TB-Profiler result

Run: ERR4813309
Summary

Run ID: ERR4813309

Sample name:

Date: 01-04-2023 12:40:01

Number of reads: 212535

Percentage reads mapped: 99.02

Strain:

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
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
pncA 2289090 p.His51Arg missense_variant 1.0 pyrazinamide
ethA 4325123 c.-1340_*880del transcript_ablation 1.0 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
gyrB 5922 p.Glu228Gly missense_variant 0.25
gyrB 7251 p.Arg671Leu missense_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8807 c.1506C>T synonymous_variant 0.29
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9388 p.Ala696Asp missense_variant 0.13
gyrA 9407 c.2106C>A synonymous_variant 0.15
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 763319 c.-51T>C upstream_gene_variant 0.14
rpoC 763380 p.Val4Ala missense_variant 0.17
rpoC 763436 c.69delG frameshift_variant 0.18
rpoC 763519 p.Lys50Asn missense_variant 0.18
rpoC 764938 c.1569G>A synonymous_variant 0.22
rpoC 766726 p.His1119Gln missense_variant 0.4
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
mmpS5 779630 c.-725T>C upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800863 p.Glu19Lys missense_variant 0.17
fbiC 1305316 p.Thr796Ser missense_variant 0.29
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473136 n.1291A>G non_coding_transcript_exon_variant 0.13
rrl 1475201 n.1544G>A non_coding_transcript_exon_variant 0.4
inhA 1674686 p.Thr162Met missense_variant 0.2
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834390 c.849G>T synonymous_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1917980 p.Arg14Leu missense_variant 0.67
katG 2154405 c.1707G>T synonymous_variant 0.29
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167677 p.Gly979Val missense_variant 0.2
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289534 c.-293G>T upstream_gene_variant 0.29
kasA 2518330 p.Met72Ile missense_variant 0.29
eis 2715340 c.-8C>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087159 p.Ser114Pro missense_variant 0.17
Rv3083 3448479 c.-25G>T upstream_gene_variant 0.33
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3613217 c.-101G>T upstream_gene_variant 0.2
fbiA 3640603 p.Gln21* stop_gained 0.2
embC 4240232 p.Gln124Lys missense_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242957 p.Pro1032Gln missense_variant 0.29
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243823 c.591G>T synonymous_variant 1.0
embA 4244589 p.Leu453Met missense_variant 0.4
embA 4244614 p.Ala461Glu missense_variant 0.33
embB 4248184 p.Met557Ile missense_variant 0.17
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267983 p.Arg285Leu missense_variant 1.0
aftB 4268652 p.Ala62Glu missense_variant 0.5
ubiA 4269703 p.Val44Ala missense_variant 0.25
ubiA 4269734 p.Ala34Ser missense_variant 0.25
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