TB-Profiler result

Run: ERR4831938
Summary

Run ID: ERR4831938

Sample name:

Date: 01-04-2023 21:13:21

Number of reads: 714383

Percentage reads mapped: 99.64

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
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 575527 c.180G>T synonymous_variant 0.13
mshA 575907 p.Ala187Val missense_variant 0.96
mshA 576751 p.Lys468Asn missense_variant 0.33
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 759620 c.-187A>C upstream_gene_variant 0.27
rpoB 760829 c.1025delT frameshift_variant 0.12
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
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpR5 778406 c.-584G>T upstream_gene_variant 0.12
mmpS5 778823 p.Ile28Asn missense_variant 0.12
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
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101692 p.Glu451Lys missense_variant 0.14
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168505 p.Gly703Val missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290039 c.-798C>A upstream_gene_variant 1.0
ahpC 2726341 p.Val50Gly missense_variant 0.25
ahpC 2726350 p.Trp53Leu missense_variant 0.29
ahpC 2726525 c.333C>A synonymous_variant 0.11
ahpC 2726599 p.Phe136Ser missense_variant 0.1
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339499 p.Ala128Pro missense_variant 0.1
Rv3083 3449101 p.Asn200Asp missense_variant 0.18
Rv3083 3449116 p.Ala205Thr missense_variant 1.0
Rv3083 3449212 p.Arg237Ser missense_variant 0.12
Rv3083 3449259 c.756A>G synonymous_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474814 c.810delG frameshift_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3613141 c.-25C>A upstream_gene_variant 0.12
rpoA 3877753 p.Asp252Gly missense_variant 0.12
embC 4240648 c.786C>T synonymous_variant 0.3
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243217 c.-16C>A upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4249630 c.3117C>A synonymous_variant 0.29
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267807 p.Phe344Leu missense_variant 0.15
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
gid 4408285 c.-83C>A upstream_gene_variant 0.11