TB-Profiler result

Run: ERR2229255
Summary

Run ID: ERR2229255

Sample name:

Date: 31-03-2023 16:53:30

Number of reads: 1453899

Percentage reads mapped: 99.31

Strain: lineage4.8

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
lineage4.8 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
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 0.98
mshA 575153 c.-195C>A upstream_gene_variant 0.15
mshA 575259 c.-89G>T upstream_gene_variant 0.22
mshA 576108 p.Ala254Gly missense_variant 0.31
rpoC 765287 p.Leu640Met missense_variant 0.15
rpoC 765588 p.Pro740Leu missense_variant 0.14
rpoC 766823 p.Lys1152* stop_gained 0.12
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
fbiC 1304075 p.Ala382Val 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
inhA 1674784 p.Arg195Trp missense_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102965 c.78G>T synonymous_variant 0.13
PPE35 2167973 c.2640A>G synonymous_variant 0.14
PPE35 2168140 p.Ala825Thr missense_variant 0.12
PPE35 2168143 p.Phe824Leu missense_variant 0.12
PPE35 2168150 c.2463T>C synonymous_variant 0.13
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169278 c.1335T>C synonymous_variant 0.12
PPE35 2169281 c.1332T>G synonymous_variant 0.17
PPE35 2169287 c.1326T>C synonymous_variant 0.14
PPE35 2169902 c.711G>C synonymous_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 0.38
PPE35 2170053 p.Thr187Ser missense_variant 0.39
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2746816 c.783C>G synonymous_variant 0.11
pepQ 2859696 c.723G>A synonymous_variant 0.14
pepQ 2859951 p.Asp156Glu missense_variant 0.12
thyX 3068000 c.-55G>T upstream_gene_variant 0.12
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
Rv3236c 3612387 p.Ala244Thr missense_variant 0.14
fbiB 3641810 c.276G>T synonymous_variant 0.12
alr 3841546 c.-126C>A upstream_gene_variant 0.19
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242655 c.-578A>G upstream_gene_variant 0.12
embA 4244184 p.Ser318Arg missense_variant 0.14
aftB 4268955 c.-119A>G upstream_gene_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0
Rv3236c 3612912 c.-454_204del conservative_inframe_deletion 1.0