TB-Profiler result

Run: ERR2512846
Summary

Run ID: ERR2512846

Sample name:

Date: 31-03-2023 19:17:34

Number of reads: 796933

Percentage reads mapped: 98.84

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
gyrB 7170 p.Ala644Asp missense_variant 0.18
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 491308 c.534_541delCCCGGCGG frameshift_variant 0.17
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 576089 c.750_769delTGATCGGCGCGCGGCCCGGG frameshift_variant 0.12
mshA 576459 c.1117_1147delGCGGTGGGCGGGCTGCCCGTCGCGGTGCGCG frameshift_variant 0.22
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 761713 p.Val636Asp missense_variant 0.11
rpoC 764782 p.Ser471Arg missense_variant 0.11
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304801 p.Arg624Gln missense_variant 0.11
Rv1258c 1406945 c.396C>T synonymous_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.25
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.25
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.25
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.29
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.25
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.22
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.22
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.22
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.22
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.22
rrs 1472617 n.772A>T non_coding_transcript_exon_variant 0.22
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.33
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.4
rrl 1474197 n.540C>T non_coding_transcript_exon_variant 0.33
rrl 1474200 n.545delT non_coding_transcript_exon_variant 0.33
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.33
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2153894 p.Arg740Ser missense_variant 1.0
katG 2154644 p.Gly490Ser missense_variant 0.11
katG 2155100 p.Gly338Ser missense_variant 1.0
PPE35 2169902 c.711G>C synonymous_variant 0.11
PPE35 2170232 c.381T>A synonymous_variant 0.11
PPE35 2170238 c.375T>G synonymous_variant 0.11
PPE35 2170247 p.Ile122Met missense_variant 0.11
PPE35 2170454 c.159C>G synonymous_variant 0.17
PPE35 2170457 c.156G>C synonymous_variant 0.17
PPE35 2170460 c.153G>A synonymous_variant 0.17
PPE35 2170465 p.Ala50Ser missense_variant 0.17
PPE35 2170472 c.141G>A synonymous_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
folC 2747696 c.-98G>A upstream_gene_variant 0.22
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612658 c.459G>A synonymous_variant 0.18
rpoA 3878639 c.-132C>G upstream_gene_variant 0.4
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4246542 p.Ser10Asn missense_variant 0.17
embB 4246563 p.Leu17Trp missense_variant 0.12
embB 4246567 c.54G>T synonymous_variant 0.12
embB 4247068 c.555T>C synonymous_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0