TB-Profiler result

Run: ERR2229169
Summary

Run ID: ERR2229169

Sample name:

Date: 31-03-2023 16:46:36

Number of reads: 489901

Percentage reads mapped: 99.02

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.99
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
katG 2155187 p.Gly309Cys missense_variant 0.5 isoniazid
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 6124 c.888delG frameshift_variant 0.18
gyrA 7350 p.Pro17Ser missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8813 c.1512C>T synonymous_variant 0.29
gyrA 9057 p.Glu586* stop_gained 0.14
fgd1 491003 p.Val74Glu missense_variant 0.25
mshA 575315 c.-33G>T upstream_gene_variant 0.25
mshA 576755 p.Arg470Cys missense_variant 0.4
ccsA 620418 c.528G>A synonymous_variant 0.18
rpoB 760019 c.213G>T synonymous_variant 0.22
rpoB 762149 c.2343G>T synonymous_variant 0.18
rpoC 766151 p.Asp928Tyr missense_variant 0.25
rpoC 766857 p.Arg1163His missense_variant 0.4
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775927 c.2554C>T synonymous_variant 0.22
mmpL5 775931 c.2550C>T synonymous_variant 0.22
mmpL5 776517 p.Met655Lys missense_variant 0.22
mmpL5 778958 c.-478T>A upstream_gene_variant 0.2
mmpR5 778999 p.Asn4Asp missense_variant 0.2
mmpR5 779387 p.Ser133Ile missense_variant 0.67
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304360 p.Arg477His missense_variant 0.5
Rv1258c 1406338 c.1002delC frameshift_variant 0.22
Rv1258c 1406888 p.Asn151Lys missense_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472190 n.345G>T non_coding_transcript_exon_variant 0.17
rrs 1472214 n.369C>A non_coding_transcript_exon_variant 0.15
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 0.15
rrl 1473737 n.80G>T non_coding_transcript_exon_variant 0.14
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474084 n.427G>T non_coding_transcript_exon_variant 0.2
rrl 1474197 n.540C>G non_coding_transcript_exon_variant 0.14
fabG1 1673346 c.-94C>G upstream_gene_variant 0.11
fabG1 1673359 c.-81T>C upstream_gene_variant 0.11
fabG1 1673361 c.-79C>G upstream_gene_variant 0.11
fabG1 1673380 c.-60C>G upstream_gene_variant 0.42
fabG1 1673528 p.Ala30Val missense_variant 0.67
inhA 1674462 p.Lys87Asn missense_variant 0.25
rpsA 1833597 p.Ser19Ile missense_variant 0.14
rpsA 1834277 p.Asp246Tyr missense_variant 0.12
rpsA 1834315 c.774C>A synonymous_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102875 c.168C>T synonymous_variant 0.18
katG 2154551 c.1561C>T synonymous_variant 0.14
katG 2155012 p.Pro367Gln missense_variant 0.22
PPE35 2167800 p.Gly938Asp missense_variant 0.14
PPE35 2167865 c.2748G>C synonymous_variant 0.24
PPE35 2167868 c.2745A>C synonymous_variant 0.22
PPE35 2168143 p.Phe824Leu missense_variant 0.11
PPE35 2168150 c.2463T>C synonymous_variant 0.22
PPE35 2168156 p.Ile819Met missense_variant 0.13
PPE35 2168327 c.2286G>A synonymous_variant 0.17
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169890 c.723C>T synonymous_variant 0.15
PPE35 2169893 c.720C>A synonymous_variant 0.14
PPE35 2169902 p.Leu237Phe missense_variant 0.28
PPE35 2169910 p.Asn235Tyr missense_variant 0.19
PPE35 2169974 c.639T>C synonymous_variant 0.15
PPE35 2170048 p.Leu189Val missense_variant 0.31
PPE35 2170053 p.Thr187Ser missense_variant 0.33
PPE35 2170099 p.Leu172Met missense_variant 0.22
