TB-Profiler result

Run: ERR2229194
Summary

Run ID: ERR2229194

Sample name:

Date: 31-03-2023 16:48:20

Number of reads: 1422838

Percentage reads mapped: 99.21

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 576108 p.Ala254Gly missense_variant 0.2
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 1474576 n.919T>A non_coding_transcript_exon_variant 0.14
rrl 1474996 n.1339C>G non_coding_transcript_exon_variant 0.13
rrl 1476410 n.2753C>A non_coding_transcript_exon_variant 0.12
fabG1 1673346 c.-94C>G upstream_gene_variant 0.24
fabG1 1673349 c.-91G>C upstream_gene_variant 0.23
fabG1 1673357 c.-83G>A upstream_gene_variant 0.18
fabG1 1673359 c.-81T>C upstream_gene_variant 0.18
fabG1 1673361 c.-79C>G upstream_gene_variant 0.18
fabG1 1673380 c.-60C>G upstream_gene_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167745 p.Thr956Arg missense_variant 0.16
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.47
PPE35 2170053 p.Thr187Ser missense_variant 0.54
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518606 c.492G>C synonymous_variant 0.12
kasA 2518609 p.Met165Ile missense_variant 0.12
thyX 3067538 c.408C>A synonymous_variant 0.12
alr 3841612 c.-193_-192insC upstream_gene_variant 0.16
clpC1 4040144 c.561G>C synonymous_variant 0.17
embC 4242330 p.Glu823Gly missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245613 p.Asn794Thr missense_variant 0.15
embA 4246176 p.Ala982Ser missense_variant 0.2
embB 4246548 p.Pro12Gln missense_variant 0.2
embB 4246555 c.42G>C synonymous_variant 0.2
embB 4246556 p.Ala15Pro missense_variant 0.2
embB 4246567 c.54_55insT frameshift_variant 0.18
ethA 4327053 p.Tyr141His missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0