TB-Profiler result

Run: ERR5866344
Summary

Run ID: ERR5866344

Sample name:

Date: 02-04-2023 00:38:11

Number of reads: 1130229

Percentage reads mapped: 97.52

Strain: lineage2.2.1

Drug-resistance: MDR-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
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 2289057 p.Pro62Leu missense_variant 1.0 pyrazinamide
eis 2715369 c.-37G>T upstream_gene_variant 1.0 kanamycin
fbiA 3641290 p.Lys250* stop_gained 0.12 delamanid
embB 4247730 p.Gly406Asp missense_variant 1.0 ethambutol
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 9034 p.Arg578Gln missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766645 p.Glu1092Asp 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
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674267 c.66G>A synonymous_variant 0.11
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
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518046 c.-69C>T upstream_gene_variant 0.11
folC 2746896 p.Gly235Arg missense_variant 0.15
pepQ 2860569 c.-151G>T upstream_gene_variant 0.1
Rv2752c 3067118 c.-927A>T upstream_gene_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339352 p.Val79Ile missense_variant 0.11
Rv3083 3448418 c.-85A>G upstream_gene_variant 0.13
Rv3083 3448478 c.-25delG upstream_gene_variant 0.11
Rv3083 3449436 c.933G>T synonymous_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474029 p.Ile8Thr missense_variant 0.1
Rv3236c 3612645 p.Glu158Lys missense_variant 0.15
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3613225 c.-109G>T upstream_gene_variant 0.1
fbiA 3641280 p.Ile246Met missense_variant 0.11
fbiB 3641289 c.-246A>G upstream_gene_variant 0.11
rpoA 3878639 c.-132C>G upstream_gene_variant 1.0
ddn 3986815 c.-29G>A upstream_gene_variant 0.11
panD 4044005 p.Met93Val missense_variant 0.14
panD 4044163 p.Glu40Gly missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244397 p.Val389Met missense_variant 1.0
embB 4249776 p.Leu1088Pro missense_variant 0.2
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267671 p.Ala389Val missense_variant 0.17
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