TB-Profiler result

Run: ERR2515011
Summary

Run ID: ERR2515011

Sample name:

Date: 31-03-2023 20:41:59

Number of reads: 1877525

Percentage reads mapped: 98.97

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 1.0
lineage4.1.2 Euro-American T;H None 0.99
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 1472644 n.799C>T non_coding_transcript_exon_variant 0.19 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 760115 c.309C>T synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 0.98
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.2
rrs 1472150 n.305T>G non_coding_transcript_exon_variant 0.2
rrs 1472151 n.306C>A non_coding_transcript_exon_variant 0.2
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.2
rrs 1472472 n.627G>A non_coding_transcript_exon_variant 0.29
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.25
rrs 1472597 n.752G>A non_coding_transcript_exon_variant 0.25
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.2
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.31
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.25
rrs 1472682 n.837T>G non_coding_transcript_exon_variant 0.15
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.23
rrs 1472690 n.845C>T non_coding_transcript_exon_variant 0.14
rrs 1472692 n.847T>C non_coding_transcript_exon_variant 0.21
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.2
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.14
rrs 1472951 n.1106T>C non_coding_transcript_exon_variant 0.33
rrs 1472953 n.1108G>A non_coding_transcript_exon_variant 0.33
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.33
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.75
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.33
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.5
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.33
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.27
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.27
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.12
rrs 1473226 n.1381C>G non_coding_transcript_exon_variant 0.11
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.14
rrs 1473288 n.1443C>G non_coding_transcript_exon_variant 0.12
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102506 c.537C>T synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
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
whiB6 4338595 c.-75delG upstream_gene_variant 1.0