TB-Profiler result

Run: ERR2229152
Summary

Run ID: ERR2229152

Sample name:

Date: 31-03-2023 16:45:13

Number of reads: 530811

Percentage reads mapped: 98.6

Strain: lineage4.8

Drug-resistance: Sensitive

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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 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
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 6519 p.Val427Glu missense_variant 0.17
gyrA 6940 c.-362G>T upstream_gene_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8032 p.Tyr244Phe missense_variant 0.11
gyrA 8808 p.Gly503* stop_gained 0.13
mshA 575814 p.Trp156* stop_gained 0.2
mshA 576108 p.Ala254Gly missense_variant 0.6
ccsA 620232 c.344dupA frameshift_variant 0.29
rpoB 760385 c.579G>A synonymous_variant 0.13
rpoB 763140 p.Pro1112Ala missense_variant 0.11
rpoC 765265 p.Lys632Asn missense_variant 0.22
rpoC 765352 c.1983G>A synonymous_variant 0.25
rpoC 765938 p.Arg857Gly missense_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776003 c.2478C>T synonymous_variant 0.2
mmpL5 776008 p.His825Asp missense_variant 0.17
mmpL5 776009 c.2472A>G synonymous_variant 0.17
mmpL5 777035 p.Gln482His missense_variant 0.12
mmpL5 777157 c.1324C>A synonymous_variant 0.17
mmpL5 777164 c.1317C>T synonymous_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781480 c.-80A>G upstream_gene_variant 0.17
rpsL 781506 c.-53delG upstream_gene_variant 0.17
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1406240 c.1101C>A synonymous_variant 0.2
embR 1417133 p.Ile72Asn missense_variant 0.17
embR 1417504 c.-157G>T upstream_gene_variant 0.25
atpE 1460916 c.-129G>T upstream_gene_variant 0.15
atpE 1460992 c.-53A>G upstream_gene_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472508 n.663T>A non_coding_transcript_exon_variant 0.25
rrl 1474608 n.951T>C non_coding_transcript_exon_variant 0.33
fabG1 1673380 c.-60C>G upstream_gene_variant 0.29
fabG1 1674158 p.Asp240Val missense_variant 0.22
fabG1 1674183 c.744A>T stop_lost&splice_region_variant 0.2
rpsA 1833490 c.-51delA upstream_gene_variant 0.11
rpsA 1834210 c.669C>T synonymous_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101880 p.Ser388Ile missense_variant 0.22
katG 2153970 p.Asp714Glu missense_variant 0.33
PPE35 2167965 p.Ala883Gly missense_variant 0.29
PPE35 2167967 c.2646A>C synonymous_variant 0.29
PPE35 2167997 c.2616G>C synonymous_variant 0.25
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169269 c.1344A>G synonymous_variant 0.15
PPE35 2169272 c.1341C>G synonymous_variant 0.17
PPE35 2169278 c.1335T>C synonymous_variant 0.15
PPE35 2169281 c.1332T>G synonymous_variant 0.15
PPE35 2169287 c.1326T>C synonymous_variant 0.13
PPE35 2169293 c.1320T>C synonymous_variant 0.13
PPE35 2170048 p.Leu189Val missense_variant 0.65
PPE35 2170053 p.Thr187Ser missense_variant 0.61
PPE35 2170305 p.Ala103Glu missense_variant 0.2
Rv1979c 2222553 c.611delC frameshift_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288856 p.Asp129Val missense_variant 0.22
pncA 2289046 p.Ser66Thr missense_variant 0.22
pncA 2289466 c.-225T>C upstream_gene_variant 0.15
pncA 2289697 c.-456G>T upstream_gene_variant 0.33
pncA 2289912 c.-671G>T upstream_gene_variant 0.15
pncA 2289936 c.-695T>G upstream_gene_variant 0.11
kasA 2518433 p.Arg107Trp missense_variant 0.12
kasA 2518518 p.Arg135Gln missense_variant 0.15
kasA 2518818 p.Asp235Ala missense_variant 0.22
pepQ 2860608 c.-190C>A upstream_gene_variant 0.15
thyX 3067895 p.Phe17Leu missense_variant 0.18
fbiD 3339012 c.-106A>G upstream_gene_variant 0.1
Rv3236c 3612214 c.903C>G synonymous_variant 0.18
fbiA 3640423 c.-120C>A upstream_gene_variant 0.17
alr 3841131 p.Ala97Glu missense_variant 0.22
rpoA 3877591 p.Leu306Arg missense_variant 0.12
rpoA 3878395 p.Leu38Gln missense_variant 0.18
ddn 3987090 p.Glu83* stop_gained 0.15
clpC1 4039358 p.Ser449Arg missense_variant 0.25
clpC1 4039521 p.Leu395Pro missense_variant 0.22
clpC1 4039645 p.His354Asp missense_variant 0.2
clpC1 4039654 p.Thr351Ser missense_variant 0.18
clpC1 4039730 c.975C>G synonymous_variant 0.11
embC 4241724 p.Val621Ala missense_variant 0.5
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245386 c.2154C>A synonymous_variant 0.14
embB 4248374 p.Trp621Arg missense_variant 0.15
embB 4249550 p.Arg1013Cys missense_variant 0.12
ethA 4327060 p.Ser138Arg missense_variant 0.14
ethR 4327613 p.Gly22Val missense_variant 0.2
whiB6 4338196 p.His109Leu missense_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0