TB-Profiler result

Run: ERR2510812
Summary

Run ID: ERR2510812

Sample name:

Date: 31-03-2023 18:57:05

Number of reads: 919688

Percentage reads mapped: 94.13

Strain: lineage4.1.2.1

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 0.99
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
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 1.0 streptomycin
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
rpoB 759892 p.Ala29Val missense_variant 0.11
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 762260 c.2454C>A synonymous_variant 0.12
rpoC 764278 p.Gln303His missense_variant 0.2
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 778337 c.-653G>A upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304300 p.Gly457Ala missense_variant 0.15
fbiC 1304734 c.1805delA frameshift_variant 0.11
Rv1258c 1407079 c.261delC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.67
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.67
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.67
rrl 1473751 n.94C>T non_coding_transcript_exon_variant 0.33
inhA 1674794 p.Ala198Glu missense_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918643 p.Gly235Asp missense_variant 0.22
ndh 2101951 c.1092C>T synonymous_variant 0.1
PPE35 2169278 c.1335T>C synonymous_variant 0.1
PPE35 2170664 c.-52C>A upstream_gene_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289473 c.-232T>A upstream_gene_variant 0.15
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
Rv2752c 3065416 p.Val259Glu missense_variant 0.15
thyA 3073690 p.Val261Asp missense_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448740 c.237G>A synonymous_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474464 p.Ile153Asn missense_variant 0.14
whiB7 3568725 c.-46A>G upstream_gene_variant 0.12
whiB7 3568760 c.-81G>A upstream_gene_variant 0.12
alr 3841546 c.-126C>A upstream_gene_variant 0.12
panD 4043897 p.Gly129Cys missense_variant 0.12
embC 4241558 p.Arg566Ser missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243382 c.150C>T synonymous_variant 0.11
embA 4244343 p.Ala371Thr missense_variant 1.0
embA 4244778 p.Ser516Pro missense_variant 0.18
ethA 4326472 c.1002G>A synonymous_variant 1.0
ethR 4326961 c.-588G>C upstream_gene_variant 0.14
ethR 4326964 c.-585G>A upstream_gene_variant 0.13
ethR 4326970 c.-579G>T upstream_gene_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408123 p.Ala27Val missense_variant 1.0