TB-Profiler result

Run: ERR1679633
Summary

Run ID: ERR1679633

Sample name:

Date: 31-03-2023 14:55:00

Number of reads: 425780

Percentage reads mapped: 99.83

Strain: lineage4.6.2.2

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
lineage4.6 Euro-American T;LAM None 1.0
lineage4.6.2 Euro-American T;LAM RD726 1.0
lineage4.6.2.2 Euro-American (Cameroon) LAM10-CAM RD726 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.Ser450Trp missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288746 c.495dupC frameshift_variant 0.31 pyrazinamide
embB 4247574 p.Asp354Ala missense_variant 0.81 ethambutol
embB 4248003 p.Gln497Pro 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7581 p.Asp94Pro missense_variant 0.15
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7894 p.Ala198Val missense_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 762898 c.3094delG frameshift_variant 0.11
rpoC 766740 p.Val1124Gly missense_variant 0.27
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775946 c.2535C>T synonymous_variant 0.1
mmpR5 778298 c.-692C>T upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304222 p.Val431Ala missense_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475077 n.1420C>T non_coding_transcript_exon_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918069 p.Thr44Pro missense_variant 0.15
katG 2155389 c.723C>G synonymous_variant 1.0
PPE35 2167995 p.Ser873Ile missense_variant 0.2
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289042 p.Ser67Leu missense_variant 0.69
thyX 3067474 p.Pro158Ala missense_variant 1.0
thyA 3073797 c.675G>A synonymous_variant 0.11
thyA 3074645 c.-174T>G upstream_gene_variant 0.33
ald 3087195 p.Ala126Thr missense_variant 0.11
fbiD 3338958 c.-160A>G upstream_gene_variant 0.11
Rv3083 3448567 p.His22Asp missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.95
Rv3236c 3612564 p.Met185Leu missense_variant 0.22
Rv3236c 3612571 c.546C>T synonymous_variant 1.0
rpoA 3877960 p.Val183Ala missense_variant 0.48
clpC1 4039916 c.789T>G synonymous_variant 0.12
clpC1 4040140 p.Pro189Thr missense_variant 0.1
embC 4241882 p.Leu674Met missense_variant 0.13
embC 4241887 c.2025A>G synonymous_variant 0.17
embA 4242550 c.-683C>G upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246716 p.Thr68Ile missense_variant 0.14
aftB 4267272 p.Lys522Arg missense_variant 1.0
ubiA 4269514 p.Val107Gly missense_variant 0.15
ethR 4326739 c.-810G>C upstream_gene_variant 1.0
ethA 4328004 c.-531C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338599 c.-78A>C upstream_gene_variant 1.0
gid 4408085 p.Glu40Lys missense_variant 1.0