TB-Profiler result

Run: ERR2229606
Summary

Run ID: ERR2229606

Sample name:

Date: 31-03-2023 17:21:14

Number of reads: 1004548

Percentage reads mapped: 99.28

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 0.97
gyrA 7837 p.Gly179Val missense_variant 0.13
fgd1 491030 p.Pro83His missense_variant 0.12
mshA 576108 p.Ala254Gly missense_variant 0.33
ccsA 619806 c.-85G>A upstream_gene_variant 0.12
ccsA 620311 p.Leu141Met missense_variant 0.15
rpoC 766790 p.Val1141Phe missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775945 p.Val846Phe missense_variant 0.18
mmpL5 776261 c.2220C>G synonymous_variant 0.22
mmpL5 776291 c.2190G>T synonymous_variant 0.14
mmpL5 776305 p.Pro726Thr missense_variant 0.12
mmpL5 777696 p.Ala262Glu missense_variant 0.12
mmpL5 777720 p.Arg254Gln missense_variant 0.15
mmpL5 777983 c.498G>T synonymous_variant 0.14
mmpL5 778952 c.-472T>C upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304381 p.Ala484Val missense_variant 0.12
embR 1417000 c.348T>C synonymous_variant 0.15
embR 1417095 p.Gly85Ser missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473062 n.1217T>C non_coding_transcript_exon_variant 0.1
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474785 n.1128T>C non_coding_transcript_exon_variant 0.14
fabG1 1673380 c.-60C>G upstream_gene_variant 0.14
fabG1 1674047 p.Leu203Pro missense_variant 0.13
inhA 1674639 c.438C>G synonymous_variant 0.15
rpsA 1834682 p.Ala381Ser missense_variant 0.12
rpsA 1834699 p.Glu386Asp missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102358 p.Gly229Cys missense_variant 0.2
PPE35 2167965 p.Ala883Gly missense_variant 0.12
PPE35 2167967 c.2646A>C synonymous_variant 0.12
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169902 p.Leu237Phe missense_variant 0.16
PPE35 2169910 p.Asn235Tyr missense_variant 0.15
PPE35 2170048 p.Leu189Val missense_variant 0.6
PPE35 2170053 p.Thr187Ser missense_variant 0.53
Rv1979c 2222066 c.1099C>T synonymous_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289481 c.-240G>T upstream_gene_variant 0.12
pncA 2289921 c.-680A>G upstream_gene_variant 0.14
folC 2747402 p.Ser66* stop_gained 0.13
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
Rv3083 3448500 c.-4A>G upstream_gene_variant 1.0
Rv3083 3448501 c.-3G>T upstream_gene_variant 1.0
whiB7 3568428 c.252A>G synonymous_variant 0.22
Rv3236c 3612150 c.966delG frameshift_variant 0.15
fbiB 3642375 p.Ala281Thr missense_variant 0.13
alr 3841546 c.-126C>A upstream_gene_variant 0.34
clpC1 4038603 p.Leu701Arg missense_variant 0.2
clpC1 4039003 p.Asn568Asp missense_variant 0.14
clpC1 4040144 c.561G>C synonymous_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245215 c.1983A>G synonymous_variant 0.18
embB 4247395 c.882C>T synonymous_variant 0.13
embB 4249710 p.Lys1066Met missense_variant 0.33
aftB 4267787 c.1050G>T synonymous_variant 0.2
ethA 4326017 p.Pro486Gln missense_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448508 c.6_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0