TB-Profiler result

Run: ERR1950085
Summary

Run ID: ERR1950085

Sample name:

Date: 31-03-2023 15:39:26

Number of reads: 493731

Percentage reads mapped: 99.68

Strain: lineage4.8

Drug-resistance: RR-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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.99
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
rpoB 761167 p.Pro454His missense_variant 0.17 rifampicin
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 8662 p.Asp454Gly missense_variant 0.11
fgd1 491068 p.Leu96Val missense_variant 0.12
mshA 576676 c.1329T>G synonymous_variant 0.2
rpoB 761868 p.Asp688Tyr missense_variant 0.2
rpoB 763305 p.Ser1167Gly missense_variant 0.29
rpoC 763472 p.Asn35Tyr missense_variant 0.12
rpoC 764028 p.Glu220Gly missense_variant 0.17
rpoC 764541 p.Val391Gly missense_variant 0.25
rpoC 764543 p.Thr392Asp missense_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776689 p.Trp598Arg missense_variant 0.12
mmpS5 778899 p.Gly3* stop_gained 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1303911 c.981G>A synonymous_variant 0.2
fbiC 1304152 p.Pro408Thr missense_variant 0.2
fbiC 1305216 p.Ser762Arg missense_variant 0.19
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473702 n.45G>A non_coding_transcript_exon_variant 0.12
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474221 n.564T>A non_coding_transcript_exon_variant 0.22
rrl 1475375 n.1718G>A non_coding_transcript_exon_variant 0.11
rrl 1475578 n.1921C>T non_coding_transcript_exon_variant 0.18
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.15
fabG1 1674017 p.Ala193Glu missense_variant 0.2
inhA 1674109 c.-93C>T upstream_gene_variant 0.15
rpsA 1834743 p.Asn401Ser missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101765 c.1278C>T synonymous_variant 0.2
ndh 2102500 c.543C>A synonymous_variant 0.2
ndh 2102508 p.Gly179Ser missense_variant 0.17
katG 2154015 c.2097G>A synonymous_variant 0.18
katG 2155294 p.Gly273Asp missense_variant 0.17
katG 2155553 c.559C>A synonymous_variant 0.14
PPE35 2168728 p.Gly629Arg missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518648 c.534C>A synonymous_variant 0.17
ahpC 2726399 p.Ser69Arg missense_variant 0.12
ahpC 2726464 p.Phe91Tyr missense_variant 0.25
folC 2747291 p.Ser103* stop_gained 0.12
pepQ 2859396 c.1023A>G synonymous_variant 0.11
pepQ 2860096 p.Asp108Ala missense_variant 0.29
pepQ 2860560 c.-142T>A upstream_gene_variant 0.2
Rv2752c 3065127 c.1065G>A synonymous_variant 0.11
Rv2752c 3066197 c.-6C>A upstream_gene_variant 0.4
thyX 3068031 c.-86A>C upstream_gene_variant 0.12
ald 3086652 c.-168C>A upstream_gene_variant 0.17
fbiD 3339067 c.-51G>C upstream_gene_variant 0.2
fprA 3474310 p.Tyr102Asn missense_variant 0.11
fprA 3474700 p.Gly232Arg missense_variant 0.1
whiB7 3568624 p.Pro19Gln missense_variant 0.15
Rv3236c 3612933 p.Ala62Ser missense_variant 0.11
rpoA 3877819 p.Glu230Val missense_variant 0.17
rpoA 3878490 c.18C>G synonymous_variant 0.5
clpC1 4038773 p.Asp644Glu missense_variant 0.1
clpC1 4038776 p.Glu643Asp missense_variant 0.11
clpC1 4038782 c.1923G>C synonymous_variant 0.1
clpC1 4039935 p.Ala257Glu missense_variant 0.15
clpC1 4040442 p.Leu88Pro missense_variant 0.11
embC 4241035 c.1173G>A synonymous_variant 0.15
embC 4241043 p.Asn394Thr missense_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245071 c.1839G>C synonymous_variant 0.17
embA 4245150 p.Val640Leu missense_variant 0.12
embA 4245658 p.Ser809Tyr missense_variant 0.22
embB 4247037 p.Gly175Asp missense_variant 0.29
aftB 4268728 p.Thr37Ser missense_variant 0.25
ubiA 4269392 p.Val148Met missense_variant 0.11
ubiA 4269917 c.-84G>A upstream_gene_variant 0.14
ethA 4326621 p.His285Asn missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408413 c.-211C>T upstream_gene_variant 0.11
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0