TB-Profiler result

Run: ERR2229556

Summary

Run ID: ERR2229556

Sample name:

Date: 31-03-2023 17:18:34

Number of reads: 968702

Percentage reads mapped: 99.46

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 576100 p.Asp251Glu missense_variant 0.23
mshA 576108 p.Ala254Gly missense_variant 0.21
mshA 576113 p.Arg256Gly missense_variant 0.13
mshA 576186 p.Pro280His missense_variant 0.12
ccsA 620184 c.294C>G synonymous_variant 0.17
ccsA 620512 p.Gly208Cys missense_variant 0.12
rpoC 765359 p.Ala664Ser missense_variant 0.12
rpoC 766284 p.Thr972Ile missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775694 c.2787C>T synonymous_variant 0.18
mmpL5 775697 c.2784G>C synonymous_variant 0.18
mmpL5 777978 p.Ala168Glu missense_variant 0.12
mmpS5 778845 p.Ala21Thr missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801241 p.His145Asn missense_variant 0.13
fbiC 1303747 p.Thr273Ala missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.13
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475234 n.1577C>A non_coding_transcript_exon_variant 0.12
rrl 1475236 n.1579A>C non_coding_transcript_exon_variant 0.12
rrl 1476383 n.2728delG non_coding_transcript_exon_variant 0.12
fabG1 1673380 c.-60C>G upstream_gene_variant 0.19
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918034 p.Val32Glu missense_variant 0.15
katG 2154400 p.Arg571Pro missense_variant 0.15
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2168865 p.Thr583Met missense_variant 0.15
PPE35 2169212 p.Ile467Met missense_variant 0.11
PPE35 2170048 p.Leu189Val missense_variant 0.33
PPE35 2170053 p.Thr187Ser missense_variant 0.33
PPE35 2170532 c.81G>C synonymous_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518809 p.Lys232Arg missense_variant 0.19
kasA 2518864 c.750G>C synonymous_variant 0.12
kasA 2519087 p.Ala325Thr missense_variant 0.12
folC 2746772 p.Val276Gly missense_variant 0.22
Rv2752c 3065702 p.Thr164Ser missense_variant 0.15
thyX 3067860 p.Ala29Gly missense_variant 0.12
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
fprA 3474981 c.975C>A synonymous_variant 0.15
Rv3236c 3612717 p.Ala134Thr missense_variant 0.12
alr 3840662 c.759G>C synonymous_variant 0.11
rpoA 3877804 p.Gly235Val missense_variant 0.12
rpoA 3878490 c.18C>G synonymous_variant 0.22
clpC1 4038303 p.Thr801Asn missense_variant 0.11
clpC1 4039645 p.His354Asp missense_variant 0.12
clpC1 4040144 c.561G>C synonymous_variant 0.18
clpC1 4040180 c.525C>T synonymous_variant 0.12
panD 4044156 c.126A>G synonymous_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246548 p.Pro12Gln missense_variant 0.27
embB 4246555 c.42G>C synonymous_variant 0.38
embB 4246556 p.Ala15Pro missense_variant 0.38
embB 4246584 p.Arg24Pro missense_variant 0.44
embB 4246608 p.Ile32Asn missense_variant 0.12
embB 4249537 c.3024A>G synonymous_variant 0.11
ubiA 4269339 c.494delG frameshift_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0