TB-Profiler result

Run: ERR1950052
Summary

Run ID: ERR1950052

Sample name:

Date: 31-03-2023 15:38:35

Number of reads: 708782

Percentage reads mapped: 99.63

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
gyrB 6591 p.Arg451His missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
mshA 575207 c.-141A>G upstream_gene_variant 0.13
mshA 576535 c.1188T>C synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775795 p.Ala896Ser missense_variant 0.13
mmpL5 777370 p.Lys371* stop_gained 0.29
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303273 p.Arg115Cys missense_variant 0.15
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1407130 p.Arg71Cys missense_variant 0.15
Rv1258c 1407423 c.-83G>C upstream_gene_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475962 n.2305G>A non_coding_transcript_exon_variant 0.33
fabG1 1673346 c.-94C>G upstream_gene_variant 0.11
fabG1 1673349 c.-91G>C upstream_gene_variant 0.13
fabG1 1673620 p.Asp61His missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156519 c.-408T>C upstream_gene_variant 0.14
PPE35 2167955 c.2658A>C synonymous_variant 0.22
PPE35 2167965 p.Ala883Gly missense_variant 0.22
PPE35 2167967 c.2646A>C synonymous_variant 0.22
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2168989 p.Thr542Ser missense_variant 0.23
PPE35 2169049 p.Ile522Phe missense_variant 0.22
PPE35 2169144 p.Val490Glu missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
fprA 3474084 c.78C>T synonymous_variant 0.12
fprA 3474140 p.Pro45His missense_variant 0.11
whiB7 3568523 c.157T>C synonymous_variant 0.13
Rv3236c 3612456 c.661C>A synonymous_variant 0.12
fbiA 3640509 c.-34T>C upstream_gene_variant 0.11
clpC1 4040106 p.Val200Gly missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243864 p.Val211Gly missense_variant 0.18
embA 4244613 p.Ala461Thr missense_variant 0.22
aftB 4267895 p.Phe314Leu missense_variant 0.17
aftB 4268557 p.Gly94Arg missense_variant 0.1
ethA 4328473 c.-1000G>T upstream_gene_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