TB-Profiler result

Run: ERR2228823
Summary

Run ID: ERR2228823

Sample name:

Date: 31-03-2023 16:22:14

Number of reads: 324635

Percentage reads mapped: 98.61

Strain: lineage4

Drug-resistance: Sensitive

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
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 7562 c.261C>T synonymous_variant 0.5
gyrA 9473 c.2172G>T synonymous_variant 0.15
rpoB 763083 p.Arg1093Ser missense_variant 0.29
rpoC 765674 p.Glu769Gln missense_variant 0.67
mmpL5 777119 p.His454Gln missense_variant 0.33
mmpL5 777122 c.1359C>T synonymous_variant 0.33
mmpL5 777128 c.1353A>G synonymous_variant 0.29
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304268 c.1338G>T synonymous_variant 0.4
embR 1416506 p.Thr281Ile missense_variant 0.29
embR 1417487 c.-140T>C upstream_gene_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472043 n.198T>C non_coding_transcript_exon_variant 0.5
rrs 1473088 n.1243A>T non_coding_transcript_exon_variant 0.33
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.17
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475719 n.2062G>A non_coding_transcript_exon_variant 0.22
fabG1 1673346 c.-94C>G upstream_gene_variant 0.33
fabG1 1673349 c.-91G>C upstream_gene_variant 0.33
fabG1 1673380 c.-60C>G upstream_gene_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102422 c.621C>A synonymous_variant 0.5
PPE35 2167955 c.2658A>C synonymous_variant 0.5
PPE35 2167965 p.Ala883Gly missense_variant 0.5
PPE35 2167967 c.2646A>C synonymous_variant 0.5
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169269 c.1344A>G synonymous_variant 0.25
PPE35 2169272 c.1341C>G synonymous_variant 0.29
PPE35 2169278 c.1335T>C synonymous_variant 0.33
PPE35 2169281 c.1332T>G synonymous_variant 0.33
PPE35 2169457 p.His386Asp missense_variant 0.15
PPE35 2169462 p.Val384Pro missense_variant 0.14
PPE35 2169902 p.Leu237Phe missense_variant 0.18
PPE35 2169910 p.Asn235Tyr missense_variant 0.22
PPE35 2169986 p.Leu209Phe missense_variant 0.22
PPE35 2170048 p.Leu189Val missense_variant 0.29
PPE35 2170053 p.Thr187Ser missense_variant 0.33
PPE35 2170066 p.Ala183Thr missense_variant 0.14
PPE35 2170147 p.Ser156Ala missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289182 c.60G>T synonymous_variant 0.25
kasA 2518864 c.750G>C synonymous_variant 0.5
kasA 2518879 c.765A>G synonymous_variant 0.5
kasA 2518882 c.768C>A synonymous_variant 0.5
kasA 2518896 c.783_784delGT frameshift_variant 0.5
kasA 2519140 c.1026G>C synonymous_variant 0.4
kasA 2519143 c.1029G>C synonymous_variant 0.4
kasA 2519153 p.Ile347Val missense_variant 0.4
kasA 2519338 c.1224T>C synonymous_variant 1.0
ahpC 2725938 c.-255_-254insA upstream_gene_variant 0.15
ribD 2986803 c.-36A>T upstream_gene_variant 0.33
Rv2752c 3066128 p.Gly22Cys missense_variant 0.5
thyA 3074660 c.-189C>A upstream_gene_variant 0.25
alr 3841539 c.-119C>T upstream_gene_variant 0.15
alr 3841546 c.-126C>A upstream_gene_variant 0.23
clpC1 4038182 c.2523C>G synonymous_variant 0.4
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4248883 c.2370C>A synonymous_variant 1.0
embB 4249449 p.Gly979Val missense_variant 0.2
aftB 4268228 c.609C>T synonymous_variant 0.5
aftB 4269735 c.-899G>T upstream_gene_variant 0.12
ethA 4327064 p.Cys137Ser missense_variant 0.4
whiB6 4338205 p.Val106Ala missense_variant 0.4
whiB6 4338595 c.-75delG upstream_gene_variant 1.0