TB-Profiler result

Run: ERR2229296
Summary

Run ID: ERR2229296

Sample name:

Date: 31-03-2023 16:58:19

Number of reads: 1090070

Percentage reads mapped: 99.14

Strain: 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 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
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 575298 c.-50T>A upstream_gene_variant 0.4
mshA 575336 c.-12G>T upstream_gene_variant 0.29
rpoC 764284 c.915G>A synonymous_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775955 p.Ile842Val missense_variant 0.15
mmpL5 777914 c.567G>T synonymous_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
embR 1416927 p.Ala141Ser missense_variant 0.15
embR 1416963 p.Gly129Cys missense_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 0.99
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475059 n.1402G>C non_coding_transcript_exon_variant 0.12
fabG1 1673380 c.-60C>G upstream_gene_variant 0.19
rpsA 1834809 p.Arg423Leu missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918588 p.Glu217* stop_gained 0.2
ndh 2103076 c.-34C>A upstream_gene_variant 0.11
PPE35 2167745 p.Thr956Arg missense_variant 0.21
PPE35 2167965 p.Ala883Gly missense_variant 0.22
PPE35 2167967 c.2646A>C synonymous_variant 0.22
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169902 p.Leu237Phe missense_variant 0.19
PPE35 2169910 p.Asn235Tyr missense_variant 0.16
PPE35 2170048 p.Leu189Val missense_variant 0.27
PPE35 2170053 p.Thr187Ser missense_variant 0.28
PPE35 2170528 p.Ser29Ala missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519167 c.1053T>C synonymous_variant 0.18
kasA 2519171 p.Leu353Val missense_variant 0.18
folC 2746548 p.Asp351Asn missense_variant 0.15
pepQ 2860617 c.-199C>T upstream_gene_variant 0.12
ald 3087896 c.1077G>C synonymous_variant 0.14
alr 3841546 c.-126C>A upstream_gene_variant 0.39
rpoA 3877859 p.Glu217* stop_gained 0.17
clpC1 4039730 c.975C>G synonymous_variant 0.13
clpC1 4040144 c.561G>C synonymous_variant 0.27
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242799 c.-434T>C upstream_gene_variant 0.11
embB 4246555 c.42G>C synonymous_variant 0.33
embB 4246556 p.Ala15Pro missense_variant 0.36
embB 4246563 p.Leu17Trp missense_variant 0.3
embB 4246567 c.54G>T synonymous_variant 0.22
embB 4246584 p.Arg24Pro missense_variant 0.15
embB 4247512 c.999T>C synonymous_variant 0.14
embB 4247516 p.Asn335Asp missense_variant 0.14
ubiA 4269575 p.Lys87Glu missense_variant 0.1
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0