TB-Profiler result

Run: ERR3828631

Summary

Run ID: ERR3828631

Sample name:

Date: 01-04-2023 03:28:07

Number of reads: 1176316

Percentage reads mapped: 91.65

Strain: lineage4.3.4.2

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
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.18
ccsA 620122 c.236delG frameshift_variant 0.22
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 779182 p.Gly65Arg missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304061 c.1131G>T synonymous_variant 0.12
fbiC 1305014 p.Thr695Lys missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918597 p.Trp220Arg missense_variant 1.0
katG 2154677 p.Ala479Ser missense_variant 0.12
katG 2154791 p.Pro441Ser missense_variant 0.18
PPE35 2170048 p.Leu189Val missense_variant 0.33
PPE35 2170053 p.Thr187Ser missense_variant 0.44
PPE35 2170065 p.Ala183Gly missense_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290223 c.-982C>T upstream_gene_variant 0.11
folC 2747005 p.Ser198Arg missense_variant 0.13
pepQ 2860159 p.Ala87Gly missense_variant 0.13
pepQ 2860482 c.-64A>T upstream_gene_variant 0.11
thyX 3067418 c.528C>G synonymous_variant 0.1
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448880 p.Gly126Val missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
fbiB 3641624 c.90C>T synonymous_variant 0.2
fbiB 3642315 p.Arg261Gly missense_variant 0.13
clpC1 4038287 c.2418C>T synonymous_variant 0.95
clpC1 4039003 p.Asn568Asp missense_variant 0.12
clpC1 4039523 p.Phe394Leu missense_variant 0.11
embC 4240379 p.Gln173* stop_gained 0.18
embC 4240697 p.Ala279Thr missense_variant 0.12
embC 4241203 c.1341T>C synonymous_variant 0.12
embC 4241635 c.1773G>A synonymous_variant 0.22
embC 4242176 p.Pro772Ala missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243287 p.Val19Phe missense_variant 0.18
embA 4243707 p.Ala159Ser missense_variant 0.14
embA 4243722 p.Pro164Ser missense_variant 0.17
embA 4244591 c.1359G>C synonymous_variant 0.17
embA 4244711 c.1479C>T synonymous_variant 0.17
embA 4246350 p.Ser1040Pro missense_variant 0.11
embB 4246544 p.Thr11Pro missense_variant 0.67
embB 4247470 c.957T>C synonymous_variant 0.14
embB 4247472 p.Phe320Tyr missense_variant 0.14
embB 4247828 p.Ala439Thr missense_variant 0.2
embB 4248324 p.Ala604Gly missense_variant 0.22
aftB 4267640 c.1197C>G synonymous_variant 0.13
aftB 4267736 c.1101C>T synonymous_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0