TB-Profiler result

Run: ERR2229065
Summary

Run ID: ERR2229065

Sample name:

Date: 31-03-2023 16:34:43

Number of reads: 696524

Percentage reads mapped: 99.52

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 0.22
ccsA 620250 c.360C>A synonymous_variant 0.12
ccsA 620773 p.Ile295Val missense_variant 0.2
rpoB 759762 c.-45T>A upstream_gene_variant 0.17
rpoB 760847 c.1041C>A synonymous_variant 0.15
rpoC 765589 c.2220G>T synonymous_variant 0.17
rpoC 765823 c.2456dupG frameshift_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775927 c.2554C>T synonymous_variant 0.13
mmpL5 775931 c.2550C>T synonymous_variant 0.14
mmpL5 777486 p.Phe332Ser missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303331 p.Arg134Leu missense_variant 0.22
fbiC 1303396 p.Arg156Cys missense_variant 0.13
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304869 p.Leu647Met missense_variant 0.2
atpE 1460983 c.-62A>T upstream_gene_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474079 n.423delA non_coding_transcript_exon_variant 0.18
rrl 1475430 n.1773T>C non_coding_transcript_exon_variant 0.2
fabG1 1673357 c.-83G>A upstream_gene_variant 0.14
fabG1 1673359 c.-81T>C upstream_gene_variant 0.14
fabG1 1673361 c.-79C>G upstream_gene_variant 0.14
fabG1 1673380 c.-60C>G upstream_gene_variant 0.4
inhA 1673526 c.-676G>A upstream_gene_variant 0.15
inhA 1674754 p.Arg185Ser missense_variant 0.22
rpsA 1833643 c.102C>T synonymous_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101727 p.Arg439Leu missense_variant 0.18
PPE35 2167746 p.Thr956Phe missense_variant 0.13
PPE35 2168160 p.Glu818Val missense_variant 0.11
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169281 c.1332T>G synonymous_variant 0.11
PPE35 2169293 c.1320T>C synonymous_variant 0.11
PPE35 2170048 p.Leu189Val missense_variant 0.31
PPE35 2170053 p.Thr187Ser missense_variant 0.29
Rv1979c 2222581 p.Thr195Met missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518619 p.Ser169Pro missense_variant 0.15
kasA 2518806 p.Asp231Val missense_variant 0.12
Rv2752c 3064760 p.Val478Met missense_variant 0.12
Rv2752c 3066107 p.Arg29Cys missense_variant 0.12
thyA 3073843 p.Asp210Gly missense_variant 0.12
panD 4044182 p.Asp34Tyr missense_variant 0.17
embC 4242375 p.Arg838Gln missense_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243854 p.Leu208Phe missense_variant 0.12
embB 4246686 p.Trp58* stop_gained 0.25
embB 4247028 p.Leu172Arg missense_variant 0.21
embB 4249170 p.Asn886Ser missense_variant 0.17
embB 4249173 p.Ser887Asn missense_variant 0.17
aftB 4267476 p.Ser454Leu missense_variant 0.15
aftB 4268776 p.Ser21Gly missense_variant 0.12
ethA 4326924 p.Gly184Ser missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408330 c.-128G>T upstream_gene_variant 0.13
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0