TB-Profiler result

Run: ERR2229115
Summary

Run ID: ERR2229115

Sample name:

Date: 31-03-2023 16:40:59

Number of reads: 666324

Percentage reads mapped: 99.45

Strain: lineage4.8

Drug-resistance: Other

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
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
pncA 2289030 p.His71Arg missense_variant 0.11 pyrazinamide
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 7413 p.Gly38Ser missense_variant 0.17
mshA 576108 p.Ala254Gly missense_variant 0.23
rpoB 759841 p.Ser12Asn missense_variant 0.29
rpoB 761504 c.1698C>A synonymous_variant 0.14
rpoB 761746 p.Val647Ala missense_variant 0.12
rpoB 762393 p.Val863Met missense_variant 0.17
rpoC 766219 p.Asp950Glu missense_variant 0.17
rpoC 766932 p.Ala1188Val missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776209 p.Leu758Met missense_variant 0.22
mmpL5 777128 c.1353A>G synonymous_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304498 p.Pro523Leu missense_variant 0.15
fbiC 1305183 p.Leu751Phe missense_variant 0.17
embR 1416481 c.867G>A synonymous_variant 0.18
embR 1416798 p.Cys184Arg missense_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472378 n.533G>T non_coding_transcript_exon_variant 0.4
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474302 n.645G>A non_coding_transcript_exon_variant 0.29
rrl 1475951 n.2294G>A non_coding_transcript_exon_variant 0.22
fabG1 1673380 c.-60C>G upstream_gene_variant 0.23
inhA 1674661 p.Ala154Thr missense_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102696 p.Ile116Asn missense_variant 0.15
katG 2155959 p.Asn51Lys missense_variant 0.13
PPE35 2167955 c.2658A>C synonymous_variant 0.14
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169902 c.711G>C synonymous_variant 0.11
PPE35 2170048 p.Leu189Val missense_variant 0.33
PPE35 2170053 p.Thr187Ser missense_variant 0.35
PPE35 2170368 p.Gln82Arg missense_variant 0.14
PPE35 2170372 p.Thr81Ala missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223333 c.-169G>A upstream_gene_variant 0.12
kasA 2518899 p.Leu262Trp missense_variant 0.2
Rv2752c 3064875 c.1317C>T synonymous_variant 0.17
thyX 3067340 c.606G>A synonymous_variant 0.42
whiB7 3568757 c.-78A>G upstream_gene_variant 0.5
fbiA 3640880 p.Leu113Arg missense_variant 0.2
fbiA 3640888 c.349delC frameshift_variant 0.2
fbiB 3641899 p.Pro122Leu missense_variant 0.12
alr 3840558 p.Arg288Leu missense_variant 0.22
clpC1 4039094 c.1611C>T synonymous_variant 0.18
embC 4240859 c.997C>T synonymous_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4248976 c.2463G>C synonymous_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408197 c.6T>A synonymous_variant 0.17
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0