TB-Profiler result

Run: ERR2503379
Summary

Run ID: ERR2503379

Sample name:

Date: 31-03-2023 18:25:30

Number of reads: 524514

Percentage reads mapped: 99.55

Strain: lineage4.1.2

Drug-resistance: Other

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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
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
ethR 4327876 p.Phe110Leu missense_variant 1.0 ethionamide
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 9206 c.1905C>G synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575310 c.-38G>T upstream_gene_variant 0.13
ccsA 619831 c.-60T>G upstream_gene_variant 0.31
ccsA 620327 p.Leu146Pro missense_variant 0.11
ccsA 620436 c.546T>C synonymous_variant 0.11
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766746 c.3382delC frameshift_variant 0.1
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800889 c.81C>A synonymous_variant 1.0
Rv1258c 1406887 p.Leu152Met missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475313 n.1656G>A non_coding_transcript_exon_variant 0.17
rrl 1475392 n.1735C>A non_coding_transcript_exon_variant 0.18
inhA 1674147 c.-55C>T upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918377 c.438T>C synonymous_variant 0.11
ndh 2102690 p.Ala118Gly missense_variant 0.1
PPE35 2168303 c.2310G>T synonymous_variant 1.0
PPE35 2169776 p.Phe279Leu missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518618 c.504G>T synonymous_variant 0.11
kasA 2518761 p.Met216Thr missense_variant 0.12
kasA 2519269 c.1155C>G synonymous_variant 0.11
folC 2746673 p.Val309Ala missense_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474145 p.Gly47Trp missense_variant 0.12
alr 3840263 c.1158C>T synonymous_variant 1.0
embC 4240168 p.Lys102Asn missense_variant 1.0
embC 4240793 p.Ala311Ser missense_variant 0.13
embC 4240801 c.939C>T synonymous_variant 0.14
embC 4240803 p.Tyr314Phe missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243780 p.Pro183Leu missense_variant 0.11
embB 4249051 c.2538C>G synonymous_variant 0.11
aftB 4267891 c.943_945delATC conservative_inframe_deletion 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0