TB-Profiler result

Run: ERR2229398

Summary

Run ID: ERR2229398

Sample name:

Date: 31-03-2023 17:09:27

Number of reads: 864305

Percentage reads mapped: 98.95

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
fgd1 491511 c.729G>A synonymous_variant 0.11
mshA 576108 p.Ala254Gly missense_variant 0.2
mshA 576521 p.Gly392Trp missense_variant 0.15
rpoB 761837 c.2031C>T synonymous_variant 0.14
rpoC 763394 p.Glu9Gln missense_variant 0.1
rpoC 765894 p.Glu842Gly missense_variant 0.12
rpoC 766695 p.Gln1109Leu missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776382 p.Asp700Val missense_variant 0.15
mmpR5 779336 p.Asp116Ala missense_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800732 c.-77G>A upstream_gene_variant 0.14
fbiC 1303747 p.Thr273Ala missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475917 n.2260T>C non_coding_transcript_exon_variant 0.1
fabG1 1673380 c.-60C>G upstream_gene_variant 0.32
fabG1 1673560 p.Lys41Gln missense_variant 0.11
inhA 1674019 c.-183C>T upstream_gene_variant 0.25
inhA 1674369 c.168A>G synonymous_variant 0.25
inhA 1674690 c.489C>A synonymous_variant 0.12
rpsA 1834672 c.1131G>A synonymous_variant 0.15
rpsA 1834860 p.Ala440Val missense_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101673 p.Ala457Gly missense_variant 0.12
PPE35 2167814 c.2799C>T synonymous_variant 0.2
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2168865 p.Thr583Lys missense_variant 0.2
PPE35 2169278 c.1335T>C synonymous_variant 0.1
PPE35 2169281 c.1332T>G synonymous_variant 0.1
PPE35 2169596 p.Phe339Trp missense_variant 0.12
PPE35 2169725 c.888T>C synonymous_variant 0.1
PPE35 2170048 p.Leu189Val missense_variant 0.66
PPE35 2170053 p.Thr187Ser missense_variant 0.71
Rv1979c 2222750 c.415C>T synonymous_variant 0.13
Rv1979c 2222826 c.338delT frameshift_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289762 c.-521G>T upstream_gene_variant 0.25
kasA 2518610 p.Thr166Pro missense_variant 0.25
pepQ 2860024 p.Arg132Pro missense_variant 0.22
ribD 2987052 p.Asn72Asp missense_variant 0.12
Rv2752c 3065524 p.His223Leu missense_variant 0.17
thyX 3067475 p.Gln157His missense_variant 0.18
ald 3087437 p.Gln206His missense_variant 0.2
Rv3236c 3613249 c.-133A>T upstream_gene_variant 0.11
fbiB 3641361 c.-174C>A upstream_gene_variant 0.11
fbiB 3641998 p.Ala155Asp missense_variant 0.15
alr 3840810 p.Asp204Gly missense_variant 0.12
alr 3841546 c.-126C>A upstream_gene_variant 0.14
clpC1 4038396 c.2307_2308delGG frameshift_variant 0.22
embC 4240234 c.372A>G synonymous_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.17
embB 4246555 c.42G>C synonymous_variant 0.27
embB 4246556 p.Ala15Pro missense_variant 0.3
embB 4246563 p.Leu17Trp missense_variant 0.33
embB 4246567 c.54G>T synonymous_variant 0.43
ethR 4327793 p.Gln82Arg missense_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0