TB-Profiler result

Run: ERR4815367
Summary

Run ID: ERR4815367

Sample name:

Date: 01-04-2023 13:49:25

Number of reads: 601332

Percentage reads mapped: 99.6

Strain: lineage3.1.1

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 1.0
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
ethA 4327400 c.73delG frameshift_variant 0.11 ethionamide
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 7860 p.Thr187Ala missense_variant 0.1
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576246 p.Gly300Glu missense_variant 0.18
ccsA 619921 p.Ala11Thr missense_variant 0.17
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 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpR5 778451 c.-539C>T upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1407083 c.258G>T synonymous_variant 0.33
atpE 1461162 p.Ala40Ser missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918673 p.Thr245Met missense_variant 0.13
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169536 c.1077C>T synonymous_variant 0.11
PPE35 2169854 c.759T>G synonymous_variant 0.25
PPE35 2170279 p.Ala112Thr missense_variant 0.17
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 2518147 c.33C>T synonymous_variant 0.3
kasA 2518918 c.804C>A synonymous_variant 0.13
eis 2715053 p.Arg94Cys missense_variant 0.2
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726338 p.Val49Gly missense_variant 0.3
thyX 3067319 c.627G>A synonymous_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612041 p.Val359Ala missense_variant 0.11
Rv3236c 3612393 p.Val242Leu missense_variant 0.2
clpC1 4040241 p.Thr155Phe missense_variant 0.13
clpC1 4040249 p.Glu152Gly missense_variant 0.14
clpC1 4040254 p.Ala151Thr missense_variant 0.14
embC 4240172 p.Val104Met missense_variant 1.0
embC 4241562 p.Arg567His missense_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245714 p.Leu828Met missense_variant 0.13
embB 4247236 p.Gln241His missense_variant 0.17
aftB 4267135 p.Cys568Ser missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0