TB-Profiler result

Run: ERR2229079
Summary

Run ID: ERR2229079

Sample name:

Date: 31-03-2023 16:36:53

Number of reads: 1470979

Percentage reads mapped: 99.34

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 4326005 c.1468delT frameshift_variant&stop_lost&splice_region_variant 0.17 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.23
mshA 576113 p.Arg256Gly missense_variant 0.18
mshA 576482 p.Val379Leu missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
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 1474008 n.351G>T non_coding_transcript_exon_variant 0.17
fabG1 1673380 c.-60C>G upstream_gene_variant 0.15
inhA 1674659 p.Arg153Gln missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169322 c.1291T>C synonymous_variant 0.1
PPE35 2169323 c.1290C>G synonymous_variant 0.1
PPE35 2170048 p.Leu189Val missense_variant 0.45
PPE35 2170053 p.Thr187Ser missense_variant 0.41
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714836 p.Val166Asp missense_variant 0.12
thyX 3067340 c.606G>A synonymous_variant 0.17
fbiD 3339531 p.Ser138Arg missense_variant 0.12
fbiD 3339734 p.Ala206Gly missense_variant 0.57
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
whiB7 3568431 c.249C>A synonymous_variant 0.18
Rv3236c 3613124 c.-8C>A upstream_gene_variant 0.2
alr 3841546 c.-126C>A upstream_gene_variant 0.27
clpC1 4039714 p.Tyr331His missense_variant 0.1
embA 4242436 c.-797G>T upstream_gene_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243569 p.Thr113Ala missense_variant 0.11
embB 4246544 p.Thr11Pro missense_variant 0.25
embB 4246548 p.Pro12Gln missense_variant 0.25
embB 4246555 c.42G>C synonymous_variant 0.25
embB 4246556 p.Ala15Pro missense_variant 0.22
embB 4246563 p.Leu17Trp missense_variant 0.2
embB 4246567 c.54G>T synonymous_variant 0.18
embB 4247095 c.582G>T synonymous_variant 0.14
embB 4247192 p.Val227Leu missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0