TB-Profiler result

Run: ERR2229376
Summary

Run ID: ERR2229376

Sample name:

Date: 31-03-2023 17:07:56

Number of reads: 928079

Percentage reads mapped: 98.89

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
tlyA 1918030 c.92_95delAGGT frameshift_variant 0.15 capreomycin
tlyA 1918048 c.109_110insACCT frameshift_variant 0.17 capreomycin
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
gyrA 7365 p.Gln22Lys missense_variant 0.13
fgd1 491431 p.Ala217Ser missense_variant 0.5
mshA 576108 p.Ala254Gly missense_variant 0.6
mshA 576527 p.Glu394* stop_gained 0.25
mshA 576620 p.Ala425Ser missense_variant 0.18
ccsA 620220 p.Met110Ile missense_variant 0.14
ccsA 620783 p.Ala298Val missense_variant 0.12
ccsA 620837 p.Gly316Val missense_variant 0.17
rpoB 760575 p.Glu257Gln missense_variant 0.12
rpoB 761890 p.Val695Glu missense_variant 0.12
rpoB 762541 p.Asn912Ser missense_variant 0.22
rpoB 762555 p.Pro917Thr missense_variant 0.2
rpoC 763841 p.Glu158* stop_gained 0.2
rpoC 764588 p.Lys407Gln missense_variant 0.67
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776018 c.2463G>C synonymous_variant 0.15
mmpL5 776021 c.2460G>C synonymous_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1406400 p.Ile314Thr missense_variant 0.15
atpE 1461116 c.72C>A synonymous_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473617 n.-41T>A upstream_gene_variant 0.27
rrl 1473895 n.238C>A non_coding_transcript_exon_variant 0.18
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474837 n.1182delC non_coding_transcript_exon_variant 0.15
rrl 1475013 n.1356G>A non_coding_transcript_exon_variant 0.33
rrl 1475376 n.1719A>G non_coding_transcript_exon_variant 0.29
fabG1 1673380 c.-60C>G upstream_gene_variant 0.2
rpsA 1833397 c.-145G>A upstream_gene_variant 0.2
rpsA 1834175 c.634C>A synonymous_variant 0.14
rpsA 1834212 p.Ala224Glu missense_variant 0.14
rpsA 1834645 p.Asp368Glu missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918037 p.Arg33Pro missense_variant 0.15
tlyA 1918039 p.Ile34Val missense_variant 0.15
tlyA 1918044 c.105C>T synonymous_variant 0.17
tlyA 1918046 p.Gly36Ala missense_variant 0.17
PPE35 2167965 p.Ala883Gly missense_variant 0.17
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169027 p.Leu529* stop_gained 0.18
PPE35 2169269 c.1344A>G synonymous_variant 0.19
PPE35 2169272 c.1341C>G synonymous_variant 0.2
PPE35 2169278 c.1335T>C synonymous_variant 0.21
PPE35 2169281 c.1332T>G synonymous_variant 0.2
PPE35 2169902 c.711G>C synonymous_variant 0.15
PPE35 2170048 p.Leu189Val missense_variant 0.69
PPE35 2170053 p.Thr187Ser missense_variant 0.7
PPE35 2170392 p.Gly74Ala missense_variant 0.16
PPE35 2170400 c.213G>C synonymous_variant 0.14
Rv1979c 2222785 p.Trp127Leu missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289963 c.-722A>G upstream_gene_variant 0.13
kasA 2518525 c.411G>T synonymous_variant 0.2
kasA 2519140 c.1026G>C synonymous_variant 0.2
kasA 2519143 c.1029G>C synonymous_variant 0.2
kasA 2519236 p.Glu374Asp missense_variant 0.33
eis 2714458 p.Asp292Val missense_variant 0.15
eis 2714541 c.792A>G synonymous_variant 0.11
eis 2714989 p.Val115Asp missense_variant 0.17
folC 2747599 c.-1A>T upstream_gene_variant 0.15
ribD 2987188 p.Leu117Pro missense_variant 0.11
ribD 2987315 c.477C>T synonymous_variant 0.17
thyA 3074431 p.Thr14Lys missense_variant 0.13
thyA 3074454 c.18C>T synonymous_variant 0.15
ald 3087271 p.Arg151Leu missense_variant 0.18
ald 3087280 p.Gly154Glu missense_variant 0.2
Rv3236c 3612103 p.Leu338Phe missense_variant 0.12
fbiA 3641378 p.Arg279Gln missense_variant 0.14
fbiB 3642027 c.494delT frameshift_variant 0.12
fbiB 3642031 p.Gly166Ala missense_variant 0.12
fbiB 3642033 c.499_500insA frameshift_variant 0.12
fbiB 3642037 c.503_504insGGCAT frameshift_variant 0.12
alr 3841546 c.-126C>A upstream_gene_variant 0.24
alr 3841612 c.-193_-192insC upstream_gene_variant 0.14
rpoA 3877853 p.Phe219Leu missense_variant 0.4
clpC1 4039018 p.Ser563Ala missense_variant 0.18
clpC1 4039022 c.1683A>G synonymous_variant 0.18
clpC1 4039031 c.1674T>C synonymous_variant 0.2
clpC1 4039730 c.975C>G synonymous_variant 0.37
clpC1 4040144 c.561G>C synonymous_variant 0.23
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244214 p.Ala328Thr missense_variant 0.12
embA 4244654 p.Gln474His missense_variant 0.18
embA 4244759 c.1527C>T synonymous_variant 0.17
embB 4246544 p.Thr11Pro missense_variant 0.18
embB 4246548 p.Pro12Gln missense_variant 0.45
embB 4246555 c.42G>C synonymous_variant 0.8
embB 4246556 p.Ala15Pro missense_variant 0.8
embB 4246563 p.Leu17Trp missense_variant 0.56
embB 4246567 c.54G>T synonymous_variant 0.64
embB 4246881 p.Val123Gly missense_variant 0.15
embB 4247516 p.Asn335Asp missense_variant 0.12
embB 4249588 c.3075C>A synonymous_variant 0.17
aftB 4268022 p.Leu272Pro missense_variant 0.2
aftB 4268481 p.Pro119Gln missense_variant 0.13
ubiA 4269044 p.Val264Leu missense_variant 0.12
ubiA 4269426 c.407delT frameshift_variant 0.18
ethR 4326961 c.-588G>C upstream_gene_variant 0.2
ethR 4326964 c.-585G>A upstream_gene_variant 0.19
ethR 4326970 c.-579G>T upstream_gene_variant 0.19
ethA 4327662 c.-189C>T upstream_gene_variant 0.15
ethR 4327924 p.Ala126Ser missense_variant 0.14
ethR 4327954 p.Glu136Lys missense_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