TB-Profiler result

Run: ERR2229764
Summary

Run ID: ERR2229764

Sample name:

Date: 31-03-2023 17:34:19

Number of reads: 825174

Percentage reads mapped: 99.53

Strain: lineage4.8

Drug-resistance: HR-TB

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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
katG 2155795 p.Ala106Val missense_variant 0.12 isoniazid
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 575378 p.Gly11Trp missense_variant 0.12
rpoB 761482 p.Ala559Val missense_variant 0.14
rpoB 761929 p.Ala708Val missense_variant 0.11
rpoC 764541 p.Val391Gly missense_variant 0.13
rpoC 764543 p.Thr392Asp missense_variant 0.13
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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673357 c.-83G>A upstream_gene_variant 0.14
fabG1 1673359 c.-81T>C upstream_gene_variant 0.15
fabG1 1673361 c.-79C>G upstream_gene_variant 0.15
fabG1 1673380 c.-60C>G upstream_gene_variant 0.31
tlyA 1917830 c.-110C>A upstream_gene_variant 0.13
tlyA 1917934 c.-6T>C upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102875 c.168C>T synonymous_variant 0.11
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169269 c.1344A>G synonymous_variant 0.18
PPE35 2169272 c.1341C>G synonymous_variant 0.19
PPE35 2169278 c.1335T>C synonymous_variant 0.14
PPE35 2169281 c.1332T>G synonymous_variant 0.14
PPE35 2169902 p.Leu237Phe missense_variant 0.18
PPE35 2170048 p.Leu189Val missense_variant 0.55
PPE35 2170053 p.Thr187Ser missense_variant 0.55
PPE35 2170147 p.Ser156Ala missense_variant 0.21
PPE35 2170159 p.Ala152Ser missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726338 p.Val49Gly missense_variant 0.27
Rv3236c 3612454 c.663G>T synonymous_variant 0.13
alr 3841546 c.-126C>A upstream_gene_variant 0.25
rpoA 3878352 c.156C>A synonymous_variant 0.11
clpC1 4039042 p.Ser555Thr missense_variant 0.17
clpC1 4039730 c.975C>G synonymous_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243691 p.Met153Ile missense_variant 0.17
ethR 4327335 c.-214A>G upstream_gene_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0