TB-Profiler result

Run: ERR2228868

Summary

Run ID: ERR2228868

Sample name:

Date: 31-03-2023 16:24:32

Number of reads: 870861

Percentage reads mapped: 99.27

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
gyrA 7812 p.Pro171Thr missense_variant 0.13
mshA 576108 p.Ala254Gly missense_variant 0.18
mshA 576711 p.Arg455Gln missense_variant 0.13
mshA 576745 c.1398G>C synonymous_variant 0.18
mshA 576752 p.Pro469Ala missense_variant 0.22
rpoB 759702 c.-105T>G upstream_gene_variant 0.11
rpoB 762502 p.Pro899Gln missense_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775927 c.2554C>T synonymous_variant 0.25
mmpL5 775931 c.2550C>T synonymous_variant 0.25
mmpL5 776231 c.2250G>T synonymous_variant 0.33
mmpL5 776401 p.Glu694Lys missense_variant 0.18
mmpL5 776729 c.1752C>T synonymous_variant 0.13
mmpL5 777119 p.His454Gln missense_variant 0.19
mmpL5 777122 c.1359C>T synonymous_variant 0.19
mmpL5 777128 c.1353A>G synonymous_variant 0.19
mmpR5 778121 c.-869G>T upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801275 p.Thr156Lys missense_variant 0.12
fbiC 1303747 p.Thr273Ala missense_variant 1.0
embR 1417446 c.-99G>T upstream_gene_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673380 c.-60C>G upstream_gene_variant 0.16
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918701 p.Lys254Asn missense_variant 0.15
katG 2155039 p.Gly358Asp missense_variant 0.12
katG 2155267 p.Asp282Val missense_variant 0.25
PPE35 2167814 c.2799C>T synonymous_variant 0.17
PPE35 2167865 c.2748G>C synonymous_variant 0.18
PPE35 2167868 c.2745A>C synonymous_variant 0.18
PPE35 2167997 c.2616G>C synonymous_variant 0.2
PPE35 2168140 p.Ala825Thr missense_variant 0.15
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169269 c.1344A>G synonymous_variant 0.23
PPE35 2169272 c.1341C>G synonymous_variant 0.25
PPE35 2169278 c.1335T>C synonymous_variant 0.23
PPE35 2169281 c.1332T>G synonymous_variant 0.24
PPE35 2169717 p.Asn299Ile missense_variant 0.15
PPE35 2169725 c.888T>C synonymous_variant 0.14
PPE35 2169902 p.Leu237Phe missense_variant 0.24
PPE35 2170048 p.Leu189Val missense_variant 0.53
PPE35 2170053 p.Thr187Ser missense_variant 0.53
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518606 c.492G>C synonymous_variant 0.2
kasA 2518809 p.Lys232Arg missense_variant 0.18
kasA 2518839 p.Ala242Gly missense_variant 0.17
kasA 2519140 c.1026G>C synonymous_variant 0.29
kasA 2519143 c.1029G>C synonymous_variant 0.31
eis 2714499 c.834G>T synonymous_variant 0.13
eis 2715000 c.333C>A synonymous_variant 0.12
folC 2746484 p.Phe372Ser missense_variant 0.33
Rv2752c 3064629 c.1563C>T synonymous_variant 0.2
thyA 3074571 c.-100T>C upstream_gene_variant 0.13
ald 3087847 p.Leu343Pro missense_variant 0.14
fbiD 3339725 p.Val203Ala missense_variant 0.33
fprA 3474653 p.Ala216Val missense_variant 0.12
fprA 3474865 p.Ile287Val missense_variant 0.17
Rv3236c 3612591 p.Gly176Cys missense_variant 0.17
Rv3236c 3612931 c.186G>T synonymous_variant 0.18
alr 3841546 c.-126C>A upstream_gene_variant 0.37
ddn 3986737 c.-107G>T upstream_gene_variant 0.14
clpC1 4039645 p.His354Asp missense_variant 0.17
clpC1 4039730 c.975C>G synonymous_variant 0.19
clpC1 4039829 p.Leu292Phe missense_variant 0.14
clpC1 4040144 c.561G>C synonymous_variant 0.33
clpC1 4040429 p.Leu92Phe missense_variant 0.17
clpC1 4040433 p.Ser91Thr missense_variant 0.15
clpC1 4040435 c.270G>C synonymous_variant 0.15
embC 4240801 c.939C>T synonymous_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.18
embB 4246548 p.Pro12Gln missense_variant 0.18
embB 4246555 c.42G>C synonymous_variant 0.38
embB 4246556 p.Ala15Pro missense_variant 0.38
embB 4246563 p.Leu17Trp missense_variant 0.43
embB 4246567 c.54G>T synonymous_variant 0.43
aftB 4268727 p.Thr37Lys missense_variant 0.15
ubiA 4269577 p.Thr86Ile missense_variant 0.14
ethA 4327477 c.-4A>T upstream_gene_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0