TB-Profiler result

Run: ERR4813018
Summary

Run ID: ERR4813018

Sample name:

Date: 01-04-2023 12:28:47

Number of reads: 2652060

Percentage reads mapped: 99.6

Strain: lineage4

Drug-resistance: Pre-XDR-TB

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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
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
gyrA 7582 p.Asp94Gly missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247730 p.Gly406Ala missense_variant 1.0 ethambutol
ethA 4326302 p.Trp391* stop_gained 1.0 ethionamide
gid 4407851 c.351delG frameshift_variant 1.0 streptomycin
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 490872 p.His30Gln missense_variant 0.12
fgd1 491290 p.Val170Leu missense_variant 0.18
mshA 575662 c.315C>A synonymous_variant 0.33
mshA 575692 c.345G>T synonymous_variant 0.29
mshA 576652 p.Asp435Glu missense_variant 1.0
rpoB 761712 p.Val636Phe missense_variant 0.2
rpoC 764888 p.Leu507Val missense_variant 1.0
rpoC 766323 p.Thr985Ile missense_variant 0.13
rpoC 766341 p.Ile991Thr missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_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
tlyA 1918663 p.Trp242Arg missense_variant 0.1
ndh 2102253 p.Gly264Cys missense_variant 0.29
PPE35 2170033 p.Gly194Ser missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2859558 c.861C>A synonymous_variant 0.11
ribD 2987359 p.Asp174Gly missense_variant 0.67
ald 3087095 c.276C>T synonymous_variant 1.0
fbiD 3339054 c.-64C>A upstream_gene_variant 0.5
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
fprA 3474999 c.993G>T synonymous_variant 0.18
fbiB 3641362 c.-173C>A upstream_gene_variant 0.13
fbiB 3641523 c.-12G>T upstream_gene_variant 0.33
fbiB 3642179 c.645G>A synonymous_variant 0.5
clpC1 4040159 c.546G>T synonymous_variant 0.12
embC 4241165 c.1306delC frameshift_variant 0.5
embC 4241202 p.Gly447Asp missense_variant 0.29
embC 4241254 c.1392C>T synonymous_variant 0.17
embB 4245554 c.-960C>A upstream_gene_variant 0.15
embA 4245586 p.Pro785Gln missense_variant 0.13
embB 4247012 p.Pro167Thr missense_variant 0.2
embB 4249193 p.Pro894Ser missense_variant 0.12
aftB 4267598 p.Phe413Leu missense_variant 0.14
aftB 4267860 p.Trp326Leu missense_variant 0.11
ubiA 4269015 p.Glu273Asp missense_variant 1.0
ubiA 4270012 c.-179G>T upstream_gene_variant 0.67
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0