TB-Profiler result

Run: ERR2229479
Summary

Run ID: ERR2229479

Sample name:

Date: 31-03-2023 17:14:41

Number of reads: 1079602

Percentage reads mapped: 99.42

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
mshA 575186 c.-161delG upstream_gene_variant 0.11
mshA 575382 p.Leu12* stop_gained 0.17
mshA 576108 p.Ala254Gly missense_variant 0.24
rpoB 762652 p.Trp949Leu missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775817 c.2664T>C synonymous_variant 0.12
mmpL5 775820 c.2661G>A synonymous_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
embR 1416786 c.561delC frameshift_variant 0.2
embR 1417177 c.171C>T synonymous_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474438 n.781A>G non_coding_transcript_exon_variant 0.11
fabG1 1673380 c.-60C>G upstream_gene_variant 0.26
inhA 1674081 c.-121C>T upstream_gene_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168043 p.Ala857Gly missense_variant 0.11
PPE35 2168051 c.2562G>C synonymous_variant 0.11
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.36
PPE35 2170053 p.Thr187Ser missense_variant 0.36
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518864 c.750G>C synonymous_variant 0.12
kasA 2519140 c.1026G>C synonymous_variant 0.19
kasA 2519143 c.1029G>C synonymous_variant 0.19
kasA 2519201 p.Arg363Ser missense_variant 0.13
kasA 2519356 c.1242G>A synonymous_variant 0.13
kasA 2519359 c.1245T>G synonymous_variant 0.13
pepQ 2859576 c.843C>T synonymous_variant 0.17
Rv2752c 3065809 p.Val128Ala missense_variant 0.1
Rv2752c 3065934 p.His86Gln missense_variant 0.13
thyX 3067549 p.Thr133Pro missense_variant 0.25
thyX 3067602 p.Arg115Leu missense_variant 0.15
Rv3236c 3612822 p.Leu99Val missense_variant 0.13
fbiB 3641728 p.Glu65Gly missense_variant 1.0
fbiB 3641827 p.Arg98Leu missense_variant 0.12
rpoA 3878182 p.Asp109Gly missense_variant 0.13
clpC1 4039645 p.His354Asp missense_variant 0.21
clpC1 4039654 p.Thr351Ser missense_variant 0.21
embC 4241697 p.Ala612Glu missense_variant 0.14
embC 4242350 p.Pro830Thr missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.3
embB 4246567 c.54_55insT frameshift_variant 0.25
embB 4247017 c.504G>T synonymous_variant 0.17
embB 4247024 p.Pro171Ala missense_variant 0.21
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0