TB-Profiler result

Run: ERR2229342
Summary

Run ID: ERR2229342

Sample name:

Date: 31-03-2023 17:05:12

Number of reads: 1656017

Percentage reads mapped: 98.88

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 576482 p.Val379Leu missense_variant 0.21
rpoC 764506 c.1137C>T synonymous_variant 0.12
rpoC 764509 c.1140G>T synonymous_variant 0.12
rpoC 764541 p.Val391Gly missense_variant 0.15
rpoC 764543 p.Thr392Asp missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777173 c.1308C>T synonymous_variant 0.12
mmpL5 777176 p.Glu435Asp missense_variant 0.12
mmpL5 777191 c.1290C>A synonymous_variant 0.12
mmpL5 777196 p.Glu429Gln missense_variant 0.12
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
fabG1 1673346 c.-94C>G upstream_gene_variant 0.13
fabG1 1673349 c.-91G>C upstream_gene_variant 0.13
fabG1 1673380 c.-60C>G upstream_gene_variant 0.23
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102939 p.Arg35Pro missense_variant 0.17
katG 2153970 p.Asp714Glu missense_variant 0.15
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169287 c.1326T>C synonymous_variant 0.13
PPE35 2169293 c.1320T>C synonymous_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 0.74
PPE35 2170053 p.Thr187Ser missense_variant 0.73
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290219 c.-978C>A upstream_gene_variant 0.11
kasA 2518864 c.750G>C synonymous_variant 0.17
eis 2714263 p.Gly357Ala missense_variant 0.11
eis 2714870 p.Gly155Arg missense_variant 0.17
folC 2746223 p.Asp459Val missense_variant 0.12
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
Rv3236c 3612114 p.Glu335Lys missense_variant 0.12
alr 3841546 c.-126C>A upstream_gene_variant 0.14
rpoA 3878599 c.-92C>G upstream_gene_variant 1.0
clpC1 4039730 c.975C>G synonymous_variant 0.13
clpC1 4040394 p.Gly104Val missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244821 p.Gly530Val missense_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.22
embB 4246548 p.Pro12Gln missense_variant 0.47
embB 4246555 c.42G>C synonymous_variant 0.53
embB 4246556 p.Ala15Pro missense_variant 0.53
embB 4246563 p.Leu17Trp missense_variant 0.41
embB 4246567 c.54G>T synonymous_variant 0.47
embB 4247024 p.Pro171Ala missense_variant 0.3
embB 4247028 p.Leu172Arg missense_variant 0.25
embB 4249425 p.Leu971Pro missense_variant 0.12
aftB 4269459 c.-623G>T upstream_gene_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