TB-Profiler result

Run: SRR6982034
Summary

Run ID: SRR6982034

Sample name:

Date: 04-04-2023 18:25:20

Number of reads: 509245

Percentage reads mapped: 99.68

Strain: lineage4.9

Drug-resistance: Other

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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
lineage4.9 Euro-American (H37Rv-like) T1 None 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
pncA 2288851 p.Val131Phe missense_variant 0.1 pyrazinamide
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
gyrB 5409 p.Ala57Val missense_variant 0.1
gyrB 5512 c.273C>A synonymous_variant 0.1
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7445 c.144C>T synonymous_variant 0.11
mshA 576037 c.691dupG frameshift_variant 0.12
ccsA 619757 c.-133_-132delGC upstream_gene_variant 0.12
ccsA 620076 c.186G>T synonymous_variant 0.22
ccsA 620852 p.Ala321Gly missense_variant 0.15
rpoC 763513 p.Cys48* stop_gained 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775990 c.2491C>T synonymous_variant 0.12
mmpR5 779159 p.Ala57Gly missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303824 p.Lys298Asn missense_variant 0.1
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471777 n.-68delG upstream_gene_variant 0.12
rrl 1474563 n.908_909delTG non_coding_transcript_exon_variant 0.11
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.12
fabG1 1674053 p.Phe205Tyr missense_variant 0.11
inhA 1674547 p.Val116Leu missense_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918171 p.Ala78Ser missense_variant 0.13
tlyA 1918348 p.Arg137Cys missense_variant 0.1
tlyA 1918579 p.Arg214Trp missense_variant 0.12
katG 2156250 c.-139G>A upstream_gene_variant 0.1
PPE35 2168681 p.Phe644Leu missense_variant 0.11
PPE35 2169759 p.Gly285Asp missense_variant 0.11
PPE35 2170232 c.381T>A synonymous_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2517938 c.-177C>T upstream_gene_variant 0.12
kasA 2518413 p.Ser100Ile missense_variant 0.15
folC 2746216 p.Phe461Leu missense_variant 0.14
folC 2747352 p.Asp83Asn missense_variant 0.11
Rv2752c 3064903 p.Asp430Val missense_variant 0.11
ald 3087761 c.942C>T synonymous_variant 0.14
Rv3083 3448594 p.Thr31Ser missense_variant 0.11
Rv3083 3449238 p.Arg245Ser missense_variant 0.11
fbiB 3642251 p.Asp239Glu missense_variant 0.15
rpoA 3878533 c.-26G>C upstream_gene_variant 0.18
clpC1 4040307 c.397delC frameshift_variant 0.12
embC 4242184 c.2322C>A synonymous_variant 0.14
embC 4242240 p.Asp793Val missense_variant 0.13
embA 4244624 c.1393delC frameshift_variant 0.12
embA 4244786 c.1554G>T synonymous_variant 0.17
embA 4244832 p.Val534Met missense_variant 1.0
embA 4244974 p.Ala581Asp missense_variant 0.11
embB 4248409 p.Leu632Phe missense_variant 1.0
embB 4249547 p.Phe1012Leu missense_variant 0.2
aftB 4268647 p.Thr64Ala missense_variant 0.12
whiB6 4338384 c.138C>T synonymous_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0