TB-Profiler result

Run: ERR2229359
Summary

Run ID: ERR2229359

Sample name:

Date: 31-03-2023 17:06:20

Number of reads: 1398905

Percentage reads mapped: 99.03

Strain: lineage4.8

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
lineage4.8 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
pncA 2289038 p.Trp68Cys missense_variant 0.14 pyrazinamide
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 0.23
mshA 576235 c.888C>A synonymous_variant 0.2
ccsA 620494 p.Arg202Trp missense_variant 0.13
rpoB 762179 c.2373C>A synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpS5 778778 p.Val43Asp missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1305008 p.Ile693Thr missense_variant 0.18
embR 1416851 p.Leu166Pro missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673380 c.-60C>G upstream_gene_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167965 p.Ala883Gly missense_variant 0.19
PPE35 2167967 c.2646A>C synonymous_variant 0.2
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169278 c.1335T>C synonymous_variant 0.16
PPE35 2169281 c.1332T>G synonymous_variant 0.17
PPE35 2169287 c.1326T>C synonymous_variant 0.13
PPE35 2169902 p.Leu237Phe missense_variant 0.2
PPE35 2170048 p.Leu189Val missense_variant 0.51
PPE35 2170053 p.Thr187Ser missense_variant 0.52
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518774 c.661delG frameshift_variant 0.12
kasA 2518879 c.765A>G synonymous_variant 0.31
kasA 2518882 c.768C>A synonymous_variant 0.29
kasA 2519140 c.1026G>C synonymous_variant 0.28
kasA 2519143 c.1029G>C synonymous_variant 0.28
kasA 2519276 p.Glu388Lys missense_variant 0.12
ribD 2987224 p.Asp129Gly missense_variant 0.11
alr 3841546 c.-126C>A upstream_gene_variant 0.24
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246196 c.-318C>T upstream_gene_variant 0.17
embB 4246555 c.42G>C synonymous_variant 0.56
embB 4246556 p.Ala15Pro missense_variant 0.56
embB 4246563 p.Leu17Trp missense_variant 0.5
embB 4246567 c.54G>T synonymous_variant 0.3
embB 4246863 p.Val117Asp missense_variant 0.13
aftB 4267313 c.1524C>T synonymous_variant 0.12
aftB 4268620 p.Val73Leu missense_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1407del transcript_ablation 1.0