TB-Profiler result

Run: ERR2229513
Summary

Run ID: ERR2229513

Sample name:

Date: 31-03-2023 17:16:22

Number of reads: 1032122

Percentage reads mapped: 99.46

Strain: lineage4.8

Drug-resistance: RR-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
rpoB 761135 p.Leu443Phe missense_variant 0.15 rifampicin
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
gyrA 7685 p.Arg128Ser missense_variant 0.17
rpoB 760612 p.Leu269Trp missense_variant 0.12
rpoC 766235 p.Gly956Cys missense_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777630 p.Arg284His missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1303779 p.Glu283Asp missense_variant 0.11
fbiC 1304011 p.Thr361Pro missense_variant 0.18
fbiC 1304927 p.Gly666Val missense_variant 0.15
Rv1258c 1406612 p.Glu243Asp missense_variant 0.14
embR 1416945 c.402delC frameshift_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472319 n.474C>T non_coding_transcript_exon_variant 0.15
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
inhA 1674543 c.342G>A synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918090 p.Ala51Pro missense_variant 0.1
ndh 2103109 c.-67C>T upstream_gene_variant 0.13
katG 2154635 p.Asn493Asp missense_variant 0.15
PPE35 2167806 p.Tyr936Phe missense_variant 0.12
PPE35 2167814 c.2799C>T synonymous_variant 0.21
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169269 c.1344A>G synonymous_variant 0.11
PPE35 2169272 c.1341C>G synonymous_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 0.36
PPE35 2170053 p.Thr187Ser missense_variant 0.36
PPE35 2170139 c.474G>A synonymous_variant 0.18
PPE35 2170147 p.Ser156Ala missense_variant 0.29
PPE35 2170157 p.Ala152Ser missense_variant 0.15
PPE35 2170309 p.Leu102Val missense_variant 0.1
PPE35 2170313 c.300G>C synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290174 c.-933A>G upstream_gene_variant 0.15
kasA 2518402 c.288G>A synonymous_variant 0.11
kasA 2519140 c.1026G>C synonymous_variant 0.14
kasA 2519143 c.1029G>C synonymous_variant 0.14
fbiD 3339364 p.Pro83Ala missense_variant 0.11
fprA 3474860 p.Glu285Gly missense_variant 0.11
whiB7 3568428 c.252A>G synonymous_variant 0.22
Rv3236c 3612558 p.Val187Leu missense_variant 0.12
alr 3841546 c.-126C>A upstream_gene_variant 0.15
rpoA 3877770 c.738A>G synonymous_variant 0.17
ddn 3986933 c.90C>A synonymous_variant 0.17
ddn 3987015 p.Gln58Lys missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242725 p.Gln955* stop_gained 0.18
embA 4245758 c.2527delT frameshift_variant 0.13
embA 4245918 c.2690delG frameshift_variant 0.12
embB 4246548 p.Pro12Gln missense_variant 0.2
embB 4246555 c.42G>C synonymous_variant 0.3
embB 4246556 p.Ala15Pro missense_variant 0.3
embB 4246584 p.Arg24Pro missense_variant 0.22
embB 4247028 p.Leu172Arg missense_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0