TB-Profiler result

Run: ERR1213915
Summary

Run ID: ERR1213915

Sample name:

Date: 31-03-2023 12:44:39

Number of reads: 2491214

Percentage reads mapped: 99.02

Strain: lineage4.6.2

Drug-resistance: Other

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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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.6 Euro-American T;LAM None 1.0
lineage4.6.2 Euro-American T;LAM RD726 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 781822 p.Lys88Arg missense_variant 1.0 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 6014 p.Asp259Tyr missense_variant 0.14
gyrB 6218 p.Val327Leu missense_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9055 p.Pro585Leu missense_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 762077 c.2271G>A synonymous_variant 0.33
rpoC 763486 c.117T>A synonymous_variant 0.14
rpoC 764209 c.840C>T synonymous_variant 0.17
rpoC 764606 c.1238_1257delTCCGGCAGAACCTGCTCGGC frameshift_variant 0.17
rpoC 765147 p.Pro593Arg missense_variant 0.33
mmpL5 775726 c.2755C>T synonymous_variant 0.22
mmpR5 778298 c.-692C>T upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304701 p.Ala591Thr missense_variant 0.5
fbiC 1305233 p.Ala768Val missense_variant 0.12
Rv1258c 1406623 c.718C>T synonymous_variant 0.15
Rv1258c 1407308 c.33G>T synonymous_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472405 n.560C>T non_coding_transcript_exon_variant 0.5
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.5
rrl 1473815 n.158T>C non_coding_transcript_exon_variant 0.5
rrl 1476750 n.3093T>C non_coding_transcript_exon_variant 0.2
inhA 1674430 c.229C>A synonymous_variant 0.22
rpsA 1834548 p.Gln336Leu missense_variant 0.15
tlyA 1917923 c.-17G>T upstream_gene_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.22
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 0.62
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyX 3067474 p.Pro158Ala missense_variant 0.83
thyA 3074173 p.Ser100Leu missense_variant 0.12
ald 3087692 p.His291Gln missense_variant 0.25
Rv3083 3448493 c.-11A>G upstream_gene_variant 0.5
Rv3083 3448567 p.His22Asp missense_variant 1.0
Rv3083 3449950 p.Leu483Met missense_variant 0.22
fprA 3474801 c.795C>A synonymous_variant 0.22
fprA 3475098 c.1092G>T synonymous_variant 0.12
fprA 3475100 p.Thr365Ile missense_variant 0.18
whiB7 3568810 c.-131G>T upstream_gene_variant 0.17
Rv3236c 3612571 c.546C>T synonymous_variant 1.0
Rv3236c 3612904 p.Leu71Phe missense_variant 0.2
rpoA 3878027 p.Arg161Cys missense_variant 0.12
ddn 3987156 p.Glu105Gln missense_variant 0.17
embA 4242550 c.-683C>G upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242977 c.-256C>T upstream_gene_variant 0.2
embB 4246869 p.Ser119Asn missense_variant 1.0
embB 4246933 c.420G>T synonymous_variant 1.0
embB 4248334 c.1821C>T synonymous_variant 0.33
aftB 4267272 p.Lys522Arg missense_variant 1.0
aftB 4268159 c.678C>A synonymous_variant 0.33
ethR 4326739 c.-810G>C upstream_gene_variant 1.0
ethA 4327692 c.-219G>A upstream_gene_variant 0.29
ethA 4328004 c.-531C>T upstream_gene_variant 1.0
ethR 4328024 p.Arg159Gln missense_variant 0.25
gid 4408367 c.-165G>A upstream_gene_variant 0.33