TB-Profiler result

Run: ERR2229228
Summary

Run ID: ERR2229228

Sample name:

Date: 31-03-2023 16:50:15

Number of reads: 651047

Percentage reads mapped: 99.07

Strain: lineage4.8

Drug-resistance: HR-TB

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 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
katG 2154463 p.Ala550Asp missense_variant 0.15 isoniazid
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
fgd1 490684 c.-99G>C upstream_gene_variant 0.11
fgd1 491748 p.Glu322Asp missense_variant 0.4
rpoB 761252 c.1446C>T synonymous_variant 0.13
rpoB 762076 p.Lys757Arg missense_variant 0.29
rpoC 763058 c.-312C>T upstream_gene_variant 0.29
rpoC 764009 p.Arg214Ser missense_variant 0.18
rpoC 764161 c.792G>T synonymous_variant 0.2
rpoC 764664 p.Val432Gly missense_variant 0.3
rpoC 766391 p.Thr1008Pro missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775726 c.2755C>T synonymous_variant 0.17
mmpL5 775727 c.2754C>G synonymous_variant 0.15
mmpL5 776018 c.2463G>C synonymous_variant 0.5
mmpL5 776021 c.2460G>C synonymous_variant 0.5
mmpR5 778088 c.-902C>G upstream_gene_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781481 c.-79C>T upstream_gene_variant 0.14
Rv1258c 1406168 c.1173G>A synonymous_variant 0.15
Rv1258c 1406357 c.984C>A synonymous_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 0.22
rrl 1476499 n.2842T>A non_coding_transcript_exon_variant 0.22
fabG1 1673357 c.-83G>A upstream_gene_variant 0.18
fabG1 1673359 c.-81T>C upstream_gene_variant 0.19
fabG1 1673361 c.-79C>G upstream_gene_variant 0.18
fabG1 1673380 c.-60C>G upstream_gene_variant 0.23
fabG1 1673959 p.Ala174Thr missense_variant 0.13
rpsA 1833648 p.Gly36Val missense_variant 0.17
rpsA 1833651 p.Asp37Ala missense_variant 0.17
rpsA 1834960 c.1419G>T synonymous_variant 0.33
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103048 c.-6C>T upstream_gene_variant 0.4
katG 2155104 c.1008G>T synonymous_variant 0.22
katG 2156491 c.-380C>A upstream_gene_variant 0.15
PPE35 2167745 p.Thr956Arg missense_variant 0.17
PPE35 2167955 c.2658A>C synonymous_variant 0.14
PPE35 2167965 p.Ala883Gly missense_variant 0.17
PPE35 2167967 c.2646A>C synonymous_variant 0.18
PPE35 2168250 p.Gln788Arg missense_variant 0.18
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169269 c.1344A>G synonymous_variant 0.18
PPE35 2169272 c.1341C>G synonymous_variant 0.17
PPE35 2169278 c.1335T>C synonymous_variant 0.2
PPE35 2169281 c.1332T>G synonymous_variant 0.18
PPE35 2169287 c.1326T>C synonymous_variant 0.47
PPE35 2169293 c.1320T>C synonymous_variant 0.27
PPE35 2169902 p.Leu237Phe missense_variant 0.16
PPE35 2169910 p.Asn235Tyr missense_variant 0.19
PPE35 2170048 p.Leu189Val missense_variant 0.45
PPE35 2170053 p.Thr187Ser missense_variant 0.45
PPE35 2170406 c.207A>G synonymous_variant 0.17
PPE35 2170415 c.198A>G synonymous_variant 0.38
PPE35 2170424 c.189G>C synonymous_variant 0.23
Rv1979c 2222587 p.Tyr193Ser missense_variant 0.12
Rv1979c 2223201 c.-37T>A upstream_gene_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726342 c.150G>T synonymous_variant 0.25
Rv2752c 3065910 c.282C>A synonymous_variant 0.29
Rv2752c 3066277 c.-86C>G upstream_gene_variant 0.15
ald 3087190 p.Asp124Val missense_variant 0.14
Rv3083 3448416 c.-87C>G upstream_gene_variant 0.23
fprA 3474132 c.126G>A synonymous_variant 0.4
Rv3236c 3612969 p.Gly50Trp missense_variant 0.25
fbiB 3642200 c.666G>A synonymous_variant 0.2
alr 3841546 c.-126C>A upstream_gene_variant 0.27
rpoA 3877657 p.Leu284His missense_variant 0.15
clpC1 4038715 p.Phe664Leu missense_variant 0.2
clpC1 4039356 p.Leu450Pro missense_variant 0.33
clpC1 4039934 c.771G>T synonymous_variant 0.29
clpC1 4040057 c.648C>T synonymous_variant 0.25
embC 4241720 p.Thr620Pro missense_variant 0.25
embC 4242507 p.Leu882Arg missense_variant 0.33
embC 4242533 p.Phe891Val missense_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.13
embB 4246548 p.Pro12Gln missense_variant 0.4
embB 4246555 c.42G>C synonymous_variant 0.54
embB 4246556 p.Ala15Pro missense_variant 0.54
embB 4247526 p.Ala338Val missense_variant 0.25
embB 4247868 p.Val452Gly missense_variant 0.25
embB 4248077 p.Asn522Tyr missense_variant 0.2
embB 4248920 p.Val803Leu missense_variant 0.43
aftB 4268724 p.Val38Glu missense_variant 0.22
ubiA 4269169 p.Trp222* stop_gained 0.25
ethR 4328000 p.Ala151Val missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408260 c.-58A>C upstream_gene_variant 0.22
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0