TB-Profiler result

Run: ERR3324330
Summary

Run ID: ERR3324330

Sample name:

Date: 01-04-2023 01:49:48

Number of reads: 2063393

Percentage reads mapped: 99.19

Strain: lineage5.1.1;lineage4.8

Drug-resistance: Sensitive

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 0.92
lineage5 West-Africa 1 AFRI_2;AFRI_3 RD711 0.1
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.85
lineage5.1 West-Africa 1 AFRI_2;AFRI_3 RD711 0.1
lineage5.1.1 West-Africa 1 AFRI_2;AFRI_3 RD711 0.08
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
gyrA 7585 p.Ser95Thr missense_variant 0.23
gyrA 9143 c.1842T>C synonymous_variant 0.11
fgd1 491742 c.960T>C synonymous_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 0.1
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406402 c.939C>G synonymous_variant 0.88
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.85
inhA 1673338 c.-864G>A upstream_gene_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101840 c.1203G>A synonymous_variant 0.17
ndh 2101921 c.1122G>A synonymous_variant 0.25
ndh 2103112 c.-70G>T upstream_gene_variant 0.15
PPE35 2167926 p.Leu896Ser missense_variant 0.18
PPE35 2168149 p.Pro822Ser missense_variant 0.81
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290062 c.-821G>A upstream_gene_variant 0.23
Rv3083 3449248 p.Ala249Ser missense_variant 0.2
Rv3083 3449644 p.Ala381Thr missense_variant 0.79
Rv3083 3449723 p.Cys407Phe missense_variant 0.18
Rv3083 3449735 p.Arg411Leu missense_variant 0.17
Rv3083 3449832 c.1329T>C synonymous_variant 0.11
Rv3083 3449883 p.Trp460Cys missense_variant 0.12
alr 3840932 c.489C>T synonymous_variant 0.14
rpoA 3878493 c.15G>A synonymous_variant 0.13
rpoA 3878573 c.-66G>T upstream_gene_variant 0.15
ddn 3986987 c.144G>T synonymous_variant 0.16
ddn 3987180 p.Asp113Asn missense_variant 0.19
embC 4239843 c.-20A>C upstream_gene_variant 0.1
embC 4240671 p.Thr270Ile missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244220 c.988C>T synonymous_variant 0.14
aftB 4268050 p.Pro263Thr missense_variant 0.81
ethR 4326928 c.-621G>A upstream_gene_variant 0.18
ethA 4327103 p.Gly124Asp missense_variant 0.18
whiB6 4338547 c.-26A>G upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.1
gid 4407790 p.Ala138Val missense_variant 0.8