TB-Profiler result

Run: ERR2229544
Summary

Run ID: ERR2229544

Sample name:

Date: 31-03-2023 17:18:09

Number of reads: 961522

Percentage reads mapped: 99.44

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
gyrA 7459 p.Arg53Leu missense_variant 0.17
mshA 576108 p.Ala254Gly missense_variant 0.33
mshA 576293 c.948delC frameshift_variant 0.11
ccsA 620007 c.117T>A synonymous_variant 0.14
rpoB 762353 c.2547C>A synonymous_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775736 c.2745C>G synonymous_variant 0.13
mmpL5 775741 c.2740C>T synonymous_variant 0.14
mmpL5 776009 c.2472A>G synonymous_variant 0.13
mmpL5 776172 p.Asp770Val missense_variant 0.13
mmpL5 777122 c.1359C>T synonymous_variant 0.12
mmpL5 777157 c.1324C>A synonymous_variant 0.17
mmpL5 777164 c.1317C>T synonymous_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304285 p.Ala452Val missense_variant 0.17
fbiC 1304465 p.Gly512Val missense_variant 0.4
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673380 c.-60C>G upstream_gene_variant 0.3
rpsA 1834117 p.Glu192Asp missense_variant 0.17
tlyA 1917893 c.-47G>T upstream_gene_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918057 p.Val40Leu missense_variant 0.18
tlyA 1918168 p.Phe77Leu missense_variant 0.2
katG 2156387 c.-276T>C upstream_gene_variant 0.12
PPE35 2167745 p.Thr956Arg missense_variant 0.37
PPE35 2167865 c.2748G>C synonymous_variant 0.16
PPE35 2167868 c.2745A>C synonymous_variant 0.17
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169278 c.1335T>C synonymous_variant 0.15
PPE35 2169281 c.1332T>G synonymous_variant 0.15
PPE35 2169287 c.1326T>C synonymous_variant 0.18
PPE35 2170048 p.Leu189Val missense_variant 0.5
PPE35 2170053 p.Thr187Ser missense_variant 0.46
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289800 c.-559C>T upstream_gene_variant 0.15
ribD 2987448 p.Glu204* stop_gained 0.15
thyX 3067221 p.Ala242Glu missense_variant 0.12
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 0.18
clpC1 4038773 p.Asp644Glu missense_variant 0.2
clpC1 4038776 p.Glu643Asp missense_variant 0.19
clpC1 4039508 c.1197G>C synonymous_variant 0.22
clpC1 4039645 p.His354Asp missense_variant 0.16
embC 4239752 c.-111T>C upstream_gene_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242839 p.Cys993Arg missense_variant 0.12
embA 4243096 c.-137A>C upstream_gene_variant 0.12
embA 4243248 p.Asn6Asp missense_variant 0.1
embA 4244880 p.Trp550Gly missense_variant 0.14
embB 4246584 p.Arg24Pro missense_variant 0.67
aftB 4268769 p.Gln23Leu missense_variant 0.13
ethR 4328033 p.Ala162Gly missense_variant 0.12
ethA 4328469 c.-996G>A upstream_gene_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0