TB-Profiler result

Run: ERR046889
Summary

Run ID: ERR046889

Sample name:

Date: 31-03-2023 08:55:48

Number of reads: 7423983

Percentage reads mapped: 99.44

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 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
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 0.99
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491027 p.Asn82Thr missense_variant 0.27
fgd1 491742 c.960T>C synonymous_variant 1.0
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
rpoC 764725 p.Phe452Leu missense_variant 0.24
rpoC 767305 p.Tyr1312* stop_gained 0.19
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777399 p.Thr361Arg missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406750 c.591C>A synonymous_variant 0.17
atpE 1461019 c.-26C>A upstream_gene_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102540 p.Ala168Gly missense_variant 0.19
ndh 2102891 p.Phe51Ser missense_variant 0.23
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167871 c.2742G>C synonymous_variant 0.22
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169379 p.Phe412Val missense_variant 0.22
PPE35 2169866 c.747G>C synonymous_variant 0.34
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
eis 2714366 p.Val323Leu missense_variant 0.38
eis 2715586 c.-254G>C upstream_gene_variant 0.32
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
pepQ 2859381 c.1038C>G synonymous_variant 0.25
ribD 2987307 p.Ala157Pro missense_variant 0.13
Rv2752c 3064552 p.Arg547Pro missense_variant 0.2
Rv2752c 3064741 p.Gly484Ala missense_variant 0.24
ald 3086788 c.-32T>C upstream_gene_variant 0.99
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3641955 p.Gly141Arg missense_variant 0.31
fbiB 3642734 c.1200G>C synonymous_variant 0.15
ddn 3987013 p.Gly57Ala missense_variant 0.2
clpC1 4038857 c.1848C>A synonymous_variant 0.18
clpC1 4039932 p.Gly258Val missense_variant 0.33
embC 4239973 c.111T>G synonymous_variant 0.19
embC 4240172 p.Val104Met missense_variant 0.99
embC 4241456 p.Ala532Pro missense_variant 0.32
embC 4241562 p.Arg567His missense_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 0.99
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.3
ubiA 4269529 p.Ala102Gly missense_variant 0.26
ethA 4327672 c.-199G>A upstream_gene_variant 0.24
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0