TB-Profiler result

Run: ERR4819500

Summary

Run ID: ERR4819500

Sample name:

Date: 01-04-2023 16:08:46

Number of reads: 768447

Percentage reads mapped: 99.45

Strain: lineage4.1.2.1

Drug-resistance: Sensitive


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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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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
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
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
ccsA 620852 p.Ala321Val missense_variant 0.12
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 761308 p.Asn501Ser missense_variant 0.1
rpoB 761459 c.1653G>A synonymous_variant 0.11
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777119 p.His454Gln missense_variant 0.18
mmpL5 777122 c.1359C>T synonymous_variant 0.18
mmpL5 777128 c.1353A>G synonymous_variant 0.17
mmpL5 778056 p.Ser142Asn missense_variant 0.11
mmpR5 778061 c.-929C>T upstream_gene_variant 0.1
mmpR5 778064 c.-926G>C upstream_gene_variant 0.1
mmpL5 778070 p.Thr137Ala missense_variant 0.1
mmpL5 778171 p.Ala104Thr missense_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303737 c.807G>A synonymous_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471824 n.-22T>A upstream_gene_variant 0.12
rrl 1473443 n.-215T>A upstream_gene_variant 0.33
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.67
inhA 1674452 p.Ala84Val missense_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102456 p.Thr196Met missense_variant 0.12
ndh 2103146 c.-104G>A upstream_gene_variant 0.12
PPE35 2169717 p.Asn299Ile missense_variant 0.12
PPE35 2169725 c.888T>C synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
Rv2752c 3065868 c.324C>T synonymous_variant 0.11
thyA 3074316 c.155delT frameshift_variant 0.11
thyA 3074439 c.33G>A synonymous_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448621 p.Arg40Ser missense_variant 0.1
Rv3083 3448624 p.Leu41Met missense_variant 0.1
Rv3083 3448773 c.270G>T synonymous_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612129 p.Leu330Phe missense_variant 0.14
Rv3236c 3613260 c.-144C>G upstream_gene_variant 0.1
fbiA 3640679 p.Asn46Ser missense_variant 0.12
clpC1 4040024 c.681A>G synonymous_variant 0.12
clpC1 4040027 c.678C>G synonymous_variant 0.12
clpC1 4040032 p.Val225Ile missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 0.93
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243794 p.Arg188Cys missense_variant 0.11
ethR 4327335 c.-214A>G upstream_gene_variant 0.11
ethA 4328216 c.-743C>T upstream_gene_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0