TB-Profiler result

Run: ERR2229091
Summary

Run ID: ERR2229091

Sample name:

Date: 31-03-2023 16:37:50

Number of reads: 369044

Percentage reads mapped: 99.21

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
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpS5 779650 c.-745A>G upstream_gene_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1305224 p.Asp765Val missense_variant 0.15
embR 1417178 p.Thr57Asn missense_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474748 n.1091T>A non_coding_transcript_exon_variant 0.25
fabG1 1673251 c.-189T>A upstream_gene_variant 0.2
fabG1 1673346 c.-94C>G upstream_gene_variant 0.25
fabG1 1673349 c.-91G>C upstream_gene_variant 0.25
fabG1 1673357 c.-83G>A upstream_gene_variant 0.43
fabG1 1673359 c.-81T>C upstream_gene_variant 0.43
fabG1 1673361 c.-79C>G upstream_gene_variant 0.43
fabG1 1673380 c.-60C>G upstream_gene_variant 0.5
rpsA 1834953 p.Ala471Val missense_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918729 p.Ile264Phe missense_variant 0.22
katG 2154374 p.Asp580His missense_variant 0.25
katG 2156177 c.-66T>C upstream_gene_variant 0.14
PPE35 2167865 c.2748G>C synonymous_variant 0.33
PPE35 2167868 c.2745A>C synonymous_variant 0.33
PPE35 2167955 c.2658A>C synonymous_variant 0.33
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169023 c.1590G>T synonymous_variant 0.25
PPE35 2169269 c.1344A>G synonymous_variant 0.17
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 0.22
PPE35 2169287 c.1326T>C synonymous_variant 0.2
PPE35 2169293 c.1320T>C synonymous_variant 0.22
PPE35 2169902 p.Leu237Phe missense_variant 0.26
PPE35 2169910 p.Asn235Tyr missense_variant 0.25
PPE35 2169939 p.Gly225Ala missense_variant 0.14
PPE35 2169941 c.672C>T synonymous_variant 0.14
PPE35 2169944 c.669G>C synonymous_variant 0.14
PPE35 2169947 c.666T>C synonymous_variant 0.14
PPE35 2169956 c.657T>C synonymous_variant 0.11
PPE35 2169964 p.Leu217Val missense_variant 0.11
PPE35 2170048 p.Leu189Val missense_variant 0.19
PPE35 2170053 p.Thr187Ser missense_variant 0.2
PPE35 2170232 c.381T>C synonymous_variant 0.12
PPE35 2170235 c.378T>C synonymous_variant 0.12
PPE35 2170238 c.375T>G synonymous_variant 0.12
Rv1979c 2222656 p.Lys170Met missense_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2517922 c.-193C>T upstream_gene_variant 0.29
kasA 2518360 p.Tyr82* stop_gained 0.2
ahpC 2726148 c.-45A>T upstream_gene_variant 0.25
pepQ 2859607 p.Arg271Gln missense_variant 0.2
ribD 2986934 p.Tyr32* stop_gained 0.2
ald 3087182 p.Gln121His missense_variant 0.14
fbiA 3641368 p.Tyr276His missense_variant 0.2
alr 3841546 c.-126C>A upstream_gene_variant 0.15
alr 3841612 c.-193_-192insC upstream_gene_variant 0.18
rpoA 3877996 p.Val171Ala missense_variant 0.33
clpC1 4039645 p.His354Asp missense_variant 0.22
clpC1 4039654 p.Thr351Ser missense_variant 0.22
clpC1 4040057 c.648C>T synonymous_variant 0.17
clpC1 4040320 p.Ala129Thr missense_variant 0.2
embC 4239921 p.Arg20Leu missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247198 p.Thr229Ser missense_variant 0.25
embB 4249219 p.Tyr902* stop_gained 0.4
aftB 4269132 c.-296G>A upstream_gene_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338678 c.-157G>T upstream_gene_variant 0.14
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0