TB-Profiler result

Run: ERR2229119
Summary

Run ID: ERR2229119

Sample name:

Date: 31-03-2023 16:41:43

Number of reads: 784977

Percentage reads mapped: 99.46

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
fgd1 491225 p.Val148Asp missense_variant 0.11
mshA 576108 p.Ala254Gly missense_variant 0.17
mshA 576227 p.Arg294Ser missense_variant 0.14
mshA 576282 p.Leu312Gln missense_variant 0.13
ccsA 620535 p.Met215Ile missense_variant 0.17
rpoB 761818 p.Arg671Leu missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777709 p.Leu258Ile missense_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781403 c.-157G>A upstream_gene_variant 0.14
rpsL 781804 p.Val82Glu missense_variant 0.15
fbiC 1303747 p.Thr273Ala missense_variant 1.0
embR 1416841 c.507C>T synonymous_variant 0.15
embR 1417264 c.84G>A synonymous_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472980 n.1135G>T non_coding_transcript_exon_variant 0.18
rrl 1473482 n.-176A>G upstream_gene_variant 0.25
rrl 1473535 n.-123C>A upstream_gene_variant 0.25
rrl 1473645 n.-13G>T upstream_gene_variant 0.2
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673380 c.-60C>G upstream_gene_variant 0.36
rpsA 1834858 p.Glu439Asp missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167865 c.2748G>C synonymous_variant 0.11
PPE35 2167868 c.2745A>C synonymous_variant 0.11
PPE35 2168008 p.Ile869Phe missense_variant 0.18
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169357 p.Thr419Asn missense_variant 0.12
PPE35 2169566 c.1047T>C synonymous_variant 0.11
PPE35 2170048 p.Leu189Val missense_variant 0.48
PPE35 2170053 p.Thr187Ser missense_variant 0.45
PPE35 2170349 p.Thr88Ala missense_variant 0.11
PPE35 2170385 c.228G>T synonymous_variant 0.16
PPE35 2170547 c.66A>C synonymous_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223308 c.-144T>C upstream_gene_variant 0.12
folC 2746432 c.1167C>A synonymous_variant 0.25
folC 2746489 c.1110C>T synonymous_variant 0.2
pepQ 2859943 p.Ala159Gly missense_variant 0.13
pepQ 2859966 p.Asp151Glu missense_variant 0.12
Rv2752c 3065272 p.Thr307Ile missense_variant 0.13
Rv2752c 3065882 p.Gly104Cys missense_variant 0.17
Rv2752c 3065899 p.Pro98Arg missense_variant 0.14
thyX 3067340 c.606G>A synonymous_variant 0.27
thyX 3067746 p.Val67Asp missense_variant 0.12
thyA 3073755 p.Phe239Leu missense_variant 0.13
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
rpoA 3878182 p.Asp109Gly missense_variant 0.11
ddn 3986799 c.-45G>A upstream_gene_variant 0.11
clpC1 4039042 p.Ser555Thr missense_variant 0.18
clpC1 4039645 p.His354Asp missense_variant 0.15
clpC1 4039654 p.Thr351Ser missense_variant 0.18
clpC1 4040495 c.209delG frameshift_variant 0.12
embC 4240494 p.Gly211Val missense_variant 0.12
embC 4241783 p.Trp641Arg missense_variant 0.12
embA 4242409 c.-824G>A upstream_gene_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244184 p.Ser318Leu missense_variant 0.22
embA 4246341 p.Leu1037Met missense_variant 0.12
aftB 4268318 c.519C>T synonymous_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407559 p.Ser215Leu missense_variant 0.11
gid 4407857 p.Arg116Trp missense_variant 0.12
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0