TB-Profiler result

Run: ERR2229379
Summary

Run ID: ERR2229379

Sample name:

Date: 31-03-2023 17:08:48

Number of reads: 1209632

Percentage reads mapped: 98.88

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 2155557 c.554delT frameshift_variant 0.12 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
mshA 575806 c.459G>C synonymous_variant 0.12
mshA 576108 p.Ala254Gly missense_variant 0.33
mshA 576275 p.Asp310Tyr missense_variant 0.29
mshA 576727 p.Ile460Met missense_variant 0.2
ccsA 619722 c.-169C>A upstream_gene_variant 0.14
rpoB 760348 p.Phe181Tyr missense_variant 0.12
rpoB 762852 p.Pro1016Thr missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776018 c.2463G>C synonymous_variant 0.36
mmpL5 776021 c.2460G>C synonymous_variant 0.36
mmpL5 776066 c.2415C>G synonymous_variant 0.22
mmpL5 776069 c.2412C>T synonymous_variant 0.2
mmpL5 777164 c.1317C>T synonymous_variant 0.17
mmpL5 778122 p.Thr120Ser missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472879 n.1034T>C non_coding_transcript_exon_variant 0.12
rrl 1473662 n.5A>C non_coding_transcript_exon_variant 0.18
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673346 c.-94C>G upstream_gene_variant 0.23
fabG1 1673349 c.-91G>C upstream_gene_variant 0.23
fabG1 1673357 c.-83G>A upstream_gene_variant 0.15
fabG1 1673359 c.-81T>C upstream_gene_variant 0.15
fabG1 1673361 c.-79C>G upstream_gene_variant 0.15
fabG1 1673380 c.-60C>G upstream_gene_variant 0.42
inhA 1674981 c.780C>A synonymous_variant 0.2
tlyA 1917941 p.Val1Gly missense_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918401 c.462C>T synonymous_variant 0.17
katG 2153965 p.Ala716Glu missense_variant 0.14
katG 2154088 p.Asp675Gly missense_variant 0.12
PPE35 2167865 c.2748G>C synonymous_variant 0.17
PPE35 2167868 c.2745A>C synonymous_variant 0.16
PPE35 2167965 p.Ala883Gly missense_variant 0.27
PPE35 2167967 c.2646A>C synonymous_variant 0.24
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169902 p.Leu237Phe missense_variant 0.16
PPE35 2170048 p.Leu189Val missense_variant 0.66
PPE35 2170053 p.Thr187Ser missense_variant 0.66
PPE35 2170372 p.Thr81Ala missense_variant 0.14
PPE35 2170392 p.Gly74Ala missense_variant 0.11
PPE35 2170400 c.213G>C synonymous_variant 0.11
Rv1979c 2222774 p.Glu131Lys missense_variant 0.12
Rv1979c 2223026 p.Ala47Thr missense_variant 0.12
Rv1979c 2223271 c.-107G>T upstream_gene_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518753 p.Met213Ile missense_variant 0.18
kasA 2518773 p.Asn220Ile missense_variant 0.17
kasA 2518809 p.Lys232Arg missense_variant 0.19
kasA 2518825 c.711T>C synonymous_variant 0.14
kasA 2518864 c.750G>C synonymous_variant 0.2
kasA 2518879 c.765A>G synonymous_variant 0.2
kasA 2518882 c.768C>A synonymous_variant 0.2
kasA 2519140 c.1026G>C synonymous_variant 0.15
kasA 2519143 c.1029G>C synonymous_variant 0.15
Rv2752c 3064689 c.1503C>A synonymous_variant 0.12
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
fprA 3474887 p.Leu294Pro missense_variant 0.14
fprA 3475026 c.1020C>A synonymous_variant 0.18
Rv3236c 3612616 c.501G>A synonymous_variant 0.22
fbiB 3641959 c.426delC frameshift_variant 0.12
fbiB 3642630 p.Thr366Ser missense_variant 0.12
alr 3840538 p.Tyr295His missense_variant 0.18
alr 3841239 p.Leu61Pro missense_variant 0.13
alr 3841546 c.-126C>A upstream_gene_variant 0.36
rpoA 3878599 c.-92C>G upstream_gene_variant 1.0
clpC1 4038773 p.Asp644Glu missense_variant 0.12
clpC1 4038776 p.Glu643Asp missense_variant 0.12
clpC1 4038782 c.1923G>C synonymous_variant 0.11
clpC1 4038912 p.Pro598Gln missense_variant 0.12
clpC1 4039645 p.His354Asp missense_variant 0.17
clpC1 4039654 p.Thr351Ser missense_variant 0.29
clpC1 4039730 c.975C>G synonymous_variant 0.19
panD 4044335 c.-54C>T upstream_gene_variant 0.12
embC 4241756 p.Leu632Met missense_variant 0.12
embC 4242011 p.Leu717Ile missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.25
embB 4246548 p.Pro12Gln missense_variant 0.69
embB 4246555 c.42G>C synonymous_variant 0.62
embB 4246556 p.Ala15Pro missense_variant 0.62
embB 4246567 c.54G>T synonymous_variant 0.44
aftB 4267220 c.1617C>A synonymous_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0