TB-Profiler result

Run: ERR4817790
Summary

Run ID: ERR4817790

Sample name:

Date: 01-04-2023 15:11:37

Number of reads: 772429

Percentage reads mapped: 99.58

Strain: lineage4.1.2.1

Drug-resistance: HR-TB

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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
rpsL 781822 p.Lys88Arg missense_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
folC 2747141 p.Glu153Ala missense_variant 1.0 para-aminosalicylic_acid
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 6302 p.Ala355Ser missense_variant 0.12
gyrB 6812 p.His525Tyr missense_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8684 c.1383G>A synonymous_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490904 p.Phe41Ser missense_variant 0.12
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 576464 p.Ala373Thr missense_variant 0.17
ccsA 619966 p.Val26Met missense_variant 0.15
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 761739 p.Glu645* stop_gained 0.15
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766114 p.Tyr915* stop_gained 0.11
rpoC 766323 p.Thr985Asn missense_variant 0.13
rpoC 766958 p.Gly1197Arg missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406484 p.Pro286Arg missense_variant 0.11
Rv1258c 1406570 c.771G>T synonymous_variant 0.13
embR 1416572 p.Pro259Leu missense_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473234 n.1389A>G non_coding_transcript_exon_variant 0.25
rrl 1474243 n.586G>T non_coding_transcript_exon_variant 0.5
fabG1 1673779 p.Thr114Ala missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918474 p.Pro179Ser missense_variant 0.11
PPE35 2168563 p.Pro684Thr missense_variant 0.18
PPE35 2169558 p.Phe352Ser missense_variant 0.12
PPE35 2170408 p.Ala69Thr missense_variant 0.29
Rv1979c 2222726 p.Val147Met missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289107 c.135G>A synonymous_variant 0.11
kasA 2518076 c.-39C>T upstream_gene_variant 0.93
kasA 2519218 c.1104G>T synonymous_variant 0.15
eis 2714353 p.Gly327Asp missense_variant 0.13
folC 2747344 c.255G>C synonymous_variant 0.1
Rv2752c 3064633 p.Ala520Val missense_variant 0.12
Rv2752c 3064716 c.1476A>T synonymous_variant 0.11
Rv2752c 3065755 p.Val146Ala missense_variant 0.12
thyX 3067984 c.-39C>T upstream_gene_variant 0.12
ald 3086713 c.-107_-106delCGinsTA upstream_gene_variant 0.11
ald 3086763 c.-57T>C upstream_gene_variant 0.1
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087244 p.Ala142Asp missense_variant 0.12
Rv3083 3449248 p.Ala249Pro missense_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612127 c.990C>T synonymous_variant 0.17
alr 3840610 c.810delG frameshift_variant 0.12
alr 3840635 c.786G>A synonymous_variant 0.12
rpoA 3878275 p.Leu78Pro missense_variant 0.13
rpoA 3878446 p.Phe21Ser missense_variant 0.11
rpoA 3878701 c.-194C>T upstream_gene_variant 0.33
clpC1 4038767 c.1938G>A synonymous_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embC 4242941 p.His1027Asn missense_variant 0.11
embA 4245166 p.Pro645Leu missense_variant 1.0
embA 4245168 p.Val646Leu missense_variant 0.18
embB 4246508 c.-6G>A upstream_gene_variant 0.12
embB 4246794 p.Ala94Glu missense_variant 0.12
embB 4247050 c.537C>T synonymous_variant 1.0
embB 4248795 p.Ala761Val missense_variant 0.13
ubiA 4269298 p.Ile179Thr missense_variant 0.18
ethA 4326090 p.Leu462Val missense_variant 0.13
ethA 4326630 p.Phe282Leu missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0