TB-Profiler result

Run: ERR2503399
Summary

Run ID: ERR2503399

Sample name:

Date: 31-03-2023 18:26:09

Number of reads: 417151

Percentage reads mapped: 99.54

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 0.99
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.99
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.98
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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247431 p.Met306Ile 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 9304 p.Gly668Asp missense_variant 1.0
fgd1 490751 c.-32T>G upstream_gene_variant 0.29
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
rpoB 760197 p.Ala131Thr missense_variant 0.11
rpoB 761381 c.1576delA frameshift_variant 0.12
rpoB 762090 p.Glu762Lys missense_variant 0.12
rpoC 762524 c.-846G>C upstream_gene_variant 0.25
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
fbiC 1303567 p.Met213Leu missense_variant 0.18
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1416194 p.His385Arg missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472401 n.559dupG non_coding_transcript_exon_variant 0.25
rrl 1475380 n.1723C>T non_coding_transcript_exon_variant 0.11
rrl 1475733 n.2076G>T non_coding_transcript_exon_variant 0.5
rpsA 1833414 c.-127delT upstream_gene_variant 0.18
rpsA 1834136 p.Arg199Cys missense_variant 0.17
rpsA 1834177 c.636A>C synonymous_variant 0.91
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102681 c.360_361dupTG frameshift_variant 0.13
katG 2154717 c.1395G>A synonymous_variant 0.14
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170064 c.549G>C synonymous_variant 0.17
Rv1979c 2222977 p.Ile63Thr missense_variant 0.1
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288716 p.Arg176Ser missense_variant 0.17
kasA 2519123 p.Tyr337Asn missense_variant 0.22
eis 2715057 c.276C>T synonymous_variant 0.15
eis 2715060 p.His91Met missense_variant 0.15
eis 2715065 p.Thr90Ala missense_variant 0.15
ahpC 2726265 p.Lys25Gln missense_variant 0.25
Rv2752c 3065364 c.828G>T synonymous_variant 0.12
thyX 3067917 p.Gln10Arg missense_variant 0.13
thyA 3074648 c.-177T>G upstream_gene_variant 0.4
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449408 p.Asn302Ser missense_variant 0.13
Rv3083 3449559 p.Met352Ile missense_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3641099 c.561delT frameshift_variant 0.17
fbiB 3641614 c.83_105delATCTGAGCGCCGCCGTCGCCGCG frameshift_variant 0.13
fbiB 3641815 p.Ile94Thr missense_variant 0.13
alr 3840540 c.877_880delGTGT frameshift_variant 0.1
alr 3840773 c.648C>T synonymous_variant 0.17
clpC1 4038302 c.2403C>T synonymous_variant 0.12
clpC1 4040797 c.-94delG upstream_gene_variant 0.15
embC 4239973 c.111T>G synonymous_variant 0.5
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4246577 p.Ser22Pro missense_variant 0.17
embB 4247148 p.Thr212Asn missense_variant 0.18
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.96
gid 4407927 p.Glu92Asp missense_variant 1.0