TB-Profiler result

Run: ERR2229353
Summary

Run ID: ERR2229353

Sample name:

Date: 31-03-2023 17:04:37

Number of reads: 1444404

Percentage reads mapped: 98.86

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 7934 c.633C>T synonymous_variant 0.12
mshA 575272 c.-76A>T upstream_gene_variant 0.15
mshA 576089 c.750_769delTGATCGGCGCGCGGCCCGGG frameshift_variant 0.17
mshA 576115 c.768G>T synonymous_variant 0.18
rpoB 759626 c.-181C>A upstream_gene_variant 0.12
rpoC 765627 p.Ala753Glu missense_variant 0.22
rpoC 767281 c.3912C>G synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775910 c.2571G>T synonymous_variant 0.25
mmpR5 779102 p.Arg38Gln missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781444 c.-116C>A upstream_gene_variant 0.2
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1305318 c.2388C>A synonymous_variant 0.17
Rv1258c 1406371 p.Val324Leu 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 1475029 n.1372T>C non_coding_transcript_exon_variant 0.17
rrl 1475177 n.1522delT non_coding_transcript_exon_variant 0.12
rrl 1476516 n.2859G>T non_coding_transcript_exon_variant 0.18
fabG1 1673346 c.-94C>G upstream_gene_variant 0.16
fabG1 1673349 c.-91G>C upstream_gene_variant 0.16
fabG1 1673380 c.-60C>G upstream_gene_variant 0.27
inhA 1674405 p.Glu68Asp missense_variant 0.13
rpsA 1834049 p.Glu170* stop_gained 0.15
rpsA 1834057 p.Lys172Asn missense_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103230 c.-189delG upstream_gene_variant 0.13
katG 2153970 p.Asp714Glu missense_variant 0.14
katG 2154201 p.Asn637Lys missense_variant 0.12
katG 2155191 c.921A>C synonymous_variant 0.11
katG 2156292 c.-181G>T upstream_gene_variant 0.12
katG 2156338 c.-227C>T upstream_gene_variant 0.12
PPE35 2167801 p.Gly938Cys missense_variant 0.2
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169278 c.1335T>C synonymous_variant 0.12
PPE35 2169281 c.1332T>G synonymous_variant 0.18
PPE35 2169287 c.1326T>C synonymous_variant 0.2
PPE35 2170048 p.Leu189Val missense_variant 0.54
PPE35 2170053 p.Thr187Ser missense_variant 0.53
PPE35 2170352 c.261C>A synonymous_variant 0.14
PPE35 2170357 p.Ala86Ser missense_variant 0.16
PPE35 2170359 p.Gln85Arg missense_variant 0.14
Rv1979c 2222611 p.Ile185Thr missense_variant 0.11
Rv1979c 2222619 c.545_546insTG frameshift_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289188 c.54G>T synonymous_variant 0.22
pncA 2290168 c.-927G>A upstream_gene_variant 0.17
pncA 2290186 c.-945G>C upstream_gene_variant 0.25
kasA 2518809 p.Lys232Arg missense_variant 0.25
kasA 2518864 c.750G>C synonymous_variant 0.15
folC 2746200 p.Val467Leu missense_variant 0.14
Rv2752c 3064614 c.1578G>A synonymous_variant 0.12
thyA 3074249 p.His75Tyr missense_variant 0.13
Rv3236c 3612759 p.Gly120Ser missense_variant 0.12
Rv3236c 3612979 c.138C>T synonymous_variant 0.14
rpoA 3878599 c.-92C>G upstream_gene_variant 0.5
rpoA 3878639 c.-132C>G upstream_gene_variant 0.4
clpC1 4038752 p.Gln651His missense_variant 0.13
clpC1 4039031 c.1674T>C synonymous_variant 0.14
clpC1 4039645 p.His354Asp missense_variant 0.14
clpC1 4039876 p.Asn277Asp missense_variant 0.1
embC 4240552 p.Lys230Asn missense_variant 0.11
embC 4241622 p.Thr587Asn missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4245767 c.-747G>A upstream_gene_variant 0.2
embB 4246544 p.Thr11Pro missense_variant 0.37
embB 4246548 p.Pro12Gln missense_variant 0.5
embB 4246555 c.42G>C synonymous_variant 0.47
embB 4246556 p.Ala15Pro missense_variant 0.5
embB 4246563 p.Leu17Trp missense_variant 0.21
embB 4246567 c.54G>T synonymous_variant 0.2
embB 4246958 p.Glu149* stop_gained 0.12
embB 4247028 p.Leu172Arg missense_variant 0.18
embB 4248949 p.Asp812Glu missense_variant 0.13
embB 4249301 p.Arg930Ser missense_variant 0.12
embB 4249447 c.2934G>A synonymous_variant 0.12
aftB 4268870 c.-34G>T upstream_gene_variant 0.12
aftB 4269201 c.-365A>G upstream_gene_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0