TB-Profiler result

Run: ERR2229142
Summary

Run ID: ERR2229142

Sample name:

Date: 31-03-2023 16:44:02

Number of reads: 210602

Percentage reads mapped: 98.68

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 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 2155462 c.649delG frameshift_variant 0.22 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 576547 c.1200C>T synonymous_variant 0.5
ccsA 620293 p.Arg135Trp missense_variant 0.25
rpoB 760545 p.Gly247Trp missense_variant 0.4
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777119 p.His454Gln missense_variant 0.4
mmpL5 777122 c.1359C>T synonymous_variant 0.4
mmpL5 777128 c.1353A>G synonymous_variant 0.22
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304647 p.Asp573Tyr missense_variant 0.4
fbiC 1305199 p.Ala757Ser missense_variant 0.25
embR 1417454 c.-107C>A upstream_gene_variant 0.33
atpE 1460999 c.-46C>A upstream_gene_variant 0.5
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475034 n.1378delA non_coding_transcript_exon_variant 0.5
tlyA 1918626 c.687G>T synonymous_variant 0.33
katG 2154690 c.1422G>T synonymous_variant 0.4
katG 2155906 p.Ala69Glu missense_variant 0.33
PPE35 2167745 p.Thr956Arg missense_variant 0.29
PPE35 2169269 c.1344A>G synonymous_variant 0.2
PPE35 2169272 c.1341C>G synonymous_variant 0.2
PPE35 2169278 c.1335T>C synonymous_variant 0.2
PPE35 2169281 c.1332T>G synonymous_variant 0.2
PPE35 2169287 c.1326T>C synonymous_variant 0.18
PPE35 2169293 c.1320T>C synonymous_variant 0.18
PPE35 2169533 c.1080A>C synonymous_variant 0.18
PPE35 2169537 p.Thr359Ile missense_variant 0.15
PPE35 2169539 c.1074C>T synonymous_variant 0.14
PPE35 2169544 c.1068_1069insA frameshift_variant 0.14
PPE35 2169547 c.1065delA frameshift_variant 0.14
PPE35 2169553 p.Pro354Ser missense_variant 0.14
PPE35 2169567 p.Thr349Ile missense_variant 0.13
PPE35 2169902 p.Leu237Phe missense_variant 0.13
PPE35 2169964 p.Leu217Val missense_variant 0.17
PPE35 2170048 p.Leu189Val missense_variant 0.38
PPE35 2170053 p.Thr187Ser missense_variant 0.33
pncA 2289576 c.-335C>T upstream_gene_variant 0.25
kasA 2519140 c.1026G>C synonymous_variant 1.0
kasA 2519143 c.1029G>C synonymous_variant 1.0
thyX 3067853 c.93C>A synonymous_variant 0.25
thyX 3067904 p.Lys14Asn missense_variant 0.29
ald 3087472 p.Arg218Leu missense_variant 0.4
alr 3841546 c.-126C>A upstream_gene_variant 0.29
embC 4240801 c.939C>T synonymous_variant 0.5
embC 4240803 p.Tyr314Phe missense_variant 0.5
embB 4247028 p.Leu172Arg missense_variant 0.5
embB 4249746 p.Leu1078Pro missense_variant 0.67
aftB 4266967 p.Pro624Thr missense_variant 0.67
aftB 4267166 p.Gln557His missense_variant 0.22
ethR 4326970 c.-579G>T upstream_gene_variant 0.4
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448454 c.-49_*1435del transcript_ablation 1.0