TB-Profiler result

Run: ERR2229699
Summary

Run ID: ERR2229699

Sample name:

Date: 31-03-2023 17:28:18

Number of reads: 1389315

Percentage reads mapped: 99.2

Strain: lineage4.8

Drug-resistance: HR-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 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
katG 2155166 p.Gly316Ser missense_variant 0.14 isoniazid
katG 2155272 c.839delC frameshift_variant 0.13 isoniazid
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 576108 p.Ala254Gly missense_variant 0.14
rpoC 765822 p.Ala818Gly missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474483 n.826C>A non_coding_transcript_exon_variant 0.13
fabG1 1673380 c.-60C>G upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.54
PPE35 2170053 p.Thr187Ser missense_variant 0.56
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2746583 p.Leu339Ser missense_variant 0.11
thyX 3067340 c.606G>A synonymous_variant 0.15
alr 3841546 c.-126C>A upstream_gene_variant 0.14
rpoA 3878599 c.-92C>G upstream_gene_variant 1.0
rpoA 3878639 c.-132C>G upstream_gene_variant 0.4
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244947 p.Val572Ala missense_variant 0.17
embB 4246548 p.Pro12Gln missense_variant 0.29
embB 4246555 c.42G>C synonymous_variant 0.33
embB 4246556 p.Ala15Pro missense_variant 0.33
embB 4246563 p.Leu17Trp missense_variant 0.19
embB 4246567 c.54G>T synonymous_variant 0.21
aftB 4268630 c.207G>T synonymous_variant 0.4
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0