TB-Profiler result

Run: ERR2503451

Summary

Run ID: ERR2503451

Sample name:

Date: 31-03-2023 18:28:04

Number of reads: 546645

Percentage reads mapped: 99.58

Strain: lineage4.1.2.1

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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
tlyA 1918600 c.661_662insCTTG frameshift_variant&stop_gained 0.14 capreomycin
tlyA 1918613 c.675_678delCAAG frameshift_variant 0.14 capreomycin
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 7585 p.Ser95Thr missense_variant 1.0
gyrA 7818 c.517C>T synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575205 c.-143C>G upstream_gene_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
rpoB 759620 c.-187A>C upstream_gene_variant 0.18
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 762442 p.Leu879Pro missense_variant 0.11
rpoC 765150 p.Gly594Glu missense_variant 1.0
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
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918603 p.Ser222Ala missense_variant 0.14
tlyA 1918607 p.Val223Asp missense_variant 0.14
tlyA 1918610 p.Gly224Ala missense_variant 0.14
PPE35 2170066 p.Ala183Thr missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
folC 2746533 c.1065delT frameshift_variant 0.11
folC 2746537 c.1061_1062insTGCGCTC frameshift_variant 0.11
folC 2746543 c.1056C>T synonymous_variant 0.11
folC 2746546 c.1045_1052delTTCATCGA frameshift_variant 0.11
folC 2746559 p.Thr347Trp missense_variant 0.11
folC 2746561 c.1038C>G synonymous_variant 0.12
folC 2746565 c.1033_1034insTCGATGAA frameshift_variant 0.14
folC 2746569 p.Ser344Gly missense_variant 0.14
folC 2746574 c.1018_1024delGAGCGCA frameshift_variant 0.15
folC 2746584 c.1014_1015insA frameshift_variant 0.13
folC 2746628 p.Asp324Val missense_variant 0.25
pepQ 2859574 p.Ala282Asp missense_variant 0.1
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3641361 c.-174C>A upstream_gene_variant 0.1
fbiA 3641485 p.Ala315Thr missense_variant 0.1
rpoA 3878002 p.Ser169* stop_gained 0.1
embA 4242514 c.-719G>T upstream_gene_variant 0.1
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242738 p.Ala959Gly missense_variant 0.13
embC 4242803 p.Val981Leu missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407528 c.675A>C stop_lost&splice_region_variant 1.0