TB-Profiler result

Run: ERR2229307
Summary

Run ID: ERR2229307

Sample name:

Date: 31-03-2023 16:59:48

Number of reads: 1215713

Percentage reads mapped: 99.27

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 576108 p.Ala254Gly missense_variant 0.16
rpoC 763743 p.Leu125Gln missense_variant 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 1305006 p.Glu692Asp missense_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473975 n.318G>T non_coding_transcript_exon_variant 0.12
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673349 c.-91G>C upstream_gene_variant 0.11
fabG1 1673357 c.-83G>A upstream_gene_variant 0.23
fabG1 1673359 c.-81T>C upstream_gene_variant 0.22
fabG1 1673361 c.-79C>G upstream_gene_variant 0.24
fabG1 1673380 c.-60C>G upstream_gene_variant 0.35
inhA 1674352 p.Thr51Ser missense_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101857 p.Trp396Gly missense_variant 0.12
ndh 2102954 p.Ala30Val missense_variant 0.14
ndh 2103173 c.-132delG upstream_gene_variant 0.11
PPE35 2168143 p.Phe824Leu missense_variant 0.11
PPE35 2168150 c.2463T>C synonymous_variant 0.13
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.47
PPE35 2170053 p.Thr187Ser missense_variant 0.45
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289074 p.Asp56Glu missense_variant 0.13
pncA 2289718 c.-477G>T upstream_gene_variant 0.29
kasA 2518704 p.Gly197Asp missense_variant 0.14
kasA 2519128 c.1014G>C synonymous_variant 0.29
kasA 2519131 c.1017G>C synonymous_variant 0.29
ahpC 2725938 c.-255_-254insA upstream_gene_variant 0.12
pepQ 2859845 p.Thr192Pro missense_variant 0.22
ribD 2986853 c.15T>A synonymous_variant 0.12
thyA 3074281 p.Arg64Leu missense_variant 0.13
ald 3087846 p.Leu343Ile missense_variant 0.13
fprA 3474052 p.Phe16Val missense_variant 0.15
Rv3236c 3612011 p.Leu369Gln missense_variant 0.12
fbiB 3642509 c.975C>A synonymous_variant 0.25
alr 3841546 c.-126C>A upstream_gene_variant 0.19
rpoA 3878599 c.-92C>G upstream_gene_variant 1.0
clpC1 4039645 p.His354Asp missense_variant 0.17
embC 4241561 p.Arg567Cys missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244282 c.1050C>A synonymous_variant 0.12
embB 4246544 p.Thr11Pro missense_variant 0.21
embB 4246548 p.Pro12Gln missense_variant 0.29
embB 4246555 c.42G>C synonymous_variant 0.29
embB 4246556 p.Ala15Pro missense_variant 0.29
embB 4246563 p.Leu17Trp missense_variant 0.17
embB 4246567 c.54G>T synonymous_variant 0.17
embB 4249101 p.Tyr863Cys missense_variant 0.12
aftB 4267251 p.Asp529Gly missense_variant 0.12
aftB 4268921 c.-85C>T upstream_gene_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0