TB-Profiler result

Run: ERR2229372
Summary

Run ID: ERR2229372

Sample name:

Date: 31-03-2023 17:07:41

Number of reads: 1321881

Percentage reads mapped: 98.97

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
fgd1 491340 c.558C>G synonymous_variant 0.17
mshA 576108 p.Ala254Gly missense_variant 0.46
mshA 576775 c.1428C>T synonymous_variant 0.2
ccsA 619730 c.-161A>G upstream_gene_variant 0.15
rpoB 761152 p.Leu449Gln missense_variant 0.18
rpoC 765687 p.Ala773Glu missense_variant 0.12
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
fbiC 1303848 p.Phe306Leu missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473928 n.271T>G non_coding_transcript_exon_variant 0.1
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673380 c.-60C>G upstream_gene_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103215 c.-173C>A upstream_gene_variant 0.12
ndh 2103221 c.-179C>A upstream_gene_variant 0.12
ndh 2103228 c.-186A>C upstream_gene_variant 0.12
katG 2155993 p.Pro40Arg missense_variant 0.12
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169278 c.1335T>C synonymous_variant 0.11
PPE35 2169281 c.1332T>G synonymous_variant 0.11
PPE35 2169902 c.711G>C synonymous_variant 0.13
PPE35 2169910 p.Asn235Tyr missense_variant 0.17
PPE35 2170048 p.Leu189Val missense_variant 0.61
PPE35 2170053 p.Thr187Ser missense_variant 0.59
PPE35 2170372 p.Thr81Ala missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518197 p.Asp28Ala missense_variant 0.12
kasA 2518200 p.Ile29Asn missense_variant 0.12
kasA 2518201 c.88delG frameshift_variant 0.12
kasA 2518218 p.Gly35Ala missense_variant 0.11
kasA 2518226 p.Ala38Ser missense_variant 0.12
kasA 2519140 c.1026G>C synonymous_variant 0.12
kasA 2519143 c.1029G>C synonymous_variant 0.13
folC 2746244 p.Ala452Gly missense_variant 0.11
pepQ 2859968 p.Asp151Tyr missense_variant 0.17
ribD 2987346 p.Pro170Ser missense_variant 0.11
fbiD 3339417 p.Glu100Asp missense_variant 0.12
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
rpoA 3878491 p.Arg6His missense_variant 0.12
rpoA 3878639 c.-132C>G upstream_gene_variant 0.67
clpC1 4039003 p.Asn568Asp missense_variant 0.17
clpC1 4039730 c.975C>G synonymous_variant 0.15
embC 4241662 c.1800G>T synonymous_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.33
embB 4246548 p.Pro12Gln missense_variant 0.36
embB 4246555 c.42G>C synonymous_variant 0.38
embB 4246556 p.Ala15Pro missense_variant 0.38
embB 4246563 p.Leu17Trp missense_variant 0.27
embB 4246567 c.54G>T synonymous_variant 0.21
aftB 4268619 p.Val73Gly missense_variant 0.33
ethR 4326970 c.-579G>T upstream_gene_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