TB-Profiler result

Run: ERR5866530
Summary

Run ID: ERR5866530

Sample name:

Date: 02-04-2023 00:44:49

Number of reads: 1513824

Percentage reads mapped: 98.19

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
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288762 c.479delC frameshift_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
gid 4407566 p.Arg213* stop_gained 0.29 streptomycin
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
gyrB 5081 c.-159G>T upstream_gene_variant 0.14
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 491483 p.Ser234Tyr missense_variant 0.33
fgd1 491488 p.Asp236Tyr missense_variant 0.4
fgd1 491659 p.Ala293Thr missense_variant 0.5
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 764944 p.His525Gln missense_variant 1.0
rpoC 766645 p.Glu1092Asp missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775700 c.2781G>A synonymous_variant 0.15
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
atpE 1461232 p.Ala63Glu missense_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.18
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.18
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.2
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.22
rrl 1474853 n.1196A>G non_coding_transcript_exon_variant 0.33
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.33
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.22
rrl 1474905 n.1248T>C non_coding_transcript_exon_variant 0.22
rrl 1475586 n.1929C>A non_coding_transcript_exon_variant 0.17
fabG1 1673620 p.Asp61Tyr missense_variant 0.18
inhA 1674608 p.Pro136Arg missense_variant 0.12
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834783 p.Trp414Cys missense_variant 0.17
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
PPE35 2168216 p.Phe799Leu missense_variant 0.18
PPE35 2168984 c.1629G>T synonymous_variant 0.5
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289757 c.-516C>A upstream_gene_variant 0.22
kasA 2518201 c.87C>A synonymous_variant 0.18
ald 3086718 c.-102A>G upstream_gene_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
clpC1 4039460 p.Met415Ile missense_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4326446 p.Gly343Val missense_variant 0.25
whiB6 4338563 c.-42G>T upstream_gene_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