PPE35 2170415 c.198A>G synonymous_variant 0.25
Rv1979c 2222307 p.Asp286Glu missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289385 c.-144C>A upstream_gene_variant 0.22
kasA 2518335 p.Arg74Gln missense_variant 0.25
kasA 2518615 c.501G>C synonymous_variant 1.0
kasA 2518809 p.Lys232Arg missense_variant 0.33
kasA 2518839 p.Ala242Gly missense_variant 0.33
kasA 2518864 c.750G>C synonymous_variant 0.44
kasA 2518879 c.765A>G synonymous_variant 0.22
kasA 2518882 c.768C>A synonymous_variant 0.2
eis 2715451 c.-119C>A upstream_gene_variant 0.29
ahpC 2726482 c.291delT frameshift_variant 0.2
ahpC 2726559 p.Gly123Ser missense_variant 0.25
ahpC 2726726 p.Trp178Cys missense_variant 0.2
pepQ 2859740 p.Ala227Thr missense_variant 0.33
Rv2752c 3065120 p.Ile358Phe missense_variant 0.13
Rv2752c 3065505 c.687C>T synonymous_variant 0.29
thyA 3073995 c.477G>T synonymous_variant 0.2
thyA 3074331 c.141C>A synonymous_variant 0.15
ald 3086624 c.-196T>C upstream_gene_variant 0.14
ald 3087676 p.Pro286Gln missense_variant 0.12
ald 3087838 p.Ala340Val missense_variant 0.22
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
Rv3236c 3612751 c.366C>A synonymous_variant 0.12
Rv3236c 3613038 c.79C>A synonymous_variant 0.12
Rv3236c 3613314 c.-198T>C upstream_gene_variant 0.33
fbiB 3640977 c.-558C>A upstream_gene_variant 0.25
fbiA 3641054 p.Glu171Gly missense_variant 0.17
fbiB 3641229 c.-306T>A upstream_gene_variant 0.67
fbiB 3641614 c.83_105delATCTGAGCGCCGCCGTCGCCGCG frameshift_variant 0.5
fbiB 3642240 p.Gly236Ser missense_variant 0.22
alr 3841336 p.Ser29Pro missense_variant 0.18
alr 3841546 c.-126C>A upstream_gene_variant 0.19
clpC1 4038963 p.Asp581Gly missense_variant 0.67
clpC1 4039003 p.Asn568Asp missense_variant 1.0
clpC1 4039145 c.1560G>A synonymous_variant 0.29
clpC1 4039700 p.Asp335Glu missense_variant 0.18
clpC1 4039730 c.975C>G synonymous_variant 0.4
clpC1 4040001 p.His235Ala missense_variant 0.22
clpC1 4040010 p.Ala232Arg missense_variant 0.29
clpC1 4040057 c.648C>T synonymous_variant 0.4
panD 4043909 p.Pro125Thr missense_variant 0.25
panD 4044282 c.-1G>C upstream_gene_variant 0.25
embC 4240570 c.708C>A synonymous_variant 0.4
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243713 p.Thr161Ser missense_variant 0.18
embA 4244329 p.Ala366Val missense_variant 0.33
embA 4245197 c.1965C>A synonymous_variant 0.29
embA 4245564 p.Gly778Cys missense_variant 0.67
embB 4246544 p.Thr11Pro missense_variant 0.67
embB 4246548 p.Pro12Gln missense_variant 0.67
embB 4246555 c.42G>C synonymous_variant 0.67
embB 4246556 p.Ala15Pro missense_variant 0.67
embB 4247069 p.Val186Ile missense_variant 0.33
aftB 4267110 p.Asn576Ile missense_variant 0.18
aftB 4267940 c.897T>A synonymous_variant 0.33
aftB 4268156 p.Phe227Leu missense_variant 0.18
aftB 4269186 c.-350C>A upstream_gene_variant 0.2
ubiA 4269322 p.Pro171Gln missense_variant 0.17
ubiA 4269539 p.Glu99Lys missense_variant 0.2
ubiA 4269585 p.Glu83Asp missense_variant 0.25
ethA 4328250 c.-777C>A upstream_gene_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407785 p.Ala140Ser missense_variant 0.18
gid 4407898 p.Arg102Gln missense_variant 0.13
gid 4407903 c.300T>C synonymous_variant 0.13
Rv3083 3448508 c.6_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0