TB-Profiler result

Run: ERR2229250
Summary

Run ID: ERR2229250

Sample name:

Date: 31-03-2023 16:52:57

Number of reads: 716038

Percentage reads mapped: 99.13

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 6692 p.Ile485Phe missense_variant 0.17
gyrA 7322 c.21G>A synonymous_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
fgd1 491615 p.Glu278Val missense_variant 0.13
fgd1 491705 p.Leu308Pro missense_variant 0.18
mshA 576014 p.Gln223* stop_gained 0.19
mshA 576108 p.Ala254Gly missense_variant 0.33
mshA 576377 p.Asp344Asn missense_variant 0.2
mshA 576784 c.1437C>T synonymous_variant 0.13
rpoB 760520 c.714C>T synonymous_variant 0.15
rpoB 761389 p.Asp528Val missense_variant 0.5
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777655 p.Asp276Tyr missense_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304624 p.Cys565Phe missense_variant 0.17
embR 1416872 p.Val159Ala missense_variant 0.2
embR 1417066 p.Leu94Phe missense_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473736 n.79C>A non_coding_transcript_exon_variant 0.12
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475016 n.1359C>G non_coding_transcript_exon_variant 0.2
rrl 1475044 n.1387G>A non_coding_transcript_exon_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918720 p.His261Tyr missense_variant 0.13
katG 2156169 c.-58A>T upstream_gene_variant 0.13
katG 2156506 c.-395G>C upstream_gene_variant 0.13
PPE35 2167899 p.Gly905Val missense_variant 0.29
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169570 p.Ser348Asn missense_variant 0.15
PPE35 2169573 p.Phe347Tyr missense_variant 0.15
PPE35 2169577 p.Asn346Asp missense_variant 0.15
PPE35 2170048 p.Leu189Val missense_variant 0.62
PPE35 2170053 p.Thr187Ser missense_variant 0.62
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223361 c.-197C>T upstream_gene_variant 0.25
pncA 2290054 c.-813G>C upstream_gene_variant 0.13
kasA 2519015 p.Ser301Thr missense_variant 0.25
kasA 2519342 p.Ala410Ser missense_variant 0.22
eis 2715472 c.-140A>T upstream_gene_variant 0.11
ahpC 2726393 c.201G>T synonymous_variant 0.12
thyX 3067267 p.Phe227Val missense_variant 0.33
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
alr 3841444 c.-24G>A upstream_gene_variant 0.13
rpoA 3877557 c.951C>A synonymous_variant 0.15
clpC1 4039442 c.1263A>C synonymous_variant 0.14
clpC1 4039893 p.Lys271Met missense_variant 0.13
clpC1 4040499 p.Gln69Arg missense_variant 0.22
panD 4044211 p.Gly24Val missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244799 p.Val523Leu missense_variant 0.14
embA 4245125 c.1893G>T synonymous_variant 0.13
embB 4246567 c.54_55insT frameshift_variant 0.29
embB 4247028 p.Leu172Arg missense_variant 0.18
aftB 4267078 p.Phe587Ile missense_variant 0.29
ethA 4327554 c.-81G>T upstream_gene_variant 0.22
whiB6 4338261 c.261G>C synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338632 c.-112delG upstream_gene_variant 0.17
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0