TB-Profiler result

Run: ERR2843482

Summary

Run ID: ERR2843482

Sample name:

Date: 31-03-2023 23:50:45

Number of reads: 1211302

Percentage reads mapped: 91.24

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
mshA 576108 p.Ala254Gly missense_variant 0.43
rpoC 762434 c.-936T>G upstream_gene_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 777269 c.1212T>G synonymous_variant 0.33
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474754 n.1097C>T non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154664 p.Phe483Ser missense_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156329 c.-218C>G upstream_gene_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168644 p.Phe657Leu missense_variant 1.0
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
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ribD 2987109 p.Glu91* stop_gained 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449712 c.1209C>T synonymous_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embC 4240172 p.Val104Met missense_variant 1.0
embC 4240684 p.Asp274Glu missense_variant 0.2
embC 4241562 p.Arg567His missense_variant 1.0
embC 4241726 p.Phe622Ile missense_variant 0.33
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4248228 p.Trp572* stop_gained 0.15
aftB 4268128 p.Pro237Ser missense_variant 0.12
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407924 c.278_279insA frameshift_variant 1.0
whiB6 4337754 c.-1111_*416del transcript_ablation 1.0