TB-Profiler result

Run: ERR2229543
Summary

Run ID: ERR2229543

Sample name:

Date: 31-03-2023 17:18:18

Number of reads: 1410811

Percentage reads mapped: 99.47

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
tlyA 1918050 c.113delC frameshift_variant 0.12 capreomycin
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
ccsA 620038 p.Pro50Ser missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776145 p.Ala779Asp missense_variant 0.11
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 1473977 n.320G>T non_coding_transcript_exon_variant 0.13
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673346 c.-94C>G upstream_gene_variant 0.13
fabG1 1673349 c.-91G>C upstream_gene_variant 0.13
fabG1 1673359 c.-81T>C upstream_gene_variant 0.12
fabG1 1673361 c.-79C>G upstream_gene_variant 0.12
fabG1 1673380 c.-60C>G upstream_gene_variant 0.31
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169902 c.711G>C synonymous_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 0.41
PPE35 2170053 p.Thr187Ser missense_variant 0.44
PPE35 2170392 p.Gly74Ala missense_variant 0.12
PPE35 2170400 c.213G>C synonymous_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518596 p.Arg161Leu missense_variant 0.18
kasA 2518603 c.489G>A synonymous_variant 0.18
kasA 2518606 c.492G>C synonymous_variant 0.2
kasA 2518609 p.Met165Ile missense_variant 0.2
kasA 2518635 p.Gly174Asp missense_variant 0.17
kasA 2518864 c.750G>C synonymous_variant 0.17
eis 2714151 c.1182T>A synonymous_variant 0.14
fbiD 3339736 p.Thr207Pro missense_variant 0.2
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
fprA 3474288 c.282C>A synonymous_variant 0.16
embA 4242481 c.-752C>A upstream_gene_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244286 p.Gly352Ser missense_variant 0.12
embA 4245567 p.Glu779* stop_gained 0.15
embB 4246544 p.Thr11Pro missense_variant 0.33
embB 4246548 p.Pro12Gln missense_variant 0.33
embB 4246555 c.42G>C synonymous_variant 0.38
embB 4246556 p.Ala15Pro missense_variant 0.38
embB 4246563 p.Leu17Trp missense_variant 0.33
embB 4246567 c.54G>T synonymous_variant 0.3
embB 4246584 p.Arg24Pro missense_variant 0.25
embB 4247028 p.Leu172Arg missense_variant 0.24
aftB 4268652 p.Ala62Glu 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