TB-Profiler result

Run: ERR2514486
Summary

Run ID: ERR2514486

Sample name:

Date: 31-03-2023 20:22:08

Number of reads: 667445

Percentage reads mapped: 99.6

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 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
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
gyrA 9711 p.Met804Leu missense_variant 0.15
fgd1 491304 c.522C>T synonymous_variant 0.13
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575270 c.-78G>T upstream_gene_variant 0.11
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 576715 c.1368C>T synonymous_variant 1.0
ccsA 619771 c.-120C>A upstream_gene_variant 0.17
ccsA 620748 c.858T>G synonymous_variant 0.31
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760733 p.Lys309Asn missense_variant 0.11
rpoB 760756 p.His317Arg missense_variant 0.12
rpoB 760832 p.Leu342Phe missense_variant 0.12
rpoB 762233 c.2427G>A synonymous_variant 0.12
rpoC 764592 p.Gly408Val missense_variant 0.11
rpoC 764705 p.Leu446Met missense_variant 0.12
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775634 c.2847G>T synonymous_variant 0.33
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 778166 c.-824G>T upstream_gene_variant 0.11
mmpS5 778737 p.Glu57* stop_gained 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781419 c.-140delC upstream_gene_variant 0.11
fbiC 1303911 c.981G>A synonymous_variant 0.12
embR 1416512 p.Gln279Pro missense_variant 0.12
atpE 1461084 p.Gly14Arg missense_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472049 n.204G>T non_coding_transcript_exon_variant 0.29
rrl 1476288 n.2631T>G non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918149 c.210A>T synonymous_variant 0.11
tlyