TB-Profiler result

Run: ERR2229751
Summary

Run ID: ERR2229751

Sample name:

Date: 31-03-2023 17:33:53

Number of reads: 1102778

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 1.0
mshA 575265 c.-82delG upstream_gene_variant 0.18
mshA 576108 p.Ala254Gly missense_variant 0.19
rpoB 760134 p.Lys110* stop_gained 0.12
rpoC 764551 c.1182G>T synonymous_variant 0.12
rpoC 765935 p.Ala856Ser missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775835 c.2646C>G synonymous_variant 0.25
mmpL5 776244 p.Ile746Thr missense_variant 0.15
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 1474970 n.1313G>T non_coding_transcript_exon_variant 0.12
fabG1 1673380 c.-60C>G upstream_gene_variant 0.37
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102390 p.Pro218Leu missense_variant 0.12
katG 2155264 p.Leu283Pro missense_variant 0.14
PPE35 2167772 c.2841C>T synonymous_variant 0.17
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169125 p.Val496Ile missense_variant 0.12
PPE35 2169269 c.1344A>G synonymous_variant 0.14
PPE35 2169272 c.1341C>G synonymous_variant 0.15
PPE35 2169278 c.1335T>C synonymous_variant 0.3
PPE35 2169281 c.1332T>G synonymous_variant 0.3
PPE35 2169287 c.1326T>C synonymous_variant 0.23
PPE35 2169602 c.1011C>A synonymous_variant 0.15
PPE35 2169902 p.Leu237Phe missense_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 0.38
PPE35 2170053 p.Thr187Ser missense_variant 0.41
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289443 c.-202C>T upstream_gene_variant 0.13
kasA 2518597 c.483C>T synonymous_variant 0.14
eis 2714663 p.Ala224Ser missense_variant 0.13
folC 2746576 c.1023C>T synonymous_variant 0.12
thyX 3067340 c.606G>A synonymous_variant 0.13
Rv3236c 3612854 p.His88Arg missense_variant 0.11
Rv3236c 3613103 p.Arg5Met missense_variant 0.12
rpoA 3878703 c.-196G>A upstream_gene_variant 0.15
clpC1 4040305 p.Val134Met missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243581 p.Ala117Ser missense_variant 0.11
embB 4246544 p.Thr11Pro missense_variant 0.21
embB 4246548 p.Pro12Gln missense_variant 0.29
embB 4246555 c.42G>C synonymous_variant 0.31
embB 4246556 p.Ala15Pro missense_variant 0.31
embB 4246563 p.Leu17Trp missense_variant 0.17
embB 4246567 c.54G>T synonymous_variant 0.14
embB 4246747 p.Asp78Glu missense_variant 0.13
embB 4247212 c.699G>T synonymous_variant 0.15
embB 4249644 p.Leu1044Pro missense_variant 0.11
aftB 4268791 p.Leu16Met missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0