TB-Profiler result

Run: ERR2228867
Summary

Run ID: ERR2228867

Sample name:

Date: 31-03-2023 16:23:46

Number of reads: 107980

Percentage reads mapped: 99.39

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 0.13
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 575637 p.Asp97Ala missense_variant 0.4
mshA 575924 p.Gly193Arg missense_variant 0.29
mshA 576189 p.Asp281Val missense_variant 0.25
mshA 576594 p.Val416Gly missense_variant 0.5
rpoB 760161 p.Lys119* stop_gained 0.33
rpoB 760503 p.Lys233* stop_gained 0.5
rpoB 760565 c.759A>C synonymous_variant 0.5
rpoC 766276 c.2907C>A synonymous_variant 0.5
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777087 p.Ile465Ser missense_variant 0.67
mmpR5 778993 p.Ser2Gly missense_variant 0.5
mmpR5 779432 p.Asn148Thr missense_variant 0.67
fbiC 1304356 p.Ile476Leu missense_variant 0.5
fbiC 1304992 p.Ser688Ala missense_variant 1.0
Rv1258c 1406297 c.1044A>T synonymous_variant 0.67
embR 1416518 p.Leu277Arg missense_variant 1.0
rrl 1476789 n.3132T>A non_coding_transcript_exon_variant 1.0
fabG1 1673642 p.Val68Gly missense_variant 0.5
rpsA 1834941 p.Asp467Ala missense_variant 0.67
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102673 p.Ser124Pro missense_variant 0.4
ndh 2102696 p.Ile116Thr missense_variant 0.4
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2168882 c.1731T>A synonymous_variant 0.67
PPE35 2169022 p.Gly531Trp missense_variant 0.4
PPE35 2169301 p.Asn438Tyr missense_variant 1.0
PPE35 2170540 p.Leu25Val missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289425 c.-184A>C upstream_gene_variant 0.5
kasA 2518144 c.30T>A synonymous_variant 0.5
kasA 2518742 p.Phe210Val missense_variant 0.67
ahpC 2725920 c.-273A>T upstream_gene_variant 0.4
thyA 3073913 p.Met187Leu missense_variant 0.4
thyA 3074528 c.-57T>G upstream_gene_variant 0.67
Rv3083 3448442 c.-62A>T upstream_gene_variant 0.5
fbiB 3641723 c.189T>G synonymous_variant 0.29
fbiB 3642280 p.Leu249Arg missense_variant 1.0
alr 3840892 p.Thr177Pro missense_variant 0.4
alr 3841288 p.Ile45Phe missense_variant 1.0
embC 4241532 p.Ile557Asn missense_variant 0.4
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243525 p.Val98Glu missense_variant 0.5
embA 4243824 p.Thr198Pro missense_variant 0.4
embA 4244053 p.Asp274Ala missense_variant 0.4
embB 4247028 p.Leu172Gln missense_variant 1.0
embB 4248111 p.Val533Gly missense_variant 0.33
embB 4249401 p.Val963Gly missense_variant 0.43
ethR 4327285 c.-264A>T upstream_gene_variant 0.5
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448496 c.-7_*1408del transcript_ablation 1.0