TB-Profiler result

Run: ERR11044908

Summary

Run ID: ERR11044908

Sample name:

Date: 31-03-2023 12:02:36

Number of reads: 379433

Percentage reads mapped: 99.52

Strain: lineage4.1.2.1

Drug-resistance: Sensitive


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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 1.0
lineage4.1.2 Euro-American T;H None 1.0
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 5370 p.His44Arg missense_variant 0.11
gyrB 6200 p.Arg321Cys missense_variant 0.29
gyrB 6683 p.Arg482Ser missense_variant 0.4
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 490718 c.-65G>A upstream_gene_variant 0.22
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575575 c.228G>A synonymous_variant 0.14
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 576456 p.Val370Gly missense_variant 0.67
ccsA 620300 p.Leu137Arg missense_variant 0.29
rpoB 759935 p.Glu43Asp missense_variant 0.12
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 761087 c.1281C>A synonymous_variant 0.23
rpoB 761482 p.Ala559Gly missense_variant 0.22
rpoC 762800 c.-570C>T upstream_gene_variant 0.4
rpoB 762801 p.Asp999Asn missense_variant 0.33
rpoC 764534 p.Arg389Gly missense_variant 0.4
rpoC 764963 p.Phe532Ile missense_variant 0.12
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777082 p.Lys467Glu missense_variant 0.22
mmpL5 778191 p.Gly97Asp missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303025 p.Arg32Leu missense_variant 0.15
fbiC 1303963 p.Ala345Thr missense_variant 0.4
Rv1258c 1407369 c.-29G>A upstream_gene_variant 0.25
atpE 1461104 c.60C>G synonymous_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473624 n.-34T>G upstream_gene_variant 0.2
rrl 1474635 n.978C>T non_coding_transcript_exon_variant 0.17
rrl 1475549 n.1892T>A non_coding_transcript_exon_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918621 p.Ser228Arg missense_variant 0.33
ndh 2102453 p.Leu197* stop_gained 0.29
katG 2155876 p.Asp79Gly missense_variant 0.4
katG 2156027 p.Pro29Ser missense_variant 0.25
PPE35 2167675 p.Leu980Val missense_variant 0.29
PPE35 2167792 p.Ser941Pro missense_variant 0.25
PPE35 2169692 c.921C>T synonymous_variant 0.25
Rv1979c 2223052 p.Glu38Ala missense_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518318 c.204C>T synonymous_variant 0.29
ahpC 2726397 p.Ser69Gly missense_variant 0.18
folC 2746528 c.1071C>G synonymous_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087785 c.966C>T synonymous_variant 0.29
Rv3083 3448387 c.-117C>G upstream_gene_variant 0.14
Rv3083 3448651 p.Tyr50Asp missense_variant 0.14
Rv3083 3448992 c.489C>T synonymous_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568833 c.-154C>T upstream_gene_variant 0.22
Rv3236c 3612773 p.Gly115Asp missense_variant 1.0
fbiB 3640588 c.-947C>T upstream_gene_variant 0.15
alr 3841137 p.Asp95Val missense_variant 0.29
ddn 3987196 p.Glu118Ala missense_variant 0.15
clpC1 4038895 p.Tyr604Asp missense_variant 0.18
clpC1 4039408 c.1297C>A synonymous_variant 0.15
embC 4240411 c.549G>A synonymous_variant 0.4
embC 4241174 p.Ser438Thr missense_variant 0.12
embC 4241425 c.1563G>A synonymous_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embC 4243121 p.Ser1087Arg missense_variant 0.15
embA 4245778 p.Ala849Val missense_variant 0.18
embA 4246480 p.Gly1083Asp missense_variant 0.22
embB 4247068 c.555T>C synonymous_variant 1.0
embB 4247948 p.Val479Met missense_variant 1.0
embB 4248409 p.Leu632Phe missense_variant 0.29
aftB 4268453 c.384G>C synonymous_variant 0.2
aftB 4268619 p.Val73Gly missense_variant 0.38
ubiA 4269022 p.Ala271Val missense_variant 0.12
ethA 4326975 p.Trp167Arg missense_variant 0.1
ethA 4328415 c.-942A>G upstream_gene_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0