TB-Profiler result

Run: ERR2229396
Summary

Run ID: ERR2229396

Sample name:

Date: 31-03-2023 17:09:45

Number of reads: 749963

Percentage reads mapped: 98.86

Strain: lineage4.8

Drug-resistance: Other

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
pncA 2288749 p.Ala165Thr missense_variant 0.22 pyrazinamide
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 7170 p.Ala644Asp missense_variant 0.2
gyrB 7180 p.Leu647Phe missense_variant 0.17
gyrA 7310 p.Asp3Glu missense_variant 0.25
gyrA 7362 p.Glu21Gln missense_variant 1.0
fgd1 491370 c.588C>T synonymous_variant 0.17
fgd1 491729 p.Asp316Gly missense_variant 0.15
mshA 575171 c.-177C>A upstream_gene_variant 0.29
mshA 576108 p.Ala254Gly missense_variant 0.43
rpoB 760924 p.Arg373Leu missense_variant 0.18
rpoB 761152 p.Leu449Gln missense_variant 0.18
rpoB 761442 p.Gly546Cys missense_variant 0.33
rpoB 762261 p.Phe819Leu missense_variant 0.15
rpoB 762515 p.Asp903Glu missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776303 c.2178G>T synonymous_variant 0.17
mmpL5 777623 p.Gln286His missense_variant 0.18
mmpR5 779307 p.Glu106Asp missense_variant 0.4
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781641 p.Pro28Ser missense_variant 0.18
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304268 c.1338G>A synonymous_variant 0.17
fbiC 1304490 c.1560C>A synonymous_variant 0.29
Rv1258c 1406222 c.1119C>T synonymous_variant 0.17
embR 1416381 p.Ala323Ser missense_variant 0.19
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472035 n.190G>T non_coding_transcript_exon_variant 0.14
rrs 1472537 n.692C>A non_coding_transcript_exon_variant 0.12
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474365 n.708G>T non_coding_transcript_exon_variant 0.23
rrl 1475209 n.1552G>A non_coding_transcript_exon_variant 0.12
rrl 1476085 n.2428G>T non_coding_transcript_exon_variant 0.14
fabG1 1673380 c.-60C>G upstream_gene_variant 0.28
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101677 p.Ala456Thr missense_variant 0.15
ndh 2102625 p.Ser140Thr missense_variant 0.22
PPE35 2167814 c.2799C>T synonymous_variant 0.22
PPE35 2167965 p.Ala883Gly missense_variant 0.25
PPE35 2167967 c.2646A>C synonymous_variant 0.27
PPE35 2168530 p.Gly695Cys missense_variant 0.13
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169717 p.Asn299Ile missense_variant 0.14
PPE35 2170048 p.Leu189Val missense_variant 0.76
PPE35 2170053 p.Thr187Ser missense_variant 0.72
PPE35 2170298 c.315A>G synonymous_variant 0.17
Rv1979c 2222228 p.Phe313Leu missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223352 c.-188G>A upstream_gene_variant 0.12
Rv1979c 2223359 c.-195A>T upstream_gene_variant 0.12
pncA 2288999 c.243C>T synonymous_variant 0.15
pncA 2289892 c.-651C>T upstream_gene_variant 0.33
pncA 2290120 c.-879T>C upstream_gene_variant 0.4
kasA 2519140 c.1026G>C synonymous_variant 0.25
kasA 2519143 c.1029G>C synonymous_variant 0.25
kasA 2519153 p.Ile347Val missense_variant 0.25
eis 2714627 p.Ala236Ser missense_variant 0.17
eis 2715213 c.120G>T synonymous_variant 0.22
eis 2715408 c.-76G>T upstream_gene_variant 0.13
folC 2746513 c.1086G>A synonymous_variant 0.15
folC 2746544 p.Ala352Asp missense_variant 0.12
Rv2752c 3064688 p.Lys502* stop_gained 0.25
thyA 3074104 p.Pro123His missense_variant 0.18
fprA 3475097 p.Pro364Leu missense_variant 0.2
fprA 3475185 c.1179C>T synonymous_variant 0.14
ddn 3987245 p.Gln134His missense_variant 0.12
clpC1 4038923 c.1782A>T synonymous_variant 0.14
clpC1 4039301 p.Trp468* stop_gained 0.22
clpC1 4039793 c.912C>A synonymous_variant 0.22
clpC1 4039829 p.Leu292Ile missense_variant 0.22
clpC1 4040144 c.561G>C synonymous_variant 0.25
clpC1 4040364 p.Arg114Pro missense_variant 0.25
embC 4239972 p.Gly37Val missense_variant 0.13
embC 4240757 p.Thr299Ala missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242837 p.Pro992Leu missense_variant 0.5
embA 4243344 c.115delA frameshift_variant 0.2
embA 4243391 c.159C>A synonymous_variant 0.22
embB 4246544 p.Thr11Pro missense_variant 0.57
embB 4246548 p.Pro12Gln missense_variant 0.6
embB 4246555 c.42G>C synonymous_variant 0.8
embB 4246556 p.Ala15Pro missense_variant 0.8
embB 4246563 p.Leu17Trp missense_variant 0.75
embB 4246567 c.54_55insT frameshift_variant 0.62
embB 4246764 p.Pro84Leu missense_variant 0.12
embB 4247192 p.Val227Met missense_variant 0.4
embB 4247470 c.957T>C synonymous_variant 0.13
embB 4247472 p.Phe320Tyr missense_variant 0.13
embB 4248496 c.1983G>T synonymous_variant 0.2
embB 4249175 p.Val888Met missense_variant 0.17
embB 4249535 p.Glu1008* stop_gained 0.13
aftB 4267222 p.Ala539Pro missense_variant 0.13
whiB6 4338233 p.Ser97Pro missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407793 p.Arg137Leu missense_variant 0.17
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0