TB-Profiler result

Run: ERR2653021
Summary

Run ID: ERR2653021

Sample name:

Date: 31-03-2023 22:27:04

Number of reads: 937897

Percentage reads mapped: 99.21

Strain: lineage4.1.2.1

Drug-resistance: Other

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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 0.99
lineage4.1.2 Euro-American T;H None 0.99
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.99
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 2289073 p.His57Tyr missense_variant 1.0 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490641 c.-142G>A upstream_gene_variant 0.12
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
ccsA 619850 c.-41G>C upstream_gene_variant 0.12
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 763679 p.Ile104Val missense_variant 0.12
rpoC 763784 p.Val139Phe missense_variant 0.12
rpoC 764560 c.1191T>C synonymous_variant 0.12
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766326 p.Gly986Asp missense_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777449 c.1032C>T synonymous_variant 0.14
mmpL5 777678 p.Val268Ala missense_variant 0.12
mmpL5 777830 c.651G>T synonymous_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303230 c.300C>T synonymous_variant 0.17
fbiC 1303916 p.Met329Thr missense_variant 0.17
fbiC 1304140 p.Ala404Thr missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474901 n.1244A>C non_coding_transcript_exon_variant 0.11
rpsA 1833449 c.-93G>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101810 p.Ile411Met missense_variant 0.12
ndh 2102936 c.105_106delGG frameshift_variant 0.11
ndh 2103107 c.-65G>A upstream_gene_variant 0.17
ndh 2103185 c.-143A>G upstream_gene_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
eis 2714642 p.Thr231Ala missense_variant 0.13
folC 2746426 c.1173G>T synonymous_variant 0.12
pepQ 2859551 p.Phe290Leu missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087645 c.828delA frameshift_variant 0.11
Rv3083 3449033 p.Gly177Asp missense_variant 0.11
Rv3083 3449047 p.Val182Ile missense_variant 0.12
Rv3083 3449968 c.1468delC frameshift_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3641377 p.Arg279Trp missense_variant 0.13
alr 3841206 p.His72Arg missense_variant 0.1
rpoA 3878425 p.Pro28Gln missense_variant 0.12
rpoA 3878630 c.-123G>C upstream_gene_variant 0.13
clpC1 4039213 p.Lys498Glu missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243772 c.540A>T synonymous_variant 0.11
embB 4246544 p.Thr11Pro missense_variant 0.12
embB 4246548 p.Pro12Gln missense_variant 0.17
embB 4246555 c.42G>C synonymous_variant 0.18
embB 4246556 p.Ala15Pro missense_variant 0.18
embB 4246563 p.Leu17Trp missense_variant 0.16
embB 4246567 c.54G>T synonymous_variant 0.15
embB 4247026 c.513G>C synonymous_variant 0.14
embB 4247887 c.1374C>T synonymous_variant 0.11
embB 4248434 p.Ala641Thr missense_variant 0.12
embB 4249129 c.2616T>C synonymous_variant 0.12
aftB 4267564 p.Thr425Pro missense_variant 0.2
aftB 4267988 c.849G>A synonymous_variant 0.15
ethA 4326020 p.Ala485Val missense_variant 0.15
ethA 4328334 c.-861C>T upstream_gene_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408063 p.Arg47Gln missense_variant 1.0