TB-Profiler result

Run: ERR2653026
Summary

Run ID: ERR2653026

Sample name:

Date: 31-03-2023 22:27:15

Number of reads: 1266875

Percentage reads mapped: 99.51

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 0.99
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 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
katG 2155739 c.372delC frameshift_variant 0.13 isoniazid
ahpC 2726145 c.-48G>A upstream_gene_variant 1.0 isoniazid
gid 4408100 c.102delG frameshift_variant 1.0 streptomycin
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 6547 c.-755T>A upstream_gene_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
fgd1 491709 c.930delT frameshift_variant 0.12
mshA 576114 p.Arg256Pro missense_variant 0.2
mshA 576666 p.Ser440Ile missense_variant 0.14
rpoC 765271 c.1902G>A synonymous_variant 0.13
rpoC 766085 p.Pro906Ala missense_variant 1.0
rpoC 766146 p.Gly926Asp missense_variant 0.12
rpoC 766318 p.Met983Ile missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303817 p.Arg296His missense_variant 0.13
fbiC 1305448 p.Ile840Phe missense_variant 0.12
Rv1258c 1406330 p.Gln337His missense_variant 0.15
atpE 1460992 c.-53A>C upstream_gene_variant 0.95
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473176 n.1331A>G non_coding_transcript_exon_variant 0.11
rrs 1473198 n.1353G>A non_coding_transcript_exon_variant 0.11
rrl 1473440 n.-218C>A upstream_gene_variant 0.12
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rpsA 1834945 c.1404C>T synonymous_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918285 p.Gly116Arg missense_variant 0.2
PPE35 2170048 p.Leu189Val missense_variant 0.21
PPE35 2170053 p.Thr187Ser missense_variant 0.23
Rv1979c 2222051 p.Leu372Met missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519044 c.930G>A synonymous_variant 0.22
ahpC 2726335 p.Arg48Pro missense_variant 0.67
folC 2746667 p.Ala311Val missense_variant 0.11
pepQ 2859365 p.Pro352Ser missense_variant 0.11
pepQ 2860041 c.378A>G synonymous_variant 0.11
pepQ 2860048 c.369_370delGG frameshift_variant 0.12
ribD 2986827 c.-12G>A upstream_gene_variant 1.0
ald 3087759 p.Thr314Ala missense_variant 0.14
fbiD 3339626 p.His170Arg missense_variant 0.14
fbiB 3640593 c.-942C>G upstream_gene_variant 0.1
alr 3840764 c.657G>C synonymous_variant 1.0
rpoA 3878081 p.Gly143Ser missense_variant 0.12
rpoA 3878567 c.-60C>G upstream_gene_variant 0.16
rpoA 3878630 c.-123G>C upstream_gene_variant 0.11
clpC1 4038910 p.Pro599Thr missense_variant 0.14
embC 4241433 p.Met524Lys missense_variant 0.12
embC 4241965 c.2103C>A synonymous_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244263 c.1037_1039delGGC disruptive_inframe_deletion 0.15
embA 4244498 c.1266A>G synonymous_variant 0.14
embB 4247784 p.Arg424Gln missense_variant 0.12
embB 4248005 p.Thr498Ser missense_variant 0.12
embB 4249492 c.2979C>T synonymous_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0