TB-Profiler result

Run: ERR2229511
Summary

Run ID: ERR2229511

Sample name:

Date: 31-03-2023 17:16:24

Number of reads: 739803

Percentage reads mapped: 98.07

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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7688 c.387C>T synonymous_variant 0.17
mshA 575759 p.Arg138Ser missense_variant 0.29
mshA 576108 p.Ala254Gly missense_variant 0.67
rpoB 760901 p.Asp365Glu missense_variant 0.2
rpoB 762432 p.Gly876Cys missense_variant 0.14
rpoC 764145 p.Glu259Val missense_variant 0.22
rpoC 765343 c.1974G>A synonymous_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777164 c.1317C>T synonymous_variant 0.13
mmpL5 777448 p.Ile345Phe missense_variant 0.14
mmpL5 778008 p.Gly158Val missense_variant 0.11
mmpL5 778048 p.Lys145* stop_gained 0.13
mmpR5 779473 c.486_489dupAGAG frameshift_variant 0.11
mmpS5 779631 c.-726T>C upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303561 p.Met211Val missense_variant 0.13
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1305042 c.2112A>G synonymous_variant 0.13
Rv1258c 1406591 p.Tyr250* stop_gained 0.2
embR 1416551 p.Ala266Val missense_variant 0.11
embR 1416995 p.Glu118Val missense_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472379 n.534T>G non_coding_transcript_exon_variant 0.11
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475039 n.1382A>T non_coding_transcript_exon_variant 0.25
rrl 1476056 n.2399G>T non_coding_transcript_exon_variant 0.14
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.11
rrl 1476244 n.2587G>T non_coding_transcript_exon_variant 0.12
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.21
fabG1 1673346 c.-94C>G upstream_gene_variant 0.18
fabG1 1673349 c.-91G>C upstream_gene_variant 0.18
fabG1 1673380 c.-60C>G upstream_gene_variant 0.3
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102602 c.441G>A synonymous_variant 0.12
katG 2154895 p.Asp406Val missense_variant 0.12
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169902 p.Leu237Phe missense_variant 0.16
PPE35 2170048 p.Leu189Val missense_variant 0.62
PPE35 2170053 p.Thr187Ser missense_variant 0.69
PPE35 2170363 p.Glu84Gln missense_variant 0.15
Rv1979c 2222058 c.1107C>T synonymous_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518366 p.Gln84His missense_variant 0.12
kasA 2518515 p.Pro134His missense_variant 0.12
kasA 2519153 p.Ile347Val missense_variant 0.17
kasA 2519221 c.1107G>T synonymous_variant 0.15
eis 2714331 c.1002T>A synonymous_variant 0.15
folC 2746170 p.Ala477Ser missense_variant 0.13
ribD 2987116 p.Tyr93Cys missense_variant 0.13
thyA 3074002 p.Gly157Asp missense_variant 0.14
ald 3087859 p.Glu347Val missense_variant 0.12
fbiD 3339276 c.159C>G synonymous_variant 0.15
fbiB 3642254 c.720G>T synonymous_variant 0.15
alr 3841347 p.Met25Lys missense_variant 0.12
alr 3841546 c.-126C>A upstream_gene_variant 0.16
alr 3841612 c.-193_-192insC upstream_gene_variant 0.17
clpC1 4038411 p.Asp765Val missense_variant 0.17
clpC1 4039714 p.Tyr331His missense_variant 0.11
clpC1 4039730 c.975C>G synonymous_variant 0.12
clpC1 4040045 c.660C>T synonymous_variant 0.14
embC 4240361 p.Glu167Lys missense_variant 0.15
embC 4240413 p.Leu184Gln missense_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242737 p.Ala959Ser missense_variant 0.18
embA 4244678 c.1446G>A synonymous_variant 0.33
embB 4246555 c.42G>C synonymous_variant 0.4
embB 4246556 p.Ala15Pro missense_variant 0.4
embB 4246563 p.Leu17Trp missense_variant 0.4
embB 4246567 c.54G>T synonymous_variant 0.33
embB 4247941 p.Leu476Phe missense_variant 0.15
embB 4248795 p.Ala761Glu missense_variant 0.12
embB 4248879 p.Thr789Met missense_variant 0.12
embB 4249121 p.Asp870Asn missense_variant 0.17
aftB 4269408 c.-572C>G upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0