TB-Profiler result

Run: ERR2229526
Summary

Run ID: ERR2229526

Sample name:

Date: 31-03-2023 17:17:23

Number of reads: 1210956

Percentage reads mapped: 99.37

Strain: lineage4.8

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
lineage4.8 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
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
mshA 575382 p.Leu12* stop_gained 0.13
mshA 576108 p.Ala254Gly missense_variant 0.21
rpoC 764541 p.Val391Gly missense_variant 0.21
rpoC 764543 p.Thr392Asp missense_variant 0.15
rpoC 766579 p.Asp1070Glu missense_variant 0.11
rpoC 766912 p.Ile1181Met missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpS5 779653 c.-748A>G upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801232 p.Gln142Lys missense_variant 0.15
fbiC 1303121 p.Arg64Gln missense_variant 0.14
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1406352 p.Pro330Arg missense_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473840 n.183A>G non_coding_transcript_exon_variant 0.12
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474284 n.627G>T non_coding_transcript_exon_variant 0.11
rrl 1475013 n.1356G>A non_coding_transcript_exon_variant 0.25
rrl 1475882 n.2225C>A non_coding_transcript_exon_variant 0.17
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 0.32
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102351 p.Arg231Leu missense_variant 0.13
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.41
PPE35 2170053 p.Thr187Ser missense_variant 0.41
PPE35 2170147 p.Ser156Ala missense_variant 0.12
PPE35 2170157 p.Ala152Ser missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2746574 p.Met342Thr missense_variant 0.15
pepQ 2859837 c.582G>A synonymous_variant 0.13
pepQ 2859907 p.Gln171Arg missense_variant 0.12
Rv2752c 3067062 c.-871A>G upstream_gene_variant 0.1
fbiD 3339734 p.Ala206Gly missense_variant 0.33
fbiB 3642038 c.504C>T synonymous_variant 0.18
clpC1 4040220 p.Ser162Phe missense_variant 0.12
embC 4241631 p.Phe590Tyr missense_variant 0.27
embC 4242175 c.2313G>C synonymous_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244859 p.Gly543Trp missense_variant 0.22
embB 4246555 c.42G>C synonymous_variant 0.2
embB 4246556 p.Ala15Pro missense_variant 0.2
embB 4246563 p.Leu17Trp missense_variant 0.18
embB 4246567 c.54_55insT frameshift_variant 0.2
aftB 4267989 p.Ala283Glu missense_variant 0.15
aftB 4268642 p.Tyr65* stop_gained 0.29
aftB 4268684 p.Gln51His missense_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0