TB-Profiler result

Run: ERR1194806
Summary

Run ID: ERR1194806

Sample name:

Date: 31-03-2023 12:34:09

Number of reads: 772193

Percentage reads mapped: 99.48

Strain: lineage2.2.1

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
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
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, 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 491494 p.Asp238Tyr missense_variant 0.22
fgd1 491569 p.Asp263His missense_variant 0.22
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 762419 c.-951C>G upstream_gene_variant 0.25
rpoC 762455 c.-915C>T upstream_gene_variant 0.18
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763199 c.-171G>C upstream_gene_variant 0.15
rpoC 766645 p.Glu1092Asp missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775953 p.Leu843Gln missense_variant 0.2
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 776677 p.Ser602Ala missense_variant 0.18
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
rrl 1473797 n.140G>A non_coding_transcript_exon_variant 0.14
rrl 1475088 n.1431A>G non_coding_transcript_exon_variant 0.12
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834329 p.Leu263Pro missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102375 p.Pro223Gln missense_variant 0.11
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169029 p.Asp528Glu missense_variant 0.23
PPE35 2169049 p.Ile522Phe missense_variant 0.25
PPE35 2169063 p.Met517Lys missense_variant 0.25
PPE35 2170048 p.Leu189Val missense_variant 0.23
PPE35 2170053 p.Thr187Ser missense_variant 0.25
Rv1979c 2222103 c.1062A>T synonymous_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2747539 c.60T>C synonymous_variant 0.12
pepQ 2860592 c.-174T>A upstream_gene_variant 0.27
ribD 2987121 p.Gly95Ser missense_variant 0.12
Rv2752c 3065500 p.Gly231Val missense_variant 1.0
Rv2752c 3065664 c.528G>A synonymous_variant 0.12
thyA 3074476 c.-5C>T upstream_gene_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449171 p.Val223Asp missense_variant 0.27
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612744 p.Thr125Ala missense_variant 0.29
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3641102 p.Phe187Cys missense_variant 0.15
alr 3840784 p.Gln213* stop_gained 0.11
alr 3841513 c.-93A>T upstream_gene_variant 0.14
rpoA 3877512 c.996C>T synonymous_variant 0.17
clpC1 4038473 c.2230_2231delAG frameshift_variant 0.11
embC 4241357 c.1497dupC frameshift_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4245592 p.Val787Gly missense_variant 0.25
embB 4247028 p.Leu172Gln missense_variant 0.21
embB 4247273 p.Arg254Gly missense_variant 0.11
aftB 4267519 p.Thr440Ala missense_variant 0.11
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268600 c.237G>C synonymous_variant 0.17
ubiA 4268944 c.889delG frameshift_variant 0.12
ethA 4326015 p.Val487Met missense_variant 0.11
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