TB-Profiler result

Run: SRR3675458
Summary

Run ID: SRR3675458

Sample name:

Date: 04-04-2023 05:28:28

Number of reads: 888370

Percentage reads mapped: 97.63

Strain: lineage4.5

Drug-resistance: HR-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
lineage4.5 Euro-American H;T RD122 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
katG 2154976 p.Ala379Val missense_variant 0.12 isoniazid
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 0.89
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7892 c.591G>A synonymous_variant 1.0
gyrA 7924 p.His208Arg missense_variant 0.1
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 620029 c.139C>T synonymous_variant 1.0
ccsA 620852 p.Ala321Glu missense_variant 0.22
rpoB 761401 p.Arg532Leu missense_variant 0.2
rpoB 763017 p.Gln1071Lys missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776048 c.2433G>A synonymous_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781620 p.Thr21Ala missense_variant 0.1
Rv1258c 1406101 p.Pro414Ser missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673346 c.-94C>G upstream_gene_variant 0.18
fabG1 1673349 c.-91G>C upstream_gene_variant 0.17
fabG1 1673380 c.-60C>G upstream_gene_variant 0.29
rpsA 1833423 c.-119C>A upstream_gene_variant 0.12
rpsA 1834199 p.Val220Ile missense_variant 0.12
rpsA 1834400 p.Phe287Leu missense_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918600 p.His221Asn missense_variant 0.2
ndh 2101718 p.Leu442Pro missense_variant 0.12
katG 2155034 p.Gly360Cys missense_variant 0.12
katG 2155997 p.Trp39Arg missense_variant 0.11
PPE35 2168945 c.1668T>C synonymous_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.56
PPE35 2170053 p.Thr187Ser missense_variant 0.56
PPE35 2170406 c.207A>G synonymous_variant 0.15
PPE35 2170415 p.Ala66Ser missense_variant 0.14
PPE35 2170425 p.Val63Ala missense_variant 0.12
PPE35 2170568 p.Ile15Met missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726341 p.Val50Gly missense_variant 0.23
ahpC 2726350 p.Trp53Leu missense_variant 0.25
Rv2752c 3066124 p.Gly23Val missense_variant 0.2
Rv2752c 3066304 c.-113C>A upstream_gene_variant 0.15
thyA 3074648 c.-177T>G upstream_gene_variant 0.33
Rv3083 3449297 p.Met265Thr missense_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612628 c.489G>T synonymous_variant 0.17
rpoA 3877539 p.Tyr323* stop_gained 0.12
ddn 3987052 p.Gly70Asp missense_variant 0.15
clpC1 4038318 p.Pro796Leu missense_variant 1.0
embC 4241667 p.Ala602Glu missense_variant 0.18
embC 4242038 p.Ala726Ser missense_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244036 c.804C>T synonymous_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.29
embB 4246548 p.Pro12Gln missense_variant 0.33
embB 4246555 c.42G>C synonymous_variant 0.36
embB 4246556 p.Ala15Pro missense_variant 0.36
embB 4246563 p.Leu17Trp missense_variant 0.2
embB 4249557 p.Thr1015Ile missense_variant 0.18
aftB 4268281 c.556C>A synonymous_variant 0.15
aftB 4268518 p.Ala107Ser missense_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407894 p.Glu103Asp missense_variant 0.22