TB-Profiler result

Run: ERR2229634

Summary

Run ID: ERR2229634

Sample name:

Date: 31-03-2023 17:22:52

Number of reads: 707414

Percentage reads mapped: 99.13

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 575521 c.174A>T synonymous_variant 0.2
rpoB 759921 p.Arg39Cys missense_variant 0.12
rpoB 760375 p.Asp190Val missense_variant 0.29
rpoB 762177 p.Arg791Cys missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775867 p.Arg872Cys missense_variant 0.17
mmpL5 776155 c.2325delC frameshift_variant 0.18
mmpL5 777119 p.His454Gln missense_variant 0.25
mmpL5 777122 c.1359C>T synonymous_variant 0.25
mmpL5 777128 c.1353A>G synonymous_variant 0.12
mmpL5 777202 p.Ala427Thr missense_variant 0.12
mmpL5 777348 p.Gly378Val missense_variant 0.18
mmpL5 777491 c.990G>T synonymous_variant 0.2
mmpL5 777732 p.Leu250Pro missense_variant 0.17
mmpR5 779195 p.Thr69Ile missense_variant 0.15
mmpS5 779662 c.-757G>A upstream_gene_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1305019 p.Ala697Thr missense_variant 0.22
Rv1258c 1407201 p.Val47Glu missense_variant 0.12
embR 1416842 p.Asp169Val missense_variant 0.15
embR 1417176 p.Ala58Ser missense_variant 0.11
embR 1417281 p.Ile23Val missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472961 n.1116T>C non_coding_transcript_exon_variant 0.11
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1476275 n.2618T>A non_coding_transcript_exon_variant 0.17
rrl 1476686 n.3029C>T non_coding_transcript_exon_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918742 p.Pro268Gln missense_variant 0.13
ndh 2102882 p.Leu54Pro missense_variant 0.22
katG 2154516 c.1596G>C synonymous_variant 0.11
PPE35 2167965 p.Ala883Gly missense_variant 0.21
PPE35 2167967 c.2646A>C synonymous_variant 0.21
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169725 c.888T>C synonymous_variant 0.17
PPE35 2169902 p.Leu237Phe missense_variant 0.14
PPE35 2169910 p.Asn235Tyr missense_variant 0.19
PPE35 2170048 p.Leu189Val missense_variant 0.59
PPE35 2170053 p.Thr187Ser missense_variant 0.58
PPE35 2170147 p.Ser156Ala missense_variant 0.16
Rv1979c 2221878 c.1287A>T synonymous_variant 0.14
Rv1979c 2221907 p.Val420Ile missense_variant 0.12
Rv1979c 2222641 p.Ser175Leu missense_variant 0.18
Rv1979c 2222930 p.Tyr79His missense_variant 0.12
Rv1979c 2223137 p.Ala10Pro missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518884 p.Arg257His missense_variant 0.18
kasA 2519140 c.1026G>C synonymous_variant 0.14
kasA 2519143 c.1029G>C synonymous_variant 0.17
eis 2714699 p.Arg212Cys missense_variant 0.33
ahpC 2726155 c.-38A>G upstream_gene_variant 0.11
ahpC 2726615 p.Asn141Lys missense_variant 0.18
folC 2746442 p.Asp386Gly missense_variant 0.25
folC 2747663 c.-65C>A upstream_gene_variant 0.22
pepQ 2859621 c.797delC frameshift_variant 0.18
Rv2752c 3065612 p.Thr194Ala missense_variant 0.4
fprA 3474313 p.Ala103Ser missense_variant 0.13
fprA 3474796 p.His264Asn missense_variant 0.12
fprA 3474931 p.Glu309* stop_gained 0.12
fprA 3475285 p.Asp427Tyr missense_variant 0.15
whiB7 3568581 c.99G>A synonymous_variant 0.12
Rv3236c 3612247 p.Met290Ile missense_variant 0.22
alr 3840344 c.1077A>G synonymous_variant 0.12
alr 3841546 c.-126C>A upstream_gene_variant 0.5
rpoA 3878438 p.Glu24Lys missense_variant 0.12
clpC1 4038340 p.Ile789Val missense_variant 0.12
clpC1 4039221 p.Pro495Leu missense_variant 0.12
clpC1 4039645 p.His354Asp missense_variant 0.18
clpC1 4039654 p.Thr351Ser missense_variant 0.12
clpC1 4040001 p.His235Ala missense_variant 0.15
clpC1 4040010 p.Ala232Arg missense_variant 0.15
embC 4240472 p.Leu204Val missense_variant 0.14
embC 4240566 p.Ile235Asn missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242791 p.Ala977Ser missense_variant 0.18
embA 4244718 p.Tyr496His missense_variant 0.17
embA 4245537 p.Pro769Ser missense_variant 0.15
embB 4248131 p.Arg540Cys missense_variant 0.14
aftB 4268483 c.354T>C synonymous_variant 0.11
whiB6 4338374 p.Lys50Glu missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0