TB-Profiler result

Run: ERR2706966
Summary

Run ID: ERR2706966

Sample name:

Date: 31-03-2023 23:11:45

Number of reads: 4019803

Percentage reads mapped: 99.58

Strain: lineage4.6.1.2;lineage4.3.3

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
lineage4.3 Euro-American (LAM) mainly-LAM None 0.44
lineage4.6 Euro-American T;LAM None 0.59
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.43
lineage4.6.1 Euro-American (Uganda) T2 RD724 0.55
lineage4.6.1.2 Euro-American T2 RD724 0.57
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 0.12 rifampicin
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.15 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.14 isoniazid
pncA 2289091 p.His51Tyr missense_variant 0.2 pyrazinamide
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 5723 p.Ala162Ser missense_variant 0.32
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7539 p.Thr80Ala missense_variant 0.72
gyrA 7570 p.Ala90Gly missense_variant 0.69
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 0.47
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575240 c.-108G>A upstream_gene_variant 0.22
mshA 576108 p.Ala254Gly missense_variant 0.17
rpoC 764810 p.Pro481Thr missense_variant 0.42
rpoC 764995 c.1626C>G synonymous_variant 0.45
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpS5 779675 c.-770G>A upstream_gene_variant 0.16
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304608 p.Thr560Ala missense_variant 0.17
embR 1416410 p.Leu313Arg missense_variant 0.55
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475373 n.1716G>A non_coding_transcript_exon_variant 0.63
fabG1 1673277 c.-163_-162insT upstream_gene_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 0.46
eis 2715432 c.-100C>T upstream_gene_variant 0.13
ribD 2987533 p.Gly232Ala missense_variant 0.15
Rv2752c 3065920 p.Pro91Leu missense_variant 0.57
thyA 3073868 p.Thr202Ala missense_variant 0.28
ald 3086788 c.-32T>C upstream_gene_variant 0.4
Rv3083 3449301 c.798G>A synonymous_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
ddn 3987215 c.372A>G synonymous_variant 0.58
clpC1 4038287 c.2418C>T synonymous_variant 0.45
embC 4242182 p.Ala774Ser missense_variant 0.28
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245055 p.Thr608Asn missense_variant 0.65
embB 4246584 p.Arg24Pro missense_variant 0.24
embB 4247209 c.696A>G synonymous_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407926 p.Pro93Ser missense_variant 0.16
gid 4408156 p.Leu16Arg missense_variant 0.37