TB-Profiler result

Run: ERR2229508
Summary

Run ID: ERR2229508

Sample name:

Date: 31-03-2023 17:16:17

Number of reads: 1090949

Percentage reads mapped: 99.38

Strain: lineage4.8

Drug-resistance: HR-TB

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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
katG 2155276 p.Gly279Asp missense_variant 0.12 isoniazid
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 7322 c.23delC frameshift_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7908 c.610delG frameshift_variant 0.14
mshA 575160 c.-187delT upstream_gene_variant 0.14
mshA 575772 c.427delC frameshift_variant 0.17
mshA 576052 c.705C>A synonymous_variant 0.15
mshA 576108 p.Ala254Gly missense_variant 0.33
mshA 576622 c.1275C>A synonymous_variant 0.12
rpoC 762377 c.-993C>T upstream_gene_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776192 c.2289G>T synonymous_variant 0.22
mmpS5 778822 p.Ile28Met missense_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801153 c.345G>T synonymous_variant 0.15
fbiC 1303747 p.Thr273Ala missense_variant 1.0
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 0.2
fabG1 1673349 c.-91G>C upstream_gene_variant 0.21
fabG1 1673359 c.-81T>C upstream_gene_variant 0.13
fabG1 1673361 c.-79C>G upstream_gene_variant 0.13
fabG1 1673380 c.-60C>G upstream_gene_variant 0.27
rpsA 1834567 c.1026C>T synonymous_variant 0.12
rpsA 1834595 p.Asp352Asn missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167814 c.2799C>T synonymous_variant 0.14
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.43
PPE35 2170053 p.Thr187Ser missense_variant 0.43
PPE35 2170147 p.Ser156Ala missense_variant 0.19
PPE35 2170159 p.Ala152Ser missense_variant 0.18
PPE35 2170169 c.444A>G synonymous_variant 0.1
PPE35 2170175 c.438G>C synonymous_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289474 c.-233C>T upstream_gene_variant 0.12
kasA 2519140 c.1026G>C synonymous_variant 0.14
kasA 2519143 c.1029G>C synonymous_variant 0.14
eis 2714267 p.Leu356Met missense_variant 0.14
folC 2746214 p.Ser462* stop_gained 0.29
folC 2746607 p.Ala331Val missense_variant 0.22
folC 2747022 p.Val193Phe missense_variant 0.12
fbiD 3339523 c.406C>A synonymous_variant 0.15
fbiD 3339680 p.Asp188Gly missense_variant 0.14
whiB7 3568428 c.252A>G synonymous_variant 0.22
Rv3236c 3613142 c.-26A>G upstream_gene_variant 0.11
fbiB 3641665 p.Asp44Val missense_variant 0.12
fbiB 3641932 p.Arg133His missense_variant 0.12
alr 3841546 c.-126C>A upstream_gene_variant 0.16
clpC1 4039314 p.Arg464His missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243443 p.Asp71Asn missense_variant 0.12
embB 4246544 p.Thr11Pro missense_variant 0.5
embB 4246548 p.Pro12Gln missense_variant 0.4
embB 4246555 c.42G>C synonymous_variant 0.57
embB 4246556 p.Ala15Pro missense_variant 0.57
embB 4246563 p.Leu17Trp missense_variant 0.5
embB 4246567 c.54G>T synonymous_variant 0.5
embB 4246801 c.288G>T synonymous_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0