TB-Profiler result

Run: ERR2229136
Summary

Run ID: ERR2229136

Sample name:

Date: 31-03-2023 16:43:48

Number of reads: 815662

Percentage reads mapped: 99.44

Strain: lineage4.8

Drug-resistance: RR-TB

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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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
rpoB 761151 p.Leu449Met missense_variant 0.12 rifampicin
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
mshA 575870 p.His175Asn missense_variant 0.11
mshA 576108 p.Ala254Gly missense_variant 0.29
ccsA 620208 c.318G>A synonymous_variant 0.17
rpoC 766259 p.Ser964Pro missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303427 p.Gly166Ala missense_variant 0.13
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304046 c.1116C>A synonymous_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473305 n.1460G>A non_coding_transcript_exon_variant 0.13
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474552 n.895C>T non_coding_transcript_exon_variant 0.14
rrl 1474558 n.901G>A non_coding_transcript_exon_variant 0.14
rrl 1474582 n.925T>A non_coding_transcript_exon_variant 0.18
rrl 1475729 n.2072C>T non_coding_transcript_exon_variant 0.12
fabG1 1673380 c.-60C>G upstream_gene_variant 0.27
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167746 p.Thr956Ser missense_variant 0.15
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.44
PPE35 2170053 p.Thr187Ser missense_variant 0.44
PPE35 2170371 p.Thr81Val missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518809 p.Lys232Arg missense_variant 0.17
kasA 2518812 c.700delC frameshift_variant 0.18
thyX 3067591 p.Pro119Ser missense_variant 0.12
Rv3083 3448348 c.-156G>T upstream_gene_variant 0.13
fbiA 3640888 c.349delC frameshift_variant 0.12
alr 3841546 c.-126C>A upstream_gene_variant 0.14
clpC1 4040144 c.561G>C synonymous_variant 0.25
embC 4241777 p.Gly639Arg missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243072 c.-161C>T upstream_gene_variant 0.14
embA 4243968 p.Val246Leu missense_variant 0.14
embA 4246312 p.Gly1027Asp missense_variant 0.15
embB 4246859 p.Val116Phe missense_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0