TB-Profiler result

Run: ERR2229491
Summary

Run ID: ERR2229491

Sample name:

Date: 31-03-2023 17:14:52

Number of reads: 185107

Percentage reads mapped: 98.89

Strain: lineage4.8

Drug-resistance: HR-TB

Download CSV Download TXT Download PDF Download JSON
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 0.06
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 2155529 p.Glu195Lys missense_variant 0.4 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
gyrB 5083 c.-157C>A upstream_gene_variant 0.2
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7804 p.Ser168Asn missense_variant 1.0
gyrA 7999 p.Leu233Pro missense_variant 0.5
gyrA 8165 c.864C>A synonymous_variant 0.5
gyrA 8977 p.Phe559Tyr missense_variant 0.29
fgd1 490816 p.Ala12Thr missense_variant 0.15
mshA 576008 p.Ala221Thr missense_variant 0.4
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775862 c.2619G>T synonymous_variant 1.0
mmpL5 777164 c.1317C>T synonymous_variant 0.4
mmpL5 777173 c.1308C>T synonymous_variant 0.4
mmpL5 777176 p.Glu435Asp missense_variant 0.4
mmpL5 777191 c.1290C>A synonymous_variant 0.4
mmpL5 777196 p.Glu429Gln missense_variant 0.4
mmpL5 777201 c.1279_1280insACTTCATACCCG conservative_inframe_insertion 0.4
mmpL5 777482 c.999G>A synonymous_variant 0.29
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
embR 1416410 p.Leu313Gln missense_variant 0.22
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 0.46
rpsA 1833553 c.12C>T synonymous_variant 0.29
rpsA 1833940 c.399C>T synonymous_variant 0.33
katG 2154162 c.1950C>A synonymous_variant 0.22
katG 2154426 c.1686C>T synonymous_variant 0.18
PPE35 2167919 c.2694T>C synonymous_variant 0.4
PPE35 2168051 p.Val854Ile missense_variant 0.5
PPE35 2168059 p.Gln852Glu missense_variant 0.5
PPE35 2168702 c.1911T>A synonymous_variant 0.12
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169239 c.1374T>C synonymous_variant 0.17
PPE35 2169293 c.1320T>C synonymous_variant 0.2
PPE35 2169308 c.1305C>T synonymous_variant 0.29
PPE35 2169322 c.1291T>C synonymous_variant 0.29
PPE35 2169323 c.1290C>G synonymous_variant 0.29
PPE35 2169326 c.1287C>T synonymous_variant 0.22
PPE35 2169351 p.Ala421Ser missense_variant 0.2
PPE35 2169368 c.1245A>C synonymous_variant 0.2
PPE35 2169371 c.1242A>C synonymous_variant 0.2
PPE35 2169379 p.Phe412Ile missense_variant 0.2
PPE35 2169380 p.Trp411Ser missense_variant 0.2
PPE35 2169596 c.1017T>C synonymous_variant 0.17
PPE35 2169602 c.1011C>A synonymous_variant 0.15
PPE35 2169605 p.Asn336Thr missense_variant 0.15
PPE35 2169608 c.1005C>G synonymous_variant 0.15
PPE35 2169890 c.723C>T synonymous_variant 0.29
PPE35 2169893 c.720C>A synonymous_variant 0.33
PPE35 2169897 p.Ser239Phe missense_variant 0.33
PPE35 2169902 p.Leu237Phe missense_variant 0.33
PPE35 2169910 p.Asn235Tyr missense_variant 0.4
PPE35 2170159 p.Ala152Ser missense_variant 0.4
PPE35 2170164 p.Ala150Val missense_variant 0.4
PPE35 2170169 c.444A>G synonymous_variant 0.4
PPE35 2170175 p.Leu146Ile missense_variant 0.4
PPE35 2170178 c.435T>C synonymous_variant 0.5
PPE35 2170189 p.Glu142Gln missense_variant 0.4
PPE35 2170190 c.423G>A synonymous_variant 0.33
PPE35 2170406 c.207A>G synonymous_variant 0.67
PPE35 2170412 c.201G>C synonymous_variant 0.67
PPE35 2170415 c.198A>G synonymous_variant 0.67
PPE35 2170425 p.Val63Ala missense_variant 0.67
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ribD 2986869 p.Asp11Tyr missense_variant 0.25
ribD 2987114 c.276C>A synonymous_variant 0.67
fprA 3473836 c.-171C>G upstream_gene_variant 0.22
alr 3841501 c.-81G>T upstream_gene_variant 0.14
alr 3841546 c.-126C>A upstream_gene_variant 0.18
clpC1 4039729 p.Asp326Asn missense_variant 0.4
panD 4043937 c.345C>A synonymous_variant 0.5
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247470 c.957T>C synonymous_variant 0.29
embB 4247472 p.Phe320Tyr missense_variant 0.29
aftB 4269768 c.-932C>G upstream_gene_variant 0.5
ethR 4326789 c.-760G>A upstream_gene_variant 0.4
whiB6 4338595 c.-75delG upstream_gene_variant 1.0