TB-Profiler result

Run: ERR4817111
Summary

Run ID: ERR4817111

Sample name:

Date: 01-04-2023 14:48:37

Number of reads: 886739

Percentage reads mapped: 99.61

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 0.99
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
gyrB 5867 p.Asp210Tyr missense_variant 0.12
gyrB 5987 p.Thr250Ala missense_variant 0.17
gyrB 6194 p.Gly319Cys missense_variant 0.11
gyrB 6200 p.Arg321Cys missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8742 p.Asp481His missense_variant 0.17
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490717 c.-66C>G upstream_gene_variant 0.11
fgd1 491142 c.360C>A synonymous_variant 0.14
fgd1 491282 p.Asp167Val missense_variant 0.13
fgd1 491322 c.540G>A synonymous_variant 0.12
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
ccsA 619830 c.-61G>T upstream_gene_variant 0.11
ccsA 620270 p.Val127Asp missense_variant 0.12
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 761285 c.1479G>T synonymous_variant 0.13
rpoC 763886 c.517C>A synonymous_variant 0.12
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766368 p.Ala1000Asp missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpS5 778593 p.Ala105Ser missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303924 p.Gln332* stop_gained 0.13
Rv1258c 1406999 c.342C>T synonymous_variant 0.12
Rv1258c 1407371 c.-31C>A upstream_gene_variant 0.12
embR 1416770 p.Glu193Gly missense_variant 0.11
embR 1417540 c.-193C>T upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472562 n.717C>A non_coding_transcript_exon_variant 0.33
rrs 1473281 n.1436C>T non_coding_transcript_exon_variant 0.14
rrs 1473292 n.1447G>T non_coding_transcript_exon_variant 0.11
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.33
rrl 1476448 n.2791G>T non_coding_transcript_exon_variant 0.4
fabG1 1673719 p.Asp94Tyr missense_variant 0.22
tlyA 1917882 c.-58G>A upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918210 p.Ala91Thr missense_variant 0.14
tlyA 1918311 p.Asn124Lys missense_variant 0.14
ndh 2101747 c.1296C>T synonymous_variant 0.12
ndh 2102506 c.537C>T synonymous_variant 1.0
katG 2154165 c.1947C>A synonymous_variant 0.11
PPE35 2167673 c.2940G>T synonymous_variant 0.11
PPE35 2168446 p.Pro723Ala missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288746 p.Asp166His missense_variant 0.14
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518883 p.Arg257Cys missense_variant 0.17
folC 2746586 p.Arg338Leu missense_variant 0.14
folC 2746780 c.819C>A synonymous_variant 0.13
folC 2747756 c.-158G>T upstream_gene_variant 0.15
ribD 2987200 p.Thr121Asn missense_variant 0.11
Rv2752c 3064756 p.Val479Ala missense_variant 0.17
thyA 3073712 p.His254Asn missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448368 c.-136C>G upstream_gene_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568568 p.Val38Ile missense_variant 0.12
Rv3236c 3612037 c.1080C>T synonymous_variant 0.18
Rv3236c 3612255 p.Val288Ile missense_variant 0.12
fbiB 3641710 p.Arg59Leu missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4245786 p.Ala852Thr missense_variant 1.0
embB 4247795 p.Leu428Phe missense_variant 0.11
aftB 4268991 c.-155C>T upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0