TB-Profiler result

Run: ERR2041702
Summary

Run ID: ERR2041702

Sample name:

Date: 18-08-2022 09:23:30

Number of reads: 519869

Percentage reads mapped: 98.64

Strain: lineage4.7

Drug-resistance: MDR-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
lineage4.7 Euro-American (mainly T) T1;T5 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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288835 c.395_406delGTATTGCCACCG disruptive_inframe_deletion 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4326721 c.752dupG frameshift_variant 1.0 ethionamide
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 6358 c.-944C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
rpoB 762433 p.Gly876Asp missense_variant 0.13
rpoB 762777 p.Asp991Asn missense_variant 0.18
rpoC 764004 p.Ala212Val missense_variant 0.14
rpoC 764916 p.Leu516Pro missense_variant 1.0
mmpR5 779034 c.46_47delAT frameshift_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471778 n.-68G>C upstream_gene_variant 1.0
rrs 1471895 n.50C>G non_coding_transcript_exon_variant 0.1
rrs 1471934 n.89A>G non_coding_transcript_exon_variant 0.12
rrs 1472033 n.188A>G non_coding_transcript_exon_variant 0.12
rrs 1472362 n.517C>G non_coding_transcript_exon_variant 0.2
rrl 1474294 n.637C>G non_coding_transcript_exon_variant 1.0
fabG1 1673380 c.-60C>G upstream_gene_variant 0.19
rpsA 1834900 c.1359C>T synonymous_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154468 c.1644C>G synonymous_variant 0.1
pncA 2290005 c.-764G>T upstream_gene_variant 0.12
embC 4239984 p.Ala41Val missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244772 p.Ser514Thr missense_variant 0.17
embA 4245445 p.Asp738Val missense_variant 0.11
embB 4246070 c.-444G>T upstream_gene_variant 0.15
embB 4249732 c.3219C>G synonymous_variant 1.0
ubiA 4269012 c.822G>A synonymous_variant 0.12
ubiA 4269323 p.Pro171Ser missense_variant 1.0
ubiA 4269747 c.86dupA frameshift_variant 0.12
gid 4407980 p.Pro75Ser missense_variant 1.0
mshA 574786 c.-561_*636del transcript_ablation 1.0