TB-Profiler result

Run: ERR2229489
Summary

Run ID: ERR2229489

Sample name:

Date: 31-03-2023 17:14:38

Number of reads: 404966

Percentage reads mapped: 99.2

Strain: lineage4.8

Drug-resistance: HR-TB

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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
katG 2156056 p.Gly19Asp missense_variant 0.17 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
gyrB 7109 p.Thr624Ala missense_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8533 p.Ser411* stop_gained 0.17
rpoB 759615 c.-192A>C upstream_gene_variant 0.29
rpoB 762419 c.2615delA frameshift_variant 0.2
rpoC 762488 c.-882G>A upstream_gene_variant 0.29
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776199 p.Thr761Ser missense_variant 0.25
mmpL5 776737 p.Arg582Cys missense_variant 0.2
mmpL5 777147 p.Pro445His missense_variant 0.18
mmpR5 778301 c.-689C>T upstream_gene_variant 0.17
mmpL5 778332 p.Val50Ala missense_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1303830 p.His300Gln missense_variant 0.29
embR 1416784 c.564C>T synonymous_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471945 n.100G>T non_coding_transcript_exon_variant 0.22
rrs 1471996 n.151C>T non_coding_transcript_exon_variant 0.22
rrs 1472321 n.477delT non_coding_transcript_exon_variant 0.2
rrs 1472808 n.963C>T non_coding_transcript_exon_variant 0.15
rrl 1473597 n.-61G>A upstream_gene_variant 0.18
rrl 1473665 n.8T>A non_coding_transcript_exon_variant 0.17
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474694 n.1037C>T non_coding_transcript_exon_variant 0.29
fabG1 1673346 c.-94C>G upstream_gene_variant 0.19
fabG1 1673349 c.-91G>C upstream_gene_variant 0.21
fabG1 1673357 c.-83G>A upstream_gene_variant 0.29
fabG1 1673359 c.-81T>C upstream_gene_variant 0.29
fabG1 1673361 c.-79C>G upstream_gene_variant 0.29
fabG1 1673380 c.-60C>G upstream_gene_variant 0.46
fabG1 1674110 p.Leu224Pro missense_variant 0.15
rpsA 1834693 p.Tyr384* stop_gained 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103095 c.-53T>C upstream_gene_variant 0.29
katG 2154328 p.Arg595Leu missense_variant 0.14
PPE35 2167760 c.2853G>A synonymous_variant 0.12
PPE35 2167763 p.Ile950Val missense_variant 0.12
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169191 c.1422G>C synonymous_variant 0.12
PPE35 2169278 c.1335T>C synonymous_variant 0.12
PPE35 2169281 c.1332T>G synonymous_variant 0.12
PPE35 2169287 c.1326T>C synonymous_variant 0.18
PPE35 2169293 c.1320T>C synonymous_variant 0.12
PPE35 2169596 p.Phe339Leu missense_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 0.5
PPE35 2170053 p.Thr187Ser missense_variant 0.47
PPE35 2170125 p.Val163Ser missense_variant 0.12
PPE35 2170127 c.486T>C synonymous_variant 0.12
PPE35 2170132 p.Val161Ile missense_variant 0.12
PPE35 2170139 c.474G>A synonymous_variant 0.12
PPE35 2170147 p.Ser156Ala missense_variant 0.11
PPE35 2170159 p.Ala152Ser missense_variant 0.12
PPE35 2170460 c.153G>A synonymous_variant 0.14
PPE35 2170465 p.Ala50Ser missense_variant 0.14
PPE35 2170472 c.141G>A synonymous_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288944 p.Thr100Ser missense_variant 0.18
kasA 2519267 p.Val385Phe missense_variant 0.25
kasA 2519279 p.Pro389Thr missense_variant 0.2
Rv2752c 3066314 c.-123G>A upstream_gene_variant 0.15
thyX 3067563 p.Leu128Pro missense_variant 0.33
thyA 3073769 c.703C>A synonymous_variant 0.25
Rv3236c 3612860 p.Leu86Pro missense_variant 0.4
Rv3236c 3613097 p.Leu7Pro missense_variant 0.2
fbiB 3641733 p.Pro67Thr missense_variant 0.22
alr 3841220 c.201C>T synonymous_variant 0.18
alr 3841582 c.-162A>G upstream_gene_variant 0.14
alr 3841584 c.-164C>A upstream_gene_variant 0.14
alr 3841612 c.-193_-192insC upstream_gene_variant 0.14
rpoA 3878353 p.Thr52Ile missense_variant 0.29
clpC1 4038674 c.2031C>T synonymous_variant 0.33
clpC1 4039484 c.1221T>G synonymous_variant 0.5
clpC1 4039595 p.His370Gln missense_variant 0.33
clpC1 4039645 p.His354Asp missense_variant 0.17
clpC1 4039654 p.Thr351Ser missense_variant 0.17
clpC1 4040144 c.561G>C synonymous_variant 0.5
clpC1 4040835 c.-131G>T upstream_gene_variant 0.17
embC 4240654 c.792C>T synonymous_variant 1.0
embC 4241125 c.1263G>A synonymous_variant 0.33
embC 4241381 p.Gly507Trp missense_variant 0.18
embA 4243642 p.Ser137Asn missense_variant 0.67
embA 4244753 c.1521G>T synonymous_variant 0.22
embA 4246050 p.Arg940Ser missense_variant 0.33
embB 4246555 c.42G>C synonymous_variant 0.33
embB 4246556 p.Ala15Pro missense_variant 0.33
embB 4246563 p.Leu17Trp missense_variant 0.38
embB 4246567 c.54G>T synonymous_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0