TB-Profiler result

Run: ERR2229762
Summary

Run ID: ERR2229762

Sample name:

Date: 31-03-2023 17:33:29

Number of reads: 709101

Percentage reads mapped: 99.5

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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 2155229 c.882delG frameshift_variant 0.12 isoniazid
embB 4247703 p.Pro397Gln missense_variant 0.2 ethambutol
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 7352 c.51G>A synonymous_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 9749 c.2448G>C synonymous_variant 0.12
rpoB 761152 p.Leu449Gln missense_variant 0.18
rpoC 766197 c.2830delC frameshift_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777157 c.1324C>A synonymous_variant 0.29
mmpL5 777164 c.1317C>T synonymous_variant 0.33
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
embR 1417400 c.-53C>T upstream_gene_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673357 c.-83G>A upstream_gene_variant 0.11
fabG1 1673359 c.-81T>C upstream_gene_variant 0.12
fabG1 1673361 c.-79C>G upstream_gene_variant 0.12
fabG1 1673380 c.-60C>G upstream_gene_variant 0.31
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169269 c.1344A>G synonymous_variant 0.29
PPE35 2169272 c.1341C>G synonymous_variant 0.29
PPE35 2169278 c.1335T>C synonymous_variant 0.19
PPE35 2169281 c.1332T>G synonymous_variant 0.2
PPE35 2170048 p.Leu189Val missense_variant 0.44
PPE35 2170053 p.Thr187Ser missense_variant 0.43
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2715399 c.-67T>A upstream_gene_variant 0.11
ahpC 2726338 p.Val49Gly missense_variant 0.23
thyA 3074648 c.-177T>G upstream_gene_variant 0.3
fprA 3474143 p.Trp46Tyr missense_variant 0.19
fprA 3474165 c.159C>G synonymous_variant 0.13
fbiB 3641826 p.Arg98* stop_gained 0.12
clpC1 4040057 c.648C>T synonymous_variant 0.12
clpC1 4040144 c.561G>C synonymous_variant 0.15
panD 4044087 c.195C>A synonymous_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.18
aftB 4268340 p.Pro166Gln missense_variant 0.12
ethR 4326883 c.-666C>A upstream_gene_variant 0.15
ethR 4326964 c.-585G>A upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0