TB-Profiler result

Run: ERR4829960
Summary

Run ID: ERR4829960

Sample name:

Date: 01-04-2023 19:47:21

Number of reads: 1826604

Percentage reads mapped: 99.45

Strain: lineage4.5;lineage3

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
lineage3 East-African-Indian CAS RD750 0.7
lineage4 Euro-American LAM;T;S;X;H None 0.28
lineage4.5 Euro-American H;T RD122 0.27
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 761128 p.Ser441Leu missense_variant 0.39 rifampicin
rpoB 761139 p.His445Asn missense_variant 0.52 rifampicin
mmpR5 779181 c.198dupG frameshift_variant 0.56 clofazimine, bedaquiline
rrs 1472359 n.514A>T non_coding_transcript_exon_variant 0.31 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.32 isoniazid
embB 4247574 p.Asp354Ala missense_variant 0.36 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 7585 p.Ser95Thr missense_variant 1.0
gyrA 7892 c.591G>A synonymous_variant 0.16
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.7
ccsA 620029 c.139C>T synonymous_variant 0.28
rpoB 759746 c.-61C>T upstream_gene_variant 0.73
rpoC 762434 c.-936T>G upstream_gene_variant 0.88
rpoC 763031 c.-339T>C upstream_gene_variant 0.66
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.85
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304463 c.1533C>T synonymous_variant 0.29
Rv1258c 1406101 p.Pro414Ser missense_variant 0.24
Rv1258c 1406899 p.Ala148Thr missense_variant 0.29
Rv1258c 1407133 p.Gly70Arg missense_variant 0.55
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834985 c.1445dupG frameshift_variant&stop_lost&splice_region_variant 0.33
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102283 p.Arg254Cys missense_variant 0.38
katG 2154372 c.1740C>T synonymous_variant 0.32
katG 2154724 p.Arg463Leu missense_variant 0.61
PPE35 2167926 p.Leu896Ser missense_variant 0.78
PPE35 2170568 p.Ile15Met missense_variant 0.34
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.77
pncA 2289365 c.-125delC upstream_gene_variant 0.72
ahpC 2726105 c.-88G>A upstream_gene_variant 0.74
Rv2752c 3065643 c.549C>T synonymous_variant 0.24
ald 3086788 c.-32T>C upstream_gene_variant 0.59
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568418 c.250_261delGGACGTCCGCGC conservative_inframe_deletion 0.46
Rv3236c 3612316 c.801T>C synonymous_variant 0.14
rpoA 3878401 p.Asn36Ser missense_variant 0.14
clpC1 4038318 p.Pro796Leu missense_variant 0.2
embC 4242075 p.Arg738Gln missense_variant 0.66
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4269024 c.-188G>A upstream_gene_variant 0.6
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.81