.Gly650Val missense_variant 0.22
clpC1 4039673 c.1032G>T synonymous_variant 0.12
embC 4241562 p.Arg567His missense_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 0.95
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242751 c.-482G>A upstream_gene_variant 0.25
embA 4244254 p.Arg341His missense_variant 0.17
embA 4244395 p.Gly388Val missense_variant 0.11
aftB 4267503 p.Thr445Ile missense_variant 0.12
aftB 4268008 p.Gly277* stop_gained 0.12
aftB 4268163 p.Gln225Arg missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0