TB-Profiler result

Run: ERR2515099
Summary

Run ID: ERR2515099

Sample name:

Date: 31-03-2023 20:45:34

Number of reads: 5974339

Percentage reads mapped: 99.63

Strain: lineage3

Drug-resistance: HR-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
lineage3 East-African-Indian CAS 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
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
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 0.99
mshA 576712 c.1365G>T synonymous_variant 0.67
ccsA 619740 c.-151C>T upstream_gene_variant 0.22
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 0.99
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
fbiC 1303972 p.Gly348Ser missense_variant 0.18
fbiC 1304075 p.Ala382Val missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918093 p.Leu52Met missense_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser 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
eis 2714952 c.381C>T synonymous_variant 0.14
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
thyX 3067438 p.Ala170Ser missense_variant 0.33
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3641346 c.-189C>T upstream_gene_variant 1.0
embC 4240547 c.685C>T synonymous_variant 0.33
embC 4242075 p.Arg738Gln missense_variant 0.99
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244254 p.Arg341His missense_variant 0.13
embB 4246801 c.288G>A synonymous_variant 0.12
embB 4247666 c.1156delG frameshift_variant 0.25
embB 4247711 p.Asn400Asp missense_variant 0.12
embB 4247763 p.Val417Ala missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0