TB-Profiler result

Run: ERR2229426
Summary

Run ID: ERR2229426

Sample name:

Date: 31-03-2023 17:10:32

Number of reads: 1253449

Percentage reads mapped: 99.15

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 2155331 c.780delC frameshift_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 7362 p.Glu21Gln missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.22
mshA 576763 p.Trp472Cys missense_variant 0.14
ccsA 620375 p.Pro162Gln missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775741 c.2740C>T synonymous_variant 0.18
mmpL5 775871 c.2610C>T synonymous_variant 0.13
mmpL5 775874 c.2607C>A synonymous_variant 0.13
mmpL5 777119 p.His454Gln missense_variant 0.14
mmpL5 777122 c.1359C>T synonymous_variant 0.14
mmpL5 777128 c.1353A>G synonymous_variant 0.14
mmpL5 778201 p.Val94Leu missense_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1406501 c.840G>T synonymous_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1476084 n.2427G>C non_coding_transcript_exon_variant 0.11
fabG1 1673346 c.-94C>G upstream_gene_variant 0.11
fabG1 1673380 c.-60C>G upstream_gene_variant 0.16
inhA 1674646 p.Phe149Leu missense_variant 0.14
inhA 1674664 p.Met155Leu missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102444 p.Ala200Val missense_variant 0.2
katG 2156403 c.-292A>C upstream_gene_variant 0.11
PPE35 2167865 c.2748G>C synonymous_variant 0.16
PPE35 2167868 c.2745A>C synonymous_variant 0.16
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169397 p.Gly406Ser missense_variant 0.13
PPE35 2169575 c.1038C>T synonymous_variant 0.24
PPE35 2169581 c.1032C>G synonymous_variant 0.24
PPE35 2169902 p.Leu237Phe missense_variant 0.24
PPE35 2170048 p.Leu189Val missense_variant 0.44
PPE35 2170053 p.Thr187Ser missense_variant 0.47
PPE35 2170392 p.Gly74Ala missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2747510 p.Val30Ala missense_variant 0.2
pepQ 2859535 p.Gly295Val missense_variant 0.2
ribD 2986788 c.-50delA upstream_gene_variant 0.11
thyX 3067340 c.606G>A synonymous_variant 0.15
fprA 3474144 p.Trp46Cys missense_variant 0.12
fprA 3474165 c.159C>G synonymous_variant 0.14
fprA 3474186 c.180C>A synonymous_variant 0.17
alr 3841546 c.-126C>A upstream_gene_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243986 p.Leu252Ile missense_variant 0.12
embA 4244821 p.Gly530Val missense_variant 1.0
embA 4245813 p.Pro861Thr missense_variant 0.18
embB 4246544 p.Thr11Pro missense_variant 0.11
embB 4246555 c.42G>C synonymous_variant 0.17
embB 4246556 p.Ala15Pro missense_variant 0.18
embB 4246563 p.Leu17Trp missense_variant 0.2
embB 4246567 c.54G>T synonymous_variant 0.18
embB 4246584 p.Arg24Pro missense_variant 0.17
aftB 4269342 c.-506G>T upstream_gene_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0