TB-Profiler result

Run: ERR4818631
Summary

Run ID: ERR4818631

Sample name:

Date: 01-04-2023 15:39:56

Number of reads: 442287

Percentage reads mapped: 98.86

Strain: lineage4

Drug-resistance: RR-TB

Download CSV Download TXT Download PDF Download JSON
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
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
rpoB 761139 p.His445Asn missense_variant 0.11 rifampicin
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 5713 c.474C>G synonymous_variant 0.5
gyrB 6165 p.Asn309Ser missense_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.55
gyrA 9304 p.Gly668Asp missense_variant 0.5
fgd1 490630 c.-152delA upstream_gene_variant 0.25
fgd1 491120 p.Glu113Val missense_variant 0.17
fgd1 491501 p.Glu240Val missense_variant 0.17
fgd1 491591 p.Lys270Met missense_variant 0.42
mshA 575679 p.Asn111Ser missense_variant 0.29
rpoB 759620 c.-187A>C upstream_gene_variant 0.21
rpoB 760115 c.309C>T synonymous_variant 0.24
rpoC 764713 c.1344G>T synonymous_variant 0.12
rpoC 764716 c.1347G>C synonymous_variant 0.12
rpoC 764746 c.1377G>T synonymous_variant 0.13
rpoC 764752 c.1383G>C synonymous_variant 0.14
rpoC 764758 c.1389C>G synonymous_variant 0.17
rpoC 764764 c.1395T>C synonymous_variant 0.15
rpoC 767183 p.Val1272Met missense_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777216 p.Pro422Arg missense_variant 0.33
mmpR5 779450 c.465delG frameshift_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305296 p.Val789Ala missense_variant 0.12
Rv1258c 1406704 p.Ala213Ser missense_variant 0.18
embR 1416885 p.Asp155Asn missense_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1674077 p.Thr213Asn missense_variant 0.2
fabG1 1674170 p.Gly244Val missense_variant 0.25
inhA 1674954 c.753G>A synonymous_variant 0.33
rpsA 1833737 p.Arg66Ser missense_variant 0.11
rpsA 1833917 p.Val126Ile missense_variant 0.14
rpsA 1834628 p.Lys363Glu missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167792 p.Ser941Ala missense_variant 0.62
PPE35 2167865 c.2748G>C synonymous_variant 0.12
PPE35 2167868 c.2745A>C synonymous_variant 0.12
PPE35 2168047 p.Leu856Val missense_variant 0.12
PPE35 2168051 p.Val854Ile missense_variant 0.12
PPE35 2169356 c.1257C>T synonymous_variant 0.11
PPE35 2169902 p.Leu237Phe missense_variant 0.19
PPE35 2170048 p.Leu189Val missense_variant 0.5
PPE35 2170053 p.Thr187Ser missense_variant 0.5
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289492 c.-251C>T upstream_gene_variant 0.18
pncA 2289567 c.-326C>T upstream_gene_variant 0.11
kasA 2518076 c.-39C>T upstream_gene_variant 0.67
kasA 2518636 c.522C>T synonymous_variant 0.4
eis 2714569 p.Ala255Gly missense_variant 0.27
ahpC 2726338 p.Val49Gly missense_variant 0.25
Rv2752c 3064680 c.1512C>T synonymous_variant 0.4
thyX 3068083 c.-138T>C upstream_gene_variant 0.4
ald 3086788 c.-32T>C upstream_gene_variant 0.65
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.23
Rv3236c 3612758 p.Gly120Val missense_variant 0.29
alr 3840572 c.849G>A synonymous_variant 0.14
rpoA 3878463 c.45C>T synonymous_variant 0.2
clpC1 4038410 p.Asp765Glu missense_variant 0.13
clpC1 4038994 p.Phe571Leu missense_variant 0.2
clpC1 4039594 p.Arg371Gly missense_variant 0.29
clpC1 4039602 p.Ala368Val missense_variant 0.25
clpC1 4040478 p.Gly76Val missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 0.18
embA 4243247 c.15T>A synonymous_variant 0.17
embA 4243485 p.Asn85Asp missense_variant 0.5
embA 4244102 c.870A>G synonymous_variant 0.62
embA 4246423 p.Val1064Gly missense_variant 0.33
embB 4247031 p.Arg173Leu missense_variant 0.2
embB 4249073 p.Gln854* stop_gained 0.11
ubiA 4269922 c.-89C>T upstream_gene_variant 0.1
ethR 4328104 p.Ser186Pro missense_variant 0.15
ethA 4328239 c.-767delT upstream_gene_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407646 p.Val186Ala missense_variant 0.15