TB-Profiler result

Run: ERR11043086
Summary

Run ID: ERR11043086

Sample name:

Date: 31-03-2023 11:27:40

Number of reads: 574400

Percentage reads mapped: 99.53

Strain: lineage4.2.2.1

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
lineage4.2 Euro-American H;T;LAM None 1.0
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 1.0
lineage4.2.2.1 Euro-American LAM7-TUR None 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 761094 c.1291_1302delAGCCAATTCATG conservative_inframe_deletion 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
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
gyrB 6601 p.Glu454Asp missense_variant 0.27
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8538 p.Thr413Pro missense_variant 0.2
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575411 p.Glu22* stop_gained 1.0
mshA 576077 c.730C>T synonymous_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.31
rpoC 766391 p.Thr1008Ser missense_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416518 p.Leu277Arg missense_variant 0.23
embR 1417179 p.Thr57Pro missense_variant 0.33
embR 1417182 p.Ile56Leu missense_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475685 n.2028T>C non_coding_transcript_exon_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2222948 p.Arg73* stop_gained 0.25
Rv1979c 2223160 p.Val2Gly missense_variant 0.3
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288944 p.Thr100Pro missense_variant 1.0
ribD 2987592 p.Tyr252Asn missense_variant 0.22
Rv2752c 3066280 c.-89C>T upstream_gene_variant 1.0
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612828 p.Ile97Phe missense_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ubiA 4269817 p.Val6Gly missense_variant 0.17
ethA 4327454 p.Val7Gly missense_variant 1.0
whiB6 4338286 p.Val79Gly missense_variant 0.33
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407713 p.Gly164Cys missense_variant 1.0
gid 4407733 p.Gly157Ala missense_variant 0.15