TB-Profiler result

Run: ERR4820396

Summary

Run ID: ERR4820396

Sample name:

Date: 01-04-2023 16:39:37

Number of reads: 640536

Percentage reads mapped: 99.53

Strain: lineage4.1.2.1

Drug-resistance: Sensitive


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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 0.99
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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
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 5226 c.-14A>G upstream_gene_variant 0.5
gyrB 6178 c.939C>A synonymous_variant 0.11
gyrB 6293 p.Glu352* stop_gained 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8800 p.Ala500Glu missense_variant 0.25
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491411 p.Ala210Val missense_variant 0.22
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575562 p.Met72Thr missense_variant 0.12
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 576024 p.Ser226* stop_gained 0.17
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760532 c.726T>C synonymous_variant 0.14
rpoB 760739 p.Asn311Lys missense_variant 0.33
rpoB 762350 c.2544C>T synonymous_variant 0.11
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766157 p.Val930Phe missense_variant 0.2
rpoC 766808 p.Val1147Met missense_variant 0.25
rpoC 767147 p.Ala1260Thr missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775775 c.2706G>C synonymous_variant 0.11
mmpL5 775982 p.Trp833* stop_gained 0.14
mmpL5 776142 p.Gly780Val missense_variant 0.22
mmpL5 778168 p.Ala105Thr missense_variant 0.2
mmpR5 779174 p.Ala62Asp missense_variant 0.17
mmpS5 779581 c.-676G>A upstream_gene_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801092 c.286delC frameshift_variant 0.25
rplC 801348 c.540T>C synonymous_variant 0.13
rplC 801355 p.His183Asn missense_variant 0.13
fbiC 1303450 p.Val174Leu missense_variant 0.12
fbiC 1303635 c.708delA frameshift_variant 0.22
fbiC 1304769 c.1839C>T synonymous_variant 0.2
fbiC 1304826 c.1900delT frameshift_variant 0.22
Rv1258c 1406199 p.Leu381Pro missense_variant 0.11
embR 1416630 p.Gly240Ser missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471867 n.22C>T non_coding_transcript_exon_variant 0.4
rrl 1475241 n.1586delG non_coding_transcript_exon_variant 0.67
rpsA 1833630 p.Ile30Asn missense_variant 0.15
rpsA 1834893 p.Ala451Gly missense_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101742 p.Gln434Arg missense_variant 0.18
ndh 2102779 p.Asn88Lys missense_variant 0.15
katG 2154489 c.1623C>G synonymous_variant 0.15
katG 2156260 c.-149C>A upstream_gene_variant 0.14
PPE35 2168330 c.2283G>A synonymous_variant 0.2
PPE35 2168394 p.Ser740Ile missense_variant 0.14
PPE35 2168883 p.Gly577Ala missense_variant 1.0
Rv1979c 2222424 c.741G>A synonymous_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518763 p.Ser217Ala missense_variant 0.12
eis 2714174 p.Asp387Tyr missense_variant 0.12
eis 2714826 c.507C>T synonymous_variant 0.12
eis 2714988 c.345C>A synonymous_variant 0.18
folC 2746978 c.621C>T synonymous_variant 0.18
folC 2747743 c.-145A>G upstream_gene_variant 0.17
pepQ 2860269 c.150C>T synonymous_variant 0.11
pepQ 2860526 c.-108C>A upstream_gene_variant 0.12
Rv2752c 3065876 p.Lys106* stop_gained 0.25
thyX 3068145 c.-200C>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087541 p.Val241Glu missense_variant 0.15
fbiD 3339264 c.147C>A synonymous_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3640456 c.-87G>A upstream_gene_variant 0.14
fbiA 3640478 c.-65G>T upstream_gene_variant 0.12
fbiB 3641010 c.-525C>A upstream_gene_variant 0.15
fbiB 3642593 c.1062dupC frameshift_variant 0.11
alr 3841197 p.Thr75Lys missense_variant 0.11
clpC1 4038211 p.Leu832Met missense_variant 0.22
clpC1 4039277 c.1428C>A synonymous_variant 0.25
embC 4239900 p.Arg13Leu missense_variant 0.25
embC 4240912 c.1050G>A synonymous_variant 0.11
embC 4242197 p.Ala779Pro missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4244870 p.Ser546Arg missense_variant 0.18
embA 4245920 p.Trp896Cys missense_variant 0.14
embA 4246100 p.Phe956Leu missense_variant 0.2
embB 4247014 c.501G>A synonymous_variant 0.13
embB 4249334 p.Ala941Thr missense_variant 0.14
aftB 4268449 p.Pro130Ser missense_variant 1.0
ethA 4326116 p.Thr453Ile missense_variant 0.17
ethA 4327196 p.Gly93Glu missense_variant 0.14
whiB6 4338467 p.Val19Leu missense_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0