TB-Profiler result

Run: ERR2229406

Summary

Run ID: ERR2229406

Sample name:

Date: 31-03-2023 17:10:17

Number of reads: 831933

Percentage reads mapped: 99.25

Strain: lineage4.8

Drug-resistance: Other


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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
pncA 2289066 c.175delT frameshift_variant 0.13 pyrazinamide
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 8839 p.Arg513Pro missense_variant 0.12
gyrA 9515 p.Glu738Asp missense_variant 0.12
fgd1 491599 p.Asp273Tyr missense_variant 0.13
fgd1 491662 p.Val294Phe missense_variant 0.12
mshA 576089 p.Arg248Cys missense_variant 0.15
rpoB 761706 p.Asp634Tyr missense_variant 0.17
rpoC 764404 c.1036delA frameshift_variant 0.2
rpoC 765546 p.Arg726His missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777119 p.His454Gln missense_variant 0.25
mmpL5 777122 c.1359C>T synonymous_variant 0.26
mmpL5 777128 c.1353A>G synonymous_variant 0.29
mmpL5 777191 c.1290C>A synonymous_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304796 c.1866G>A synonymous_variant 0.12
fbiC 1305053 p.Met708Thr missense_variant 0.17
fbiC 1305352 p.Gly808Cys missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474488 n.831G>T non_coding_transcript_exon_variant 0.12
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.14
fabG1 1673380 c.-60C>G upstream_gene_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102244 p.Arg267Trp missense_variant 0.14
ndh 2102389 c.654G>C synonymous_variant 0.18
ndh 2102392 c.651C>A synonymous_variant 0.18
ndh 2102834 p.Pro70Arg missense_variant 0.12
PPE35 2167814 c.2799C>T synonymous_variant 0.21
PPE35 2167865 c.2748G>C synonymous_variant 0.21
PPE35 2167868 c.2745A>C synonymous_variant 0.22
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169203 c.1410C>A synonymous_variant 0.15
PPE35 2169206 c.1407A>G synonymous_variant 0.15
PPE35 2169209 c.1404C>G synonymous_variant 0.15
PPE35 2170048 p.Leu189Val missense_variant 0.6
PPE35 2170053 p.Thr187Ser missense_variant 0.64
PPE35 2170147 p.Ser156Ala missense_variant 0.21
PPE35 2170159 p.Ala152Ser missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288780 p.Arg154Ser missense_variant 0.17
pncA 2289637 c.-397delC upstream_gene_variant 0.22
kasA 2519128 c.1014G>C synonymous_variant 0.14
kasA 2519131 c.1017G>C synonymous_variant 0.14
kasA 2519140 c.1026G>C synonymous_variant 0.25
kasA 2519143 c.1029G>C synonymous_variant 0.25
kasA 2519153 p.Ile347Val missense_variant 0.2
kasA 2519167 c.1053T>C synonymous_variant 0.17
kasA 2519171 p.Leu353Val missense_variant 0.17
eis 2715469 c.-137T>C upstream_gene_variant 0.2
ahpC 2726470 c.281dupT frameshift_variant 0.14
folC 2747565 p.Gly12* stop_gained 0.13
Rv2752c 3064695 c.1497A>G synonymous_variant 0.2
Rv2752c 3065189 p.Val335Leu missense_variant 0.13
Rv2752c 3066301 c.-110G>T upstream_gene_variant 0.18
thyA 3074487 c.-16T>A upstream_gene_variant 0.18
ald 3087774 p.Pro319Ser missense_variant 0.14
fbiD 3339744 c.627A>C synonymous_variant 0.29
Rv3083 3448453 c.-51G>A upstream_gene_variant 0.17
fprA 3474360 p.Asp118Glu missense_variant 0.18
alr 3840932 p.Asn163Lys missense_variant 0.15
alr 3841546 c.-126C>A upstream_gene_variant 0.26
rpoA 3877482 c.1026C>T synonymous_variant 0.17
rpoA 3877719 p.Cys263* stop_gained 0.15
clpC1 4039162 p.His515Asp missense_variant 0.14
clpC1 4039645 p.His354Asp missense_variant 0.25
clpC1 4039654 p.Thr351Ser missense_variant 0.25
clpC1 4039691 c.1014G>C synonymous_variant 0.2
panD 4043918 p.Ala122Thr missense_variant 0.12
embC 4240590 p.Ala243Asp missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243029 p.Asp1056Gly missense_variant 0.2
embA 4243664 c.432T>C synonymous_variant 0.18
embA 4243739 p.Gln169His missense_variant 0.15
embA 4244076 c.844C>A synonymous_variant 0.2
embA 4244204 p.Met324Ile missense_variant 0.25
embB 4247215 c.702C>T synonymous_variant 0.29
embB 4247470 c.957T>C synonymous_variant 0.14
embB 4248731 p.Val740Leu missense_variant 0.14
aftB 4267767 p.Leu357Gln missense_variant 0.18
aftB 4268562 p.Leu92Pro missense_variant 0.22
aftB 4268657 c.180G>A synonymous_variant 0.29
aftB 4269555 c.-719C>A upstream_gene_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0