TB-Profiler result

Run: ERR11068627
Summary

Run ID: ERR11068627

Sample name:

Date: 06-04-2023 19:48:34

Number of reads: 3216939

Percentage reads mapped: 99.56

Strain: lineage2.2.1

Drug-resistance: Pre-XDR-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
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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
gyrA 7582 p.Asp94Gly missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288928 p.Gly105Val missense_variant 1.0 pyrazinamide
embB 4247399 p.Asn296His missense_variant 1.0 ethambutol
ethA 4327363 c.110delA frameshift_variant 1.0 ethionamide, 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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575416 c.69T>G synonymous_variant 0.12
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576235 c.888C>T synonymous_variant 0.15
ccsA 620151 c.261C>G synonymous_variant 0.12
ccsA 620186 p.Gly99Asp missense_variant 0.14
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764840 p.Ile491Val missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304429 p.Arg500Gln missense_variant 0.18
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155743 c.369G>T synonymous_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170026 p.Pro196Leu missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519049 p.Gly312Asp missense_variant 0.14
kasA 2519183 p.Leu357Ile missense_variant 0.14
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339333 c.216G>T synonymous_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568431 c.249C>G synonymous_variant 0.25
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
embC 4242618 p.Asp919Gly missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243346 c.114A>G synonymous_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244517 c.1285C>T synonymous_variant 0.33
embB 4246710 p.Ser66Ile missense_variant 0.1
embB 4246807 c.294G>A synonymous_variant 0.11
embB 4247036 p.Gly175Arg missense_variant 0.25
embB 4247088 p.Leu192Gln missense_variant 0.18
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethR 4328002 p.Val152Met missense_variant 0.12
ethR 4328039 p.Arg164His missense_variant 0.15
whiB6 4338371 p.Thr51Pro missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0