TB-Profiler result

Run: SRR2100123
Summary

Run ID: SRR2100123

Sample name:

Date: 03-04-2023 22:46:38

Number of reads: 4551827

Percentage reads mapped: 99.57

Strain: lineage3

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
lineage3 East-African-Indian CAS RD750 0.99
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 0.98 streptomycin
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
rpoB 759746 c.-61C>T upstream_gene_variant 0.99
rpoC 762434 c.-936T>G upstream_gene_variant 0.99
rpoC 763031 c.-339T>C upstream_gene_variant 0.98
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.99
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.96
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169317 c.1296C>T synonymous_variant 0.27
PPE35 2169320 p.Leu431Phe missense_variant 0.42
PPE35 2169866 c.747G>C synonymous_variant 0.27
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 0.98
ahpC 2726105 c.-88G>A upstream_gene_variant 0.98
ahpC 2726338 p.Val49Gly missense_variant 0.43
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086987 p.Gln56His missense_variant 0.99
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3642877 p.Lys448Arg missense_variant 0.96
clpC1 4038857 c.1848C>A synonymous_variant 0.32
embC 4242075 p.Arg738Gln missense_variant 1.0
embC 4242425 p.Arg855Gly missense_variant 0.34
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0