TB-Profiler result

Run: ERR2229236
Summary

Run ID: ERR2229236

Sample name:

Date: 31-03-2023 16:50:51

Number of reads: 720987

Percentage reads mapped: 98.98

Strain: lineage4.8

Drug-resistance: Other

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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
rpsA 1834961 p.Arg474Trp missense_variant 0.2 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 9078 p.Gly593Trp missense_variant 0.12
mshA 576755 p.Arg470Cys missense_variant 0.14
rpoC 764603 c.1234C>A synonymous_variant 0.1
rpoC 766186 p.Glu939Asp missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777811 c.670C>A synonymous_variant 0.1
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
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
fabG1 1673346 c.-94C>G upstream_gene_variant 0.13
fabG1 1673349 c.-91G>C upstream_gene_variant 0.13
fabG1 1673380 c.-60C>G upstream_gene_variant 0.15
inhA 1674915 c.714C>T synonymous_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918575 c.636G>A synonymous_variant 0.11
katG 2155137 c.975G>C synonymous_variant 0.12
PPE35 2168728 p.Gly629Arg missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290201 c.-960G>T upstream_gene_variant 0.14
kasA 2518348 c.234A>T synonymous_variant 0.11
ahpC 2726350 p.Trp53Leu missense_variant 0.15
folC 2746660 c.938delT frameshift_variant 0.25
folC 2746839 p.Ala254Thr missense_variant 0.15
thyA 3074648 c.-177T>G upstream_gene_variant 0.22
ald 3087757 p.Leu313Pro missense_variant 0.1
fprA 3473812 c.-195G>A upstream_gene_variant 0.11
fprA 3474900 c.894C>A synonymous_variant 0.11
rpoA 3878036 p.Glu158Lys missense_variant 0.11
clpC1 4039417 p.Glu430Lys missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243078 c.-155C>T upstream_gene_variant 0.11
embA 4243495 p.Leu88Pro missense_variant 0.11
embA 4244107 p.Asn292Ile missense_variant 0.12
embB 4246548 p.Pro12Gln missense_variant 0.33
embB 4246555 c.42G>C synonymous_variant 0.4
embB 4246556 p.Ala15Pro missense_variant 0.4
embB 4246777 c.264G>T synonymous_variant 0.12
embB 4247324 p.Ala271Thr missense_variant 0.15
embB 4249744 c.3231G>A synonymous_variant 0.13
embB 4249751 c.3238T>C synonymous_variant 0.11
ubiA 4269168 p.Trp222Cys missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408310 c.-108G>A upstream_gene_variant 0.15
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0