TB-Profiler result

Run: SRR12199466
Summary

Run ID: SRR12199466

Sample name:

Date: 03-04-2023 06:42:06

Number of reads: 183550

Percentage reads mapped: 94.92

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 2155168 p.Ser315Thr missense_variant 1.0 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
gyrB 6036 p.Arg266His missense_variant 0.33
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7892 c.591G>A synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491053 p.Ala91Thr missense_variant 0.29
mshA 576223 c.876G>T synonymous_variant 0.33
ccsA 620029 c.139C>T synonymous_variant 1.0
rpoC 764534 c.1165C>A synonymous_variant 0.5
rpoC 766249 c.2880C>A synonymous_variant 0.29
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776003 c.2478C>T synonymous_variant 0.4
mmpL5 776008 p.His825Asp missense_variant 0.4
mmpL5 776009 c.2472A>G synonymous_variant 0.4
mmpL5 776384 c.2097C>A synonymous_variant 0.5
mmpL5 778150 p.Gln111Glu missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406101 p.Pro414Ser missense_variant 1.0
Rv1258c 1407131 c.210G>T synonymous_variant 0.5
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834543 c.1002C>T synonymous_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101891 c.1152C>T synonymous_variant 0.22
PPE35 2168444 c.2169G>T synonymous_variant 0.33
PPE35 2169748 p.Ile289Phe missense_variant 0.5
PPE35 2169749 c.864A>C synonymous_variant 0.5
PPE35 2169974 c.639T>C synonymous_variant 0.22
PPE35 2170048 p.Leu189Val missense_variant 0.67
PPE35 2170053 p.Thr187Ser missense_variant 0.75
PPE35 2170568 p.Ile15Met missense_variant 1.0
Rv1979c 2223121 p.Gly15Val missense_variant 0.4
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2860547 c.-129C>T upstream_gene_variant 0.2
thyA 3074327 p.Lys49Glu missense_variant 0.71
Rv3083 3449977 p.His492Tyr missense_variant 0.29
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612850 p.His89Gln missense_variant 1.0
fbiA 3640631 p.Ala30Asp missense_variant 0.4
fbiB 3641851 p.Ala106Asp missense_variant 0.67
clpC1 4038318 p.Pro796Leu missense_variant 1.0
clpC1 4039498 p.Ile403Val missense_variant 0.25
clpC1 4039508 c.1197G>C synonymous_variant 0.25
clpC1 4040620 p.Gly29Ser missense_variant 0.15
embC 4240123 c.261C>A synonymous_variant 0.4
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245565 p.Gly778Val missense_variant 0.29
embB 4246548 p.Pro12Gln missense_variant 0.29
embB 4246555 c.42G>C synonymous_variant 0.38
embB 4246556 p.Ala15Pro missense_variant 0.38
embB 4247292 p.Ser260Leu missense_variant 0.33
embB 4248219 p.Gly569Val missense_variant 0.5
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407843 c.360G>A synonymous_variant 0.33
gid 4407993 c.210C>T synonymous_variant 0.4
gid 4408030 p.Leu58Pro missense_variant 1.0