TB-Profiler result

Run: ERR2515596
Summary

Run ID: ERR2515596

Sample name:

Date: 31-03-2023 21:01:00

Number of reads: 568900

Percentage reads mapped: 99.64

Strain: lineage4.1.2

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 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
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491487 p.Tyr235* stop_gained 0.12
mshA 576602 c.1258delG frameshift_variant 0.12
ccsA 619728 c.-163C>T upstream_gene_variant 0.15
rpoB 762720 p.Asp972Asn missense_variant 0.12
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766365 p.Ala999Asp missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 779425 p.Met146Leu missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305398 p.Glu823Gly missense_variant 0.1
Rv1258c 1407316 p.Ala9Ser missense_variant 0.11
embR 1417140 p.Ala70Ser missense_variant 1.0
embR 1417505 c.-158G>T upstream_gene_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473589 n.-69C>T upstream_gene_variant 0.15
rrl 1475022 n.1365T>C non_coding_transcript_exon_variant 0.11
rrl 1475260 n.1608delG non_coding_transcript_exon_variant 0.22
rrl 1476135 n.2478T>A non_coding_transcript_exon_variant 0.17
fabG1 1673249 c.-191C>T upstream_gene_variant 1.0
inhA 1673526 c.-676G>A upstream_gene_variant 0.18
fabG1 1674182 c.743G>T stop_lost&splice_region_variant 0.18
inhA 1674717 p.Asn172Lys missense_variant 0.11
rpsA 1834964 c.1428delA frameshift_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918285 p.Gly116Ser missense_variant 1.0
ndh 2102185 c.858C>A synonymous_variant 0.11
ndh 2102656 p.Asp129Glu missense_variant 0.1
katG 2155269 c.843C>A synonymous_variant 0.11
katG 2156507 c.-396T>A upstream_gene_variant 0.13
PPE35 2167744 p.Gly957Ser missense_variant 0.14
PPE35 2168044 p.Ala857Ser missense_variant 0.2
PPE35 2168696 c.1917C>T synonymous_variant 0.11
Rv1979c 2223269 c.-105G>T upstream_gene_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518098 c.-16delT upstream_gene_variant 0.12
kasA 2519155 c.1041C>T synonymous_variant 0.14
ahpC 2726516 c.324C>T synonymous_variant 0.12
folC 2746660 c.938delT frameshift_variant 0.29
folC 2746803 c.796C>T synonymous_variant 0.13
folC 2747022 p.Val193Ile missense_variant 1.0
Rv2752c 3066159 c.33G>T synonymous_variant 0.12
thyX 3067397 c.549C>A synonymous_variant 0.11
thyX 3067839 p.Val36Asp missense_variant 0.12
thyX 3068102 c.-157T>C upstream_gene_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086851 p.Asn11Thr missense_variant 0.13
Rv3083 3448894 p.Tyr131Asp missense_variant 1.0
Rv3083 3449642 p.Asn380Ser missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612211 c.906A>T synonymous_variant 0.14
Rv3236c 3612234 c.883C>T synonymous_variant 0.12
Rv3236c 3612256 c.861C>T synonymous_variant 0.13
fbiA 3641164 p.Ile208Val missense_variant 1.0
alr 3841347 p.Met25Thr missense_variant 0.11
clpC1 4038411 p.Asp765Gly missense_variant 0.1
embC 4241749 c.1889delT frameshift_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4246258 p.Pro1009Arg missense_variant 0.1
embB 4248541 c.2028T>C synonymous_variant 0.11
embB 4249289 p.Pro926Ala missense_variant 0.11
embB 4249529 c.3017delT frameshift_variant 0.13
aftB 4267452 p.Leu462Pro missense_variant 0.12
aftB 4268861 c.-25T>C upstream_gene_variant 1.0
ethR 4327117 c.-432G>A upstream_gene_variant 0.11
ethR 4327438 c.-111A>G upstream_gene_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0