TB-Profiler result

Run: ERR2229321
Summary

Run ID: ERR2229321

Sample name:

Date: 31-03-2023 17:00:47

Number of reads: 809855

Percentage reads mapped: 98.89

Strain: lineage4.8

Drug-resistance: Other

Download CSV Download TXT Download PDF Download JSON
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
pncA 2288752 p.Ser164Pro missense_variant 0.14 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
gyrB 6071 p.Phe278Leu missense_variant 0.2
gyrA 7362 p.Glu21Gln missense_variant 1.0
mshA 575644 c.297G>A synonymous_variant 0.22
rpoB 759865 p.Ser20Ile missense_variant 0.25
rpoB 761046 p.Ile414Val missense_variant 0.12
rpoB 761152 p.Leu449Gln missense_variant 0.25
rpoB 763251 p.Leu1149Met missense_variant 0.18
rpoC 765480 c.2114delC frameshift_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776507 c.1974C>A synonymous_variant 0.22
mmpL5 776862 p.His540Arg missense_variant 0.22
mmpL5 777164 c.1317C>T synonymous_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801085 c.279delC frameshift_variant 0.22
rplC 801104 p.Gln99Leu missense_variant 0.14
rplC 801190 p.Lys128Glu missense_variant 0.2
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1303819 p.Ala297Ser missense_variant 0.15
Rv1258c 1406545 p.Ala266Ser missense_variant 0.13
Rv1258c 1406840 c.501G>A synonymous_variant 0.12
Rv1258c 1407488 c.-148C>A upstream_gene_variant 0.2
embR 1416574 c.774A>G synonymous_variant 0.22
atpE 1460990 c.-55C>A upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472728 n.883G>C non_coding_transcript_exon_variant 0.12
rrl 1473812 n.155G>A non_coding_transcript_exon_variant 0.12
rrl 1473854 n.197A>T non_coding_transcript_exon_variant 0.12
rrl 1473950 n.293G>A non_coding_transcript_exon_variant 0.33
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475130 n.1473A>G non_coding_transcript_exon_variant 0.25
fabG1 1673346 c.-94C>G upstream_gene_variant 0.12
fabG1 1673357 c.-83G>A upstream_gene_variant 0.17
fabG1 1673359 c.-81T>C upstream_gene_variant 0.18
fabG1 1673361 c.-79C>G upstream_gene_variant 0.18
fabG1 1673380 c.-60C>G upstream_gene_variant 0.5
fabG1 1673439 c.-1G>T upstream_gene_variant 0.13
inhA 1673805 c.-397G>T upstream_gene_variant 0.16
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102738 p.Glu102Val missense_variant 0.18
katG 2153970 p.Asp714Glu missense_variant 0.25
katG 2155701 p.Asp137Glu missense_variant 0.14
katG 2155874 p.Ile80Phe missense_variant 0.18
PPE35 2167865 c.2748G>C synonymous_variant 0.12
PPE35 2167868 c.2745A>C synonymous_variant 0.12
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169287 c.1326T>C synonymous_variant 0.22
PPE35 2169308 c.1305C>T synonymous_variant 0.14
PPE35 2169592 p.Ile341Leu missense_variant 0.14
PPE35 2170048 p.Leu189Val missense_variant 0.7
PPE35 2170053 p.Thr187Ser missense_variant 0.71
Rv1979c 2222358 c.807C>T synonymous_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223360 c.-196G>A upstream_gene_variant 0.14
pncA 2289041 c.201G>A synonymous_variant 0.14
pncA 2289215 c.27G>A synonymous_variant 0.25
kasA 2518461 p.Leu116Pro missense_variant 0.15
kasA 2519036 p.Val308Ile missense_variant 0.15
folC 2747355 p.Val82Leu missense_variant 0.12
Rv2752c 3064858 p.Gly445Val missense_variant 0.33
fprA 3474412 p.Pro136Thr missense_variant 0.22
alr 3841546 c.-126C>A upstream_gene_variant 0.29
clpC1 4039023 p.Glu561Val missense_variant 0.17
clpC1 4039714 p.Tyr331His missense_variant 0.14
clpC1 4039760 c.945T>G synonymous_variant 0.22
panD 4044201 c.81C>G synonymous_variant 0.18
panD 4044279 c.3G>T start_lost 0.18
embC 4240096 c.234G>A synonymous_variant 0.2
embC 4240801 c.939C>T synonymous_variant 0.14
embC 4240803 p.Tyr314Phe missense_variant 0.14
embC 4241475 c.1615delG frameshift_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244006 c.774C>T synonymous_variant 0.11
embB 4246567 c.54_55insT frameshift_variant 0.4
embB 4247512 c.999T>C synonymous_variant 0.13
embB 4247516 p.Asn335Asp missense_variant 0.12
embB 4249374 p.Ser954Leu missense_variant 0.13
ubiA 4269214 p.Arg207His missense_variant 0.15
ubiA 4269695 p.Asp47Asn missense_variant 0.11
ethR 4327786 p.Val80Phe missense_variant 0.13
ethA 4328278 c.-805A>T upstream_gene_variant 0.13
whiB6 4338574 c.-53G>T 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