TB-Profiler result

Run: ERR11050292
Summary

Run ID: ERR11050292

Sample name:

Date: 02-04-2023 21:23:38

Number of reads: 3762668

Percentage reads mapped: 99.57

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 1.0
mshA 576108 p.Ala254Gly missense_variant 0.23
mshA 576113 p.Arg256Gly missense_variant 0.26
mshA 576442 p.Cys365Trp missense_variant 0.19
mshA 576456 p.Val370Gly missense_variant 0.26
mshA 576468 p.Val374Gly missense_variant 0.21
mshA 576613 c.1266A>C synonymous_variant 0.46
mshA 576616 c.1269G>C synonymous_variant 0.28
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 764367 p.Gly333Ala missense_variant 0.24
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777883 p.Gly200Arg missense_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673553 p.Asp38Glu missense_variant 0.24
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.99
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170065 p.Ala183Gly missense_variant 0.3
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 2519071 p.Asp319Glu missense_variant 0.18
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 0.99
fbiD 3339734 p.Ala206Gly missense_variant 0.53
fbiD 3339746 p.Ala210Gly missense_variant 0.6
fbiD 3339749 p.Val211Ala missense_variant 0.25
fbiD 3339751 p.Ala212Pro missense_variant 0.3
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568428 c.252A>G synonymous_variant 0.33
whiB7 3568431 c.249C>G synonymous_variant 0.26
rpoA 3878641 c.-134C>G upstream_gene_variant 0.62
embC 4240409 p.Pro183Ala missense_variant 0.26
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246527 p.Ala5Gly missense_variant 0.48
embB 4247016 p.Ser168Trp missense_variant 0.18
embB 4248328 c.1815G>C synonymous_variant 0.16
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0