TB-Profiler result

Run: ERR4011933
Summary

Run ID: ERR4011933

Sample name:

Date: 01-04-2023 03:57:13

Number of reads: 2439711

Percentage reads mapped: 99.58

Strain: lineage4.6.3;lineage3.1.1

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
lineage3 East-African-Indian CAS RD750 0.5
lineage4 Euro-American LAM;T;S;X;H None 0.51
lineage4.6 Euro-American T;LAM None 0.48
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 0.47
lineage3.1.1 East-African-Indian CAS1-Kili RD750 0.52
lineage4.6.3 Euro-American T;LAM None 0.48
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 0.43 rifampicin
rrs 1472751 n.906A>G non_coding_transcript_exon_variant 0.5 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.33 isoniazid
pncA 2288887 p.Trp119Arg missense_variant 0.58 pyrazinamide
embB 4248003 p.Gln497Arg missense_variant 0.53 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 8049 p.Ser250Ala missense_variant 0.58
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.45
ccsA 620072 p.Pro61Leu missense_variant 0.56
rpoB 759746 c.-61C>T upstream_gene_variant 0.57
rpoC 762434 c.-936T>G upstream_gene_variant 0.53
rpoC 763031 c.-339T>C upstream_gene_variant 0.54
rpoC 765462 p.Asn698Ser missense_variant 0.55
rpoC 765519 p.Lys717Thr missense_variant 0.52
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.5
mmpL5 776987 c.1493delC frameshift_variant 0.43
mmpS5 778673 p.Pro78Leu missense_variant 0.54
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.57
PPE35 2167926 p.Leu896Ser missense_variant 0.44
PPE35 2170461 p.Gly51Glu missense_variant 0.48
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.58
pncA 2289365 c.-125delC upstream_gene_variant 0.54
ahpC 2726105 c.-88G>A upstream_gene_variant 0.52
pepQ 2860371 c.48C>T synonymous_variant 0.59
ald 3086788 c.-32T>C upstream_gene_variant 0.47
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.97
fbiB 3640824 c.-711C>A upstream_gene_variant 0.56
embC 4240172 p.Val104Met missense_variant 0.53
embC 4241562 p.Arg567His missense_variant 0.59
embC 4242075 p.Arg738Gln missense_variant 0.48
embC 4242185 p.Asp775Asn missense_variant 0.4
embA 4242643 c.-590C>T upstream_gene_variant 0.99
embB 4246584 p.Arg24Pro missense_variant 0.22
aftB 4268573 p.Met88Ile missense_variant 0.51
ubiA 4269162 p.Leu224Phe missense_variant 0.54
whiB6 4338268 p.Gly85Ala missense_variant 0.46
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338635 c.-114A>G upstream_gene_variant 0.49
gid 4407588 c.615A>G synonymous_variant 0.56
gid 4407934 p.Leu90Arg missense_variant 0.48