TB-Profiler result

Run: ERR2229685
Summary

Run ID: ERR2229685

Sample name:

Date: 31-03-2023 17:25:51

Number of reads: 837241

Percentage reads mapped: 99.39

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
rpsL 781815 p.Arg86Trp missense_variant 0.14 streptomycin
fbiA 3641066 p.Arg175His missense_variant 0.13 delamanid
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 576108 p.Ala254Gly missense_variant 0.71
mshA 576113 p.Arg256Gly missense_variant 0.6
rpoB 760781 c.975G>T synonymous_variant 0.15
rpoB 761482 p.Ala559Val missense_variant 0.13
rpoC 765951 p.Ala861Glu missense_variant 0.13
rpoC 766267 c.2899_2902delACGT frameshift_variant 0.18
rpoC 766275 p.Ala969Gly missense_variant 0.18
rpoC 766278 c.2909_2910insACGT frameshift_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776734 p.Ser583Gly missense_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304178 c.1248G>T synonymous_variant 0.15
Rv1258c 1407146 c.195G>T synonymous_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673380 c.-60C>G upstream_gene_variant 0.24
inhA 1674431 p.Arg77Gln missense_variant 0.18
inhA 1674659 p.Arg153Gln missense_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918410 p.Phe157Leu missense_variant 0.17
tlyA 1918721 p.His261Arg missense_variant 0.13
katG 2155040 p.Gly358Cys missense_variant 0.13
PPE35 2167745 p.Thr956Arg missense_variant 0.29
PPE35 2167865 c.2748G>C synonymous_variant 0.16
PPE35 2167868 c.2745A>C synonymous_variant 0.16
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169013 p.Val534Leu missense_variant 0.18
PPE35 2169029 p.Asp528Glu missense_variant 0.22
PPE35 2169902 p.Leu237Phe missense_variant 0.26
PPE35 2169910 p.Asn235Tyr missense_variant 0.29
PPE35 2170048 p.Leu189Val missense_variant 0.18
PPE35 2170053 p.Thr187Ser missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518103 c.-12G>T upstream_gene_variant 0.11
kasA 2518864 c.750G>C synonymous_variant 0.14
pepQ 2860329 c.90G>T synonymous_variant 0.13
Rv2752c 3064670 p.Val508Leu missense_variant 0.12
Rv2752c 3065435 p.Val253Leu missense_variant 0.18
thyX 3067340 c.606G>A synonymous_variant 0.44
ald 3087763 p.Asn315Ser missense_variant 0.13
whiB7 3568705 c.-26A>G upstream_gene_variant 0.11
Rv3236c 3613296 c.-180T>C upstream_gene_variant 0.13
fbiB 3642162 p.Thr210Pro missense_variant 0.2
clpC1 4039602 p.Ala368Val missense_variant 0.13
embC 4239920 p.Arg20Cys missense_variant 0.15
embC 4240411 c.549G>C synonymous_variant 0.15
embC 4242331 c.2474dupG frameshift_variant 0.4
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243755 p.Thr175Pro missense_variant 0.14
embA 4244647 p.Arg472Gln missense_variant 0.25
aftB 4268847 c.-11C>T upstream_gene_variant 0.33
ethR 4326961 c.-588G>C upstream_gene_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0