TB-Profiler result

Run: ERR2446070
Summary

Run ID: ERR2446070

Sample name:

Date: 15-08-2022 11:02:47

Number of reads: 331843

Percentage reads mapped: 99.91

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 0.98
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 7869 p.Pro190Thr missense_variant 0.15
gyrA 7932 p.Asp211Tyr missense_variant 0.17
gyrA 8315 p.Gln338His missense_variant 0.18
fgd1 490739 c.-44G>T upstream_gene_variant 0.2
mshA 575534 p.Gly63Cys missense_variant 0.18
rpoB 760278 p.Gly158Cys missense_variant 0.12
rpoB 760425 p.Glu207* stop_gained 0.2
rpoB 761852 c.2046C>A synonymous_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777719 c.762G>T synonymous_variant 0.18
mmpL5 778205 p.Met92Ile missense_variant 0.14
mmpR5 778262 c.-728G>T upstream_gene_variant 0.18
mmpL5 778272 p.Pro70Gln missense_variant 0.17
mmpR5 779096 p.Ala36Glu missense_variant 0.2
rplC 801369 c.561C>A synonymous_variant 0.14
Rv1258c 1406599 p.Pro248Thr missense_variant 0.27
atpE 1461209 c.165C>A synonymous_variant 0.2
rrs 1472216 n.371C>T non_coding_transcript_exon_variant 0.15
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.11
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.09
rrs 1472736 n.891G>T non_coding_transcript_exon_variant 0.12
rrl 1473734 n.77C>A non_coding_transcript_exon_variant 0.14
rrl 1473833 n.176G>T non_coding_transcript_exon_variant 0.15
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474750 n.1093C>A non_coding_transcript_exon_variant 0.14
rrl 1475318 n.1661G>T non_coding_transcript_exon_variant 0.15
rrl 1475843 n.2186G>T non_coding_transcript_exon_variant 0.2
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.78
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.69
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.68
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.69
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.59
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.42
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.32
rrl 1476548 n.2891T>C non_coding_transcript_exon_variant 0.18
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.3
rrl 1476603 n.2946G>T non_coding_transcript_exon_variant 0.18
rrl 1476607 n.2950C>T non_coding_transcript_exon_variant 0.18
rrl 1476608 n.2951C>G non_coding_transcript_exon_variant 0.18
rrl 1476614 n.2957A>T non_coding_transcript_exon_variant 0.2
rrl 1476619 n.2962C>T non_coding_transcript_exon_variant 0.17
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.17
rrl 1476629 n.2972C>A non_coding_transcript_exon_variant 0.17
rrl 1476630 n.2973A>G non_coding_transcript_exon_variant 0.17
fabG1 1673260 c.-180C>A upstream_gene_variant 0.18
fabG1 1673684 p.Val82Asp missense_variant 0.18
inhA 1674276 c.75C>A synonymous_variant 0.2
rpsA 1833844 c.303C>A synonymous_variant 0.18
rpsA 1833869 p.Glu110* stop_gained 0.18
rpsA 1834123 c.582C>G synonymous_variant 0.2
tlyA 1917921 c.-19G>T upstream_gene_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1917981 c.42G>C synonymous_variant 0.18
pncA 2289432 c.-191C>A upstream_gene_variant 0.17
kasA 2517927 c.-188G>T upstream_gene_variant 0.2
ahpC 2726322 p.Pro44Thr missense_variant 0.17
pepQ 2860473 c.-55C>A upstream_gene_variant 0.17
ribD 2987168 c.330C>A synonymous_variant 0.17
thyX 3068090 c.-145T>C upstream_gene_variant 0.2
thyA 3073964 p.Leu170Met missense_variant 0.17
fprA 3475182 c.1176C>G synonymous_variant 0.17
clpC1 4039729 p.Asp326Asn missense_variant 1.0
clpC1 4040459 c.246C>A synonymous_variant 0.15
clpC1 4040621 c.84C>A synonymous_variant 0.15
clpC1 4040729 c.-25G>T upstream_gene_variant 0.18
embC 4239951 p.Arg30Leu missense_variant 0.13
embA 4245298 p.Pro689Gln missense_variant 0.18
embA 4245326 c.2094C>A synonymous_variant 0.17
embB 4247089 c.576G>T synonymous_variant 0.18
embB 4249299 p.Trp929Leu missense_variant 0.18
ubiA 4269948 c.-115G>T upstream_gene_variant 0.14
ethA 4326237 p.Gly413Cys missense_variant 0.2
ethA 4326538 c.936G>T synonymous_variant 0.18
ethR 4326562 c.-987G>T upstream_gene_variant 0.2