TB-Profiler result

Run: ERR2229506
Summary

Run ID: ERR2229506

Sample name:

Date: 31-03-2023 17:15:57

Number of reads: 962120

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 575929 c.582C>T synonymous_variant 0.14
mshA 576108 p.Ala254Gly missense_variant 0.18
mshA 576188 p.Asp281Tyr missense_variant 0.18
mshA 576479 p.Pro378Ala missense_variant 0.22
rpoB 761710 p.Val635Asp missense_variant 0.12
rpoB 761713 p.Val636Asp missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775832 c.2649C>T synonymous_variant 0.17
mmpL5 775981 p.Leu834Met missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1406607 p.Val245Ala missense_variant 0.12
embR 1416967 c.381C>T synonymous_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673346 c.-94C>G upstream_gene_variant 0.11
fabG1 1673380 c.-60C>G upstream_gene_variant 0.26
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918275 c.336T>C synonymous_variant 0.13
katG 2155135 p.Thr326Arg missense_variant 0.12
katG 2155184 p.Lys310Glu missense_variant 0.15
PPE35 2167814 c.2799C>T synonymous_variant 0.23
PPE35 2167865 c.2748G>C synonymous_variant 0.13
PPE35 2167868 c.2745A>C synonymous_variant 0.12
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.44
PPE35 2170053 p.Thr187Ser missense_variant 0.47
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518606 c.492G>C synonymous_variant 0.12
kasA 2518609 p.Met165Ile missense_variant 0.12
pepQ 2860140 c.279A>G synonymous_variant 0.18
Rv2752c 3065065 p.Ala376Gly missense_variant 0.1
ald 3087740 p.Lys307Asn missense_variant 0.11
fbiD 3339596 p.Pro160Gln missense_variant 0.12
alr 3841546 c.-126C>A upstream_gene_variant 0.19
clpC1 4039691 c.1014G>C synonymous_variant 0.14
clpC1 4040240 c.465C>G synonymous_variant 0.15
clpC1 4040319 p.Ala129Gly missense_variant 0.14
clpC1 4040426 c.279T>C synonymous_variant 0.11
embC 4242492 p.Arg877Gln missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242944 p.Asn1028Asp missense_variant 0.18
embA 4243168 c.-65C>T upstream_gene_variant 0.12
embB 4249480 c.2967G>A synonymous_variant 0.13
aftB 4267000 p.Cys613Arg missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0