TB-Profiler result

Run: ERR2229750
Summary

Run ID: ERR2229750

Sample name:

Date: 31-03-2023 17:35:10

Number of reads: 1129117

Percentage reads mapped: 99.25

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 0.99
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
fgd1 491308 c.534_541delCCCGGCGG frameshift_variant 0.17
mshA 576108 p.Ala254Gly missense_variant 0.2
rpoB 759742 c.-65G>A upstream_gene_variant 0.25
rpoC 765226 p.Ile619Met missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775974 p.Leu836Trp missense_variant 0.11
mmpL5 776018 c.2463G>C synonymous_variant 0.2
mmpL5 776021 c.2460G>C synonymous_variant 0.2
mmpL5 776729 c.1752C>T synonymous_variant 0.2
mmpL5 778963 c.-483G>T upstream_gene_variant 0.29
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
embR 1417156 c.192A>C synonymous_variant 0.13
embR 1417172 c.175dupC frameshift_variant 0.14
embR 1417540 c.-193C>G upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473913 n.258delA non_coding_transcript_exon_variant 0.33
rrl 1474030 n.373G>A non_coding_transcript_exon_variant 0.67
rrl 1474076 n.419C>T non_coding_transcript_exon_variant 0.25
rrl 1474093 n.436G>A non_coding_transcript_exon_variant 0.25
rrl 1476023 n.2366C>T non_coding_transcript_exon_variant 0.25
rrl 1476140 n.2485delA non_coding_transcript_exon_variant 0.25
fabG1 1673357 c.-83G>A upstream_gene_variant 0.11
fabG1 1673359 c.-81T>C upstream_gene_variant 0.11
fabG1 1673361 c.-79C>G upstream_gene_variant 0.11
fabG1 1673380 c.-60C>G upstream_gene_variant 0.32
inhA 1674199 c.-3C>T upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155326 c.786A>T synonymous_variant 0.13
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169606 p.Asn336Thr missense_variant 0.1
PPE35 2169618 p.Phe332Gly missense_variant 0.1
PPE35 2169623 c.990T>C synonymous_variant 0.22
PPE35 2169629 c.984T>C synonymous_variant 0.13
PPE35 2169671 c.942C>G synonymous_variant 0.14
PPE35 2169674 c.939T>C synonymous_variant 0.13
PPE35 2169680 c.933A>G synonymous_variant 0.11
PPE35 2170048 p.Leu189Val missense_variant 0.65
PPE35 2170053 p.Thr187Ser missense_variant 0.65
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518606 c.492G>C synonymous_variant 0.15
kasA 2518609 p.Met165Ile missense_variant 0.12
eis 2714767 p.Gly189Val missense_variant 0.14
eis 2714953 p.Gly127Val missense_variant 0.13
ahpC 2726523 p.Leu111Ile missense_variant 0.14
thyX 3067340 c.606G>A synonymous_variant 0.19
Rv3236c 3612460 c.657G>A synonymous_variant 0.13
fbiA 3640531 c.-12C>T upstream_gene_variant 0.17
rpoA 3877991 p.Lys173Glu missense_variant 0.1
embC 4241143 c.1281C>T synonymous_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244610 p.Ala460Pro missense_variant 0.11
embB 4246544 p.Thr11Pro missense_variant 0.35
embB 4246548 p.Pro12Gln missense_variant 0.5
embB 4246555 c.42G>C synonymous_variant 0.56
embB 4246556 p.Ala15Pro missense_variant 0.56
embB 4246563 p.Leu17Trp missense_variant 0.46
embB 4246567 c.54G>T synonymous_variant 0.43
aftB 4268086 p.Ser251Pro missense_variant 0.15
ethR 4327781 p.Arg78Leu missense_variant 0.12
ethA 4328465 c.-992C>A upstream_gene_variant 0.14
whiB6 4338261 c.261G>C synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0