TB-Profiler result

Run: ERR2229481
Summary

Run ID: ERR2229481

Sample name:

Date: 31-03-2023 17:14:15

Number of reads: 460771

Percentage reads mapped: 99.03

Strain: lineage4.8

Drug-resistance: Other

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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
pncA 2288806 p.Ala146Thr missense_variant 0.17 pyrazinamide
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 6885 p.Phe549Ser missense_variant 0.2
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 9523 p.Pro741Leu missense_variant 0.22
fgd1 490856 p.Val25Asp missense_variant 0.15
fgd1 491655 c.873C>T synonymous_variant 0.25
rpoB 761204 c.1398C>T synonymous_variant 0.25
rpoC 763660 c.291T>C synonymous_variant 0.25
rpoC 765091 p.Leu574Phe missense_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777609 p.Leu291Arg missense_variant 0.29
mmpL5 779169 c.-689C>A upstream_gene_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
embR 1416504 p.Met282Leu missense_variant 0.18
embR 1417209 p.Asn47Asp missense_variant 0.15
embR 1417500 c.-153C>T upstream_gene_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673346 c.-94C>G upstream_gene_variant 0.11
fabG1 1673349 c.-91G>C upstream_gene_variant 0.11
fabG1 1673357 c.-83G>A upstream_gene_variant 0.12
fabG1 1673359 c.-81T>C upstream_gene_variant 0.12
fabG1 1673361 c.-79C>G upstream_gene_variant 0.12
fabG1 1673380 c.-60C>G upstream_gene_variant 0.19
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101902 p.Lys381Glu missense_variant 0.17
ndh 2102429 p.Asp205Val missense_variant 0.29
PPE35 2167695 p.Ile973Thr missense_variant 0.18
PPE35 2167701 p.Ala971Phe missense_variant 0.18
PPE35 2167706 c.2907T>C synonymous_variant 0.2
PPE35 2168051 p.Val854Ile missense_variant 0.14
PPE35 2168059 p.Gln852Glu missense_variant 0.14
PPE35 2168208 p.Asp802Pro missense_variant 0.17
PPE35 2168215 p.Thr800Ala missense_variant 0.17
PPE35 2168220 p.Ala798Glu missense_variant 0.3
PPE35 2168231 c.2382T>C synonymous_variant 0.25
PPE35 2168234 c.2379G>T synonymous_variant 0.25
PPE35 2168237 c.2376G>A synonymous_variant 0.29
PPE35 2168642 c.1971C>T synonymous_variant 0.2
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2168888 c.1725G>T synonymous_variant 0.2
PPE35 2169587 c.1026G>A synonymous_variant 0.19
PPE35 2169902 c.711G>C synonymous_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 1.0
PPE35 2170053 p.Thr187Ser missense_variant 1.0
PPE35 2170147 p.Ser156Ala missense_variant 0.33
PPE35 2170157 p.Ala152Ser missense_variant 0.33
Rv1979c 2222421 c.744G>A synonymous_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518606 c.492G>C synonymous_variant 0.2
ahpC 2725938 c.-255_-254insA upstream_gene_variant 0.25
ribD 2986748 c.-91A>G upstream_gene_variant 0.13
thyA 3073769 c.703C>A synonymous_variant 0.19
thyA 3073867 p.Thr202Ser missense_variant 0.11
thyA 3073943 p.Asn177Asp missense_variant 0.12
thyA 3074542 c.-71T>C upstream_gene_variant 0.22
ald 3087188 c.369C>T synonymous_variant 0.2
fprA 3474540 c.534C>T synonymous_variant 0.22
whiB7 3568574 p.Leu36Ile missense_variant 0.13
rpoA 3877605 c.903G>T synonymous_variant 0.22
rpoA 3878236 p.Glu91Val missense_variant 0.18
rpoA 3878272 p.Asn79Ile missense_variant 0.22
clpC1 4038773 p.Asp644Glu missense_variant 0.14
clpC1 4038776 p.Glu643Asp missense_variant 0.13
clpC1 4038782 c.1923G>C synonymous_variant 0.13
clpC1 4039339 p.Thr456Ser missense_variant 0.17
clpC1 4040110 p.Arg199Trp missense_variant 0.17
clpC1 4040144 c.561G>C synonymous_variant 0.17
clpC1 4040319 p.Ala129Gly missense_variant 0.25
clpC1 4040325 c.379_380insACC conservative_inframe_insertion 0.25
clpC1 4040329 p.Lys126Gln missense_variant 0.25
clpC1 4040331 p.Val125Asp missense_variant 0.25
clpC1 4040333 c.372G>T synonymous_variant 0.25
clpC1 4040335 c.367_369delGTG conservative_inframe_deletion 0.25
panD 4043910 c.372G>A synonymous_variant 0.22
embC 4239978 p.Leu39Pro missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4246080 p.Pro950Ser missense_variant 0.25
embB 4246544 p.Thr11Pro missense_variant 0.5
embB 4246548 p.Pro12Gln missense_variant 0.67
embB 4246555 c.42G>C synonymous_variant 0.67
embB 4246556 p.Ala15Pro missense_variant 0.67
aftB 4267045 p.Thr598Ala missense_variant 0.14
ethR 4327902 p.Lys118Asn missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448472 c.-31_*1407del transcript_ablation 1.0