TB-Profiler result

Run: ERR4828859
Summary

Run ID: ERR4828859

Sample name:

Date: 01-04-2023 19:07:39

Number of reads: 656817

Percentage reads mapped: 99.51

Strain: lineage4.3.1

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.1 Euro-American (LAM) LAM9 None 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.Ser450Leu missense_variant 1.0 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embA 4243221 c.-12C>T upstream_gene_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 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 767232 p.Tyr1288Cys missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302957 c.27C>T synonymous_variant 0.11
atpE 1460986 c.-59A>G upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473903 n.246A>G non_coding_transcript_exon_variant 0.2
rrl 1474219 n.562G>T non_coding_transcript_exon_variant 0.12
rrl 1474264 n.607T>A non_coding_transcript_exon_variant 0.1
rrl 1476084 n.2427G>T non_coding_transcript_exon_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169650 c.962delT frameshift_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289049 p.Ser65Pro missense_variant 1.0
eis 2714993 p.Pro114Ala missense_variant 0.1
folC 2746581 p.Glu340Lys missense_variant 0.1
Rv2752c 3067008 c.-817C>A upstream_gene_variant 0.12
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449201 p.Phe233Ser missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612765 p.Ile118Val missense_variant 0.12
fbiB 3642226 p.Gln231Pro missense_variant 0.11
fbiB 3642229 p.Leu232Gln missense_variant 0.12
fbiB 3642232 p.Leu233Gln missense_variant 0.12
fbiB 3642234 p.Arg234Leu missense_variant 0.11
rpoA 3877554 c.954G>A synonymous_variant 0.12
rpoA 3878262 c.246C>T synonymous_variant 1.0
rpoA 3878420 p.Phe30Leu missense_variant 0.1
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245910 p.Lys893Arg missense_variant 0.12
embB 4246544 p.Thr11Pro missense_variant 0.25
embB 4246555 c.42G>C synonymous_variant 0.43
embB 4246556 p.Ala15Pro missense_variant 0.43
embB 4246563 p.Leu17Trp missense_variant 0.5
embB 4246567 c.54G>T synonymous_variant 0.5
embB 4246584 p.Arg24Pro missense_variant 0.43
embB 4247515 c.1002C>T synonymous_variant 1.0
embB 4248320 p.Gly603Arg missense_variant 0.92
ethR 4328102 c.555_560delGTCATT disruptive_inframe_deletion 0.1
ethR 4328113 c.565_566insAATGAC stop_gained&disruptive_inframe_insertion 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0