TB-Profiler result

Run: ERR1274714
Summary

Run ID: ERR1274714

Sample name:

Date: 31-03-2023 13:31:16

Number of reads: 582767

Percentage reads mapped: 99.46

Strain: lineage4.1.1

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 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
inhA 1674048 c.-154G>A 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
rpoB 759620 c.-187A>C upstream_gene_variant 0.33
rpoB 760493 c.687C>A synonymous_variant 1.0
rpoB 761147 c.1341C>T synonymous_variant 0.96
rpoC 763163 c.-207C>T upstream_gene_variant 0.12
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765719 p.Glu784Gln missense_variant 1.0
rpoC 766070 c.2701C>T synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 779050 c.63delA frameshift_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406413 p.Pro310Thr missense_variant 0.11
Rv1258c 1406711 c.630C>T synonymous_variant 0.12
atpE 1461130 p.Gly29Asp missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.11
rrs 1473290 n.1445C>A non_coding_transcript_exon_variant 0.1
rrl 1473856 n.200dupC non_coding_transcript_exon_variant 0.11
rrl 1475399 n.1742T>C non_coding_transcript_exon_variant 0.11
fabG1 1673346 c.-94C>G upstream_gene_variant 0.15
fabG1 1673349 c.-91G>C upstream_gene_variant 0.16
fabG1 1673380 c.-60C>G upstream_gene_variant 0.16
rpsA 1833414 c.-127delT upstream_gene_variant 0.1
rpsA 1834804 c.1263C>A synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101780 p.Phe421Leu missense_variant 0.14
ndh 2102749 p.Cys98Trp missense_variant 0.11
katG 2154370 p.Val581Ala missense_variant 0.1
PPE35 2170372 p.Thr81Ala missense_variant 0.11
PPE35 2170376 c.237G>A synonymous_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289553 c.-312C>A upstream_gene_variant 0.11
pncA 2289687 c.-446T>C upstream_gene_variant 0.11
kasA 2518519 c.407delA frameshift_variant 0.12
kasA 2518557 p.Asn148Ser missense_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339740 p.Ala208Glu missense_variant 0.1
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568785 c.-106A>G upstream_gene_variant 0.13
fbiA 3641447 p.Thr302Met missense_variant 1.0
rpoA 3877553 p.Glu319Lys missense_variant 1.0
panD 4044092 p.Arg64Cys missense_variant 0.11
embC 4240897 c.1035C>G synonymous_variant 1.0
embC 4241698 c.1837delA frameshift_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4244851 p.Arg540Leu missense_variant 0.14
embB 4249137 c.2629_2664delGTGACCGCCGCGGGCAAGATCGCCGGCAACAGCGTG conservative_inframe_deletion 0.11
embB 4249408 c.2895G>A synonymous_variant 1.0
aftB 4268040 p.Leu266Gln missense_variant 0.11
ubiA 4268929 p.Gly302Val missense_variant 0.15
ethA 4327422 p.Ser18Gly missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0