TB-Profiler result

Run: ERR2229486

Summary

Run ID: ERR2229486

Sample name:

Date: 31-03-2023 17:14:29

Number of reads: 573095

Percentage reads mapped: 99.37

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
ethA 4326426 c.1047delT frameshift_variant 0.17 ethionamide, ethionamide
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 6103 p.Glu288Asp missense_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
rpoB 761059 p.Val418Asp missense_variant 0.33
rpoB 762436 p.Asp877Val missense_variant 0.29
rpoB 763256 c.3451delC frameshift_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775782 p.Leu900Pro missense_variant 0.29
mmpL5 777482 c.999G>A synonymous_variant 0.16
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781529 c.-31C>T upstream_gene_variant 0.17
fbiC 1303734 c.804C>A synonymous_variant 0.2
fbiC 1303747 p.Thr273Ala missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.15
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.18
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.18
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.2
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.2
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.2
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.17
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.17
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.18
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.18
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.18
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.2
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.2
rrl 1476483 n.2826G>A non_coding_transcript_exon_variant 0.2
fabG1 1673357 c.-83G>A upstream_gene_variant 0.2
fabG1 1673359 c.-81T>C upstream_gene_variant 0.2
fabG1 1673361 c.-79C>G upstream_gene_variant 0.19
fabG1 1673380 c.-60C>G upstream_gene_variant 0.44
fabG1 1673825 p.Arg129Leu missense_variant 0.18
inhA 1674472 p.Val91Leu missense_variant 0.18
rpsA 1833567 p.Pro9Leu missense_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918034 p.Val32Gly missense_variant 0.67
ndh 2102875 c.168C>T synonymous_variant 0.14
ndh 2103206 c.-164T>C upstream_gene_variant 0.11
PPE35 2167955 c.2658A>C synonymous_variant 0.22
PPE35 2167965 p.Ala883Gly missense_variant 0.22
PPE35 2167967 c.2646A>C synonymous_variant 0.22
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2168803 p.Gly604* stop_gained 0.12
PPE35 2169091 p.Val508Leu missense_variant 0.17
PPE35 2169278 c.1335T>C synonymous_variant 0.17
PPE35 2169281 c.1332T>G synonymous_variant 0.17
PPE35 2169717 p.Asn299Ile missense_variant 0.24
PPE35 2169725 c.888T>C synonymous_variant 0.26
PPE35 2169902 c.711G>C synonymous_variant 0.12
PPE35 2169939 p.Gly225Ala missense_variant 0.11
PPE35 2169947 c.666T>C synonymous_variant 0.11
PPE35 2170048 p.Leu189Val missense_variant 0.54
PPE35 2170053 p.Thr187Ser missense_variant 0.57
PPE35 2170232 c.381T>A synonymous_variant 0.2
PPE35 2170430 p.Ser61Ala missense_variant 0.12
PPE35 2170434 p.Arg60Pro missense_variant 0.12
PPE35 2170440 p.Gln58Ser missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518873 p.His253Gln missense_variant 0.17
eis 2714498 p.Leu279Ile missense_variant 0.25
Rv2752c 3065342 p.Ser284Thr missense_variant 0.2
thyX 3067744 p.Gly68Arg missense_variant 0.12
thyA 3074648 c.-177T>G upstream_gene_variant 0.29
fbiB 3641668 p.Val45Ala missense_variant 0.29
fbiB 3642650 c.1118dupT frameshift_variant 0.17
alr 3840569 c.852G>T synonymous_variant 0.22
alr 3840637 p.Pro262Ser missense_variant 0.12
alr 3840899 c.522C>A synonymous_variant 0.21
alr 3841546 c.-126C>A upstream_gene_variant 0.16
rpoA 3878469 c.39C>G synonymous_variant 0.25
ddn 3986829 c.-15G>T upstream_gene_variant 0.22
clpC1 4039051 p.Ala552Thr missense_variant 0.18
clpC1 4039153 p.Ile518Val missense_variant 0.11
clpC1 4039161 p.His515Gly missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242782 p.Val974Leu missense_variant 0.29
embA 4244031 p.Ile267Val missense_variant 0.29
embB 4246544 p.Thr11Pro missense_variant 0.19
embB 4246548 p.Pro12Gln missense_variant 0.31
embB 4246555 c.42G>C synonymous_variant 0.33
embB 4246556 p.Ala15Pro missense_variant 0.33
aftB 4267415 c.1422G>T synonymous_variant 0.12
ubiA 4269134 p.Gly234Arg missense_variant 0.13
ethR 4326982 c.-567C>G upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408249 c.-47T>A upstream_gene_variant 0.33