TB-Profiler result

Run: ERR2229362
Summary

Run ID: ERR2229362

Sample name:

Date: 31-03-2023 17:06:18

Number of reads: 1225400

Percentage reads mapped: 91.51

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
gyrB 7145 p.Val636Leu missense_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.25
mshA 576427 c.1080G>A synonymous_variant 0.22
ccsA 620158 p.Leu90Ile missense_variant 0.13
ccsA 620473 c.583C>T synonymous_variant 0.13
rpoC 765415 c.2046G>A synonymous_variant 0.11
rpoC 765935 p.Ala856Thr missense_variant 0.12
rpoC 766783 c.3414C>A synonymous_variant 0.17
rpoC 766852 p.Met1161Ile missense_variant 0.18
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 1303801 p.Ile291Phe missense_variant 0.12
Rv1258c 1406544 p.Ala266Glu missense_variant 0.17
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 0.14
fabG1 1673349 c.-91G>C upstream_gene_variant 0.14
fabG1 1673359 c.-81T>C upstream_gene_variant 0.11
fabG1 1673361 c.-79C>G upstream_gene_variant 0.11
fabG1 1673380 c.-60C>G upstream_gene_variant 0.31
rpsA 1834735 c.1194C>T synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918050 c.111G>T synonymous_variant 0.13
ndh 2102718 p.Gln109Lys missense_variant 0.15
katG 2153896 p.Val739Ala missense_variant 0.15
katG 2154298 p.Pro605Gln missense_variant 0.13
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169191 c.1422G>C synonymous_variant 0.12
PPE35 2169394 p.Ala407Thr missense_variant 0.14
PPE35 2169902 p.Leu237Phe missense_variant 0.22
PPE35 2169910 p.Asn235Tyr missense_variant 0.15
PPE35 2170048 p.Leu189Val missense_variant 0.74
PPE35 2170053 p.Thr187Ser missense_variant 0.79
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289917 c.-676G>T upstream_gene_variant 0.12
kasA 2519140 c.1026G>C synonymous_variant 0.16
kasA 2519143 c.1029G>C synonymous_variant 0.2
Rv2752c 3064993 p.Trp400* stop_gained 0.2
fprA 3474063 c.57G>A synonymous_variant 0.12
fprA 3474330 c.324C>G synonymous_variant 0.25
Rv3236c 3613197 c.-81G>A upstream_gene_variant 0.12
fbiB 3641779 p.Ala82Glu missense_variant 0.12
alr 3841546 c.-126C>A upstream_gene_variant 0.15
clpC1 4040144 c.561G>C synonymous_variant 0.15
clpC1 4040457 c.247delC frameshift_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245882 p.Gly884Ser missense_variant 0.12
embA 4246153 p.Ala974Val missense_variant 0.15
embB 4246544 p.Thr11Pro missense_variant 0.33
embB 4246548 p.Pro12Gln missense_variant 0.38
embB 4246555 c.42G>C synonymous_variant 0.35
embB 4246556 p.Ala15Pro missense_variant 0.35
embB 4247472 p.Phe320Tyr missense_variant 0.14
ethR 4326961 c.-588G>C upstream_gene_variant 0.12
ethA 4327351 p.Met41Ile missense_variant 0.13
ethA 4327395 p.Cys27Ser missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0