TB-Profiler result

Run: ERR4815229
Summary

Run ID: ERR4815229

Sample name:

Date: 01-04-2023 13:44:49

Number of reads: 795012

Percentage reads mapped: 99.67

Strain: lineage4.3.2

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.2 Euro-American (LAM) LAM3 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
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 6149 p.Phe304Leu missense_variant 0.17
gyrB 6165 p.Asn309Ser missense_variant 0.22
gyrB 6488 p.Arg417Cys missense_variant 0.2
gyrB 6922 c.1688delT frameshift_variant 0.18
gyrA 7243 c.-59G>A upstream_gene_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8131 p.Gln277Leu missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491328 c.546C>A synonymous_variant 0.12
rpoB 760115 p.Asp103Glu missense_variant 0.1
rpoB 760341 p.Val179Leu missense_variant 0.1
rpoB 760537 p.Glu244Val missense_variant 0.12
rpoB 760732 p.Lys309Met missense_variant 0.22
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765592 c.2223C>A synonymous_variant 0.12
rpoC 765593 p.Lys742Glu missense_variant 0.12
rpoC 766563 p.Thr1065Ile missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776219 c.2262C>T synonymous_variant 0.14
mmpL5 778705 c.-225C>A upstream_gene_variant 0.11
mmpR5 778996 p.Val3Ile missense_variant 0.14
mmpR5 779116 p.Leu43Met missense_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781676 c.117C>T synonymous_variant 1.0
fbiC 1304534 p.Leu535Ser missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471968 n.123G>T non_coding_transcript_exon_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1917973 p.Val12Ile missense_variant 0.13
katG 2156252 c.-141C>T upstream_gene_variant 0.11
PPE35 2167907 c.2706A>G synonymous_variant 0.25
PPE35 2167979 c.2634A>T synonymous_variant 0.22
PPE35 2168981 c.1632A>G synonymous_variant 0.13
PPE35 2170497 p.Ala39Asp missense_variant 0.25
Rv1979c 2223106 p.Val20Ala missense_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289984 c.-743C>G upstream_gene_variant 0.11
pncA 2289986 c.-745T>C upstream_gene_variant 0.11
folC 2746266 p.Ser445Pro missense_variant 0.33
folC 2746746 p.Val285Phe missense_variant 0.12
folC 2746747 c.852G>A synonymous_variant 0.94
folC 2746771 c.828A>T synonymous_variant 0.11
pepQ 2859974 p.Ala149Ser missense_variant 0.14
pepQ 2859997 p.Ala141Val missense_variant 0.17
thyA 3073868 p.Thr202Ala missense_variant 1.0
thyA 3074548 c.-77T>C upstream_gene_variant 0.33
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086987 p.Gln56His missense_variant 0.22
Rv3083 3448589 p.Asp29Val missense_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474156 c.150C>T synonymous_variant 0.29
fprA 3474633 c.627G>A synonymous_variant 0.13
Rv3236c 3612555 p.Ala188Pro missense_variant 0.2
Rv3236c 3613114 c.3G>A synonymous_variant 0.14
rpoA 3878016 c.492C>T synonymous_variant 0.12
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039017 p.Ser563Cys missense_variant 0.11
embC 4240478 p.Gly206Arg missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243984 p.Arg251Pro missense_variant 0.14
embA 4245079 p.Trp616Leu missense_variant 0.15
embA 4245871 c.2640delC frameshift_variant 0.12
embA 4246111 p.Arg960Leu missense_variant 0.13
embB 4247581 c.1068C>A synonymous_variant 0.12
aftB 4267861 p.Trp326Arg missense_variant 0.11
aftB 4267878 p.Val320Gly missense_variant 0.22
ubiA 4269974 c.-141C>A upstream_gene_variant 0.1
ethR 4327222 c.-327G>A upstream_gene_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0