TB-Profiler result

Run: ERR2229635
Summary

Run ID: ERR2229635

Sample name:

Date: 31-03-2023 17:23:05

Number of reads: 985034

Percentage reads mapped: 99.16

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 576108 p.Ala254Gly missense_variant 0.25
mshA 576376 c.1029G>T synonymous_variant 0.33
rpoB 760077 p.Glu91Gln missense_variant 0.17
rpoB 761152 p.Leu449Gln missense_variant 0.19
rpoC 765353 p.Trp662Arg missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777058 p.Val475Met missense_variant 0.12
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
rrl 1473935 n.278C>T non_coding_transcript_exon_variant 0.17
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673380 c.-60C>G upstream_gene_variant 0.18
rpsA 1834023 p.Leu161Pro missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918151 p.Val71Asp missense_variant 0.12
ndh 2102254 c.789C>T synonymous_variant 0.12
PPE35 2167814 c.2799C>T synonymous_variant 0.18
PPE35 2167965 p.Ala883Gly missense_variant 0.22
PPE35 2167967 c.2646A>C synonymous_variant 0.22
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2168840 c.1773T>C synonymous_variant 0.11
PPE35 2169029 p.Asp528Glu missense_variant 0.15
PPE35 2169902 p.Leu237Phe missense_variant 0.25
PPE35 2169910 p.Asn235Tyr missense_variant 0.18
PPE35 2170048 p.Leu189Val missense_variant 0.49
PPE35 2170053 p.Thr187Ser missense_variant 0.51
PPE35 2170147 p.Ser156Ala missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519140 c.1026G>C synonymous_variant 0.13
kasA 2519143 c.1029G>C synonymous_variant 0.13
kasA 2519153 p.Ile347Val missense_variant 0.13
pepQ 2859886 p.Ala178Asp missense_variant 0.14
pepQ 2860201 c.216_217delAG frameshift_variant 0.13
Rv2752c 3064743 c.1449C>T synonymous_variant 0.2
ald 3086626 c.-194C>G upstream_gene_variant 0.12
fprA 3474475 p.Asn157Asp missense_variant 0.15
Rv3236c 3612380 p.Leu246Pro missense_variant 0.22
fbiB 3642680 p.Gln382His missense_variant 0.15
alr 3841546 c.-126C>A upstream_gene_variant 0.38
alr 3841612 c.-193_-192insC upstream_gene_variant 0.2
clpC1 4039498 p.Ile403Val missense_variant 0.2
clpC1 4039508 c.1197G>C synonymous_variant 0.18
clpC1 4040027 c.678C>G synonymous_variant 0.22
clpC1 4040144 c.561G>C synonymous_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244935 p.Thr568Ile missense_variant 0.18
embB 4246555 c.42G>C synonymous_variant 0.3
embB 4246556 p.Ala15Pro missense_variant 0.3
embB 4246563 p.Leu17Trp missense_variant 0.25
embB 4246991 p.Asn160Tyr missense_variant 0.14
embB 4247135 c.625delC frameshift_variant 0.22
aftB 4268652 p.Ala62Val missense_variant 0.17
ubiA 4268925 c.909G>T stop_lost&splice_region_variant 0.22
ubiA 4269086 p.Val250Leu missense_variant 0.14
ethR 4326970 c.-579G>T upstream_gene_variant 0.14
ethA 4327451 p.Val8Asp 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