TB-Profiler result

Run: ERR2229575

Summary

Run ID: ERR2229575

Sample name:

Date: 31-03-2023 17:19:35

Number of reads: 468891

Percentage reads mapped: 98.83

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 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
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 5659 p.Lys140Asn missense_variant 0.29
gyrB 6387 p.Phe383Tyr missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7600 p.Ala100Asp missense_variant 0.15
gyrA 9684 p.Gly795Arg missense_variant 0.14
fgd1 491660 p.Ala293Asp missense_variant 0.25
mshA 576108 p.Ala254Gly missense_variant 0.33
mshA 576611 p.Ala422Ser missense_variant 0.18
rpoB 760177 p.Ala124Glu missense_variant 0.2
rpoC 763672 c.303C>A synonymous_variant 0.33
rpoC 763983 p.Met205Thr missense_variant 0.29
rpoC 764990 p.Met541Val missense_variant 0.29
rpoC 766390 c.3021C>T synonymous_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777614 c.867C>T synonymous_variant 0.4
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781473 c.-87C>G upstream_gene_variant 0.29
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304088 c.1158C>T synonymous_variant 0.4
Rv1258c 1406240 c.1101C>T synonymous_variant 0.22
embR 1416912 p.Arg146Cys missense_variant 0.67
embR 1417442 c.-95C>A upstream_gene_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473227 n.1382C>A non_coding_transcript_exon_variant 0.2
fabG1 1673380 c.-60C>G upstream_gene_variant 0.17
fabG1 1673648 p.Arg70His missense_variant 0.25
rpsA 1834468 c.927A>T synonymous_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102071 c.972C>G synonymous_variant 0.17
katG 2154507 p.Asn535Lys missense_variant 0.14
katG 2155224 p.Met296Ile missense_variant 0.2
katG 2156105 p.Glu3* stop_gained 0.15
PPE35 2168081 c.2532C>A synonymous_variant 0.4
PPE35 2168216 p.Phe799Leu missense_variant 1.0
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169278 c.1335T>C synonymous_variant 0.33
PPE35 2169281 c.1332T>G synonymous_variant 0.36
PPE35 2169381 p.Trp411Leu missense_variant 0.18
PPE35 2169386 c.1227C>A synonymous_variant 0.15
PPE35 2169394 p.Ala407Ser missense_variant 0.13
PPE35 2169411 p.Thr401Asp missense_variant 0.13
PPE35 2169413 c.1200T>C synonymous_variant 0.13
PPE35 2169902 p.Leu237Phe missense_variant 0.32
PPE35 2169910 p.Asn235Tyr missense_variant 0.31
PPE35 2170048 p.Leu189Val missense_variant 0.45
PPE35 2170053 p.Thr187Ser missense_variant 0.5
PPE35 2170159 p.Ala152Ser missense_variant 0.16
PPE35 2170232 c.381T>C synonymous_variant 0.12
Rv1979c 2221749 c.1416C>A synonymous_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288879 c.363G>T synonymous_variant 0.17
kasA 2517984 c.-131G>T upstream_gene_variant 0.2
kasA 2518798 c.684G>C synonymous_variant 0.2
kasA 2519177 p.Ser355Thr missense_variant 0.25
eis 2714658 c.675G>T synonymous_variant 0.18
eis 2714679 c.654G>T synonymous_variant 0.15
folC 2746847 p.Arg251Pro missense_variant 0.33
folC 2747468 p.Asp44Gly missense_variant 0.4
pepQ 2860213 p.Pro69Leu missense_variant 0.29
pepQ 2860545 c.-127G>C upstream_gene_variant 0.2
ribD 2987436 p.Gly200Trp missense_variant 0.4
Rv2752c 3065181 c.1011G>T synonymous_variant 0.25
Rv2752c 3066175 p.Pro6Leu missense_variant 0.15
Rv2752c 3067177 c.-986G>T upstream_gene_variant 0.25
thyX 3067517 p.Tyr143* stop_gained 0.18
thyA 3073783 p.Leu230Gln missense_variant 0.14
ald 3087792 p.Ala325Thr missense_variant 0.29
fbiD 3339681 p.Asp188Glu missense_variant 0.25
Rv3236c 3612769 c.348T>C synonymous_variant 0.18
fbiA 3640945 p.Arg135Cys missense_variant 0.22
fbiB 3641638 p.Ala35Gly missense_variant 0.29
fbiB 3641963 c.429C>A synonymous_variant 0.33
alr 3840385 p.Phe346Leu missense_variant 0.18
alr 3840490 p.Pro311Thr missense_variant 0.18
alr 3840648 p.Tyr258Cys missense_variant 0.15
alr 3841539 c.-119C>T upstream_gene_variant 0.14
alr 3841546 c.-126C>A upstream_gene_variant 0.33
rpoA 3878318 p.Thr64Ala missense_variant 0.22
ddn 3986712 c.-132A>T upstream_gene_variant 0.18
clpC1 4038229 p.Pro826Thr missense_variant 0.4
clpC1 4038452 c.2253G>T synonymous_variant 0.22
clpC1 4038842 c.1863G>A synonymous_variant 0.14
clpC1 4039634 p.Glu357Gly missense_variant 0.25
clpC1 4039645 p.His354Asp missense_variant 0.25
panD 4044054 c.228G>A synonymous_variant 0.4
embC 4241145 p.Ala428Asp missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246548 p.Pro12Gln missense_variant 0.44
embB 4246555 c.42G>C synonymous_variant 0.4
embB 4246556 p.Ala15Pro missense_variant 0.4
embB 4247972 p.Thr487Ala missense_variant 0.12
embB 4248319 c.1806A>T synonymous_variant 0.2
embB 4248444 p.Asn644Ser missense_variant 0.17
embB 4248446 p.Gly645Arg missense_variant 0.17
embB 4249386 p.Glu958Gly missense_variant 0.15
aftB 4267444 p.Met465Val missense_variant 0.14
ethA 4326519 c.955C>A synonymous_variant 0.33
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407627 c.576C>A synonymous_variant 0.29
gid 4407635 p.Thr190Ser missense_variant 0.33
gid 4408409 c.-207T>C upstream_gene_variant 0.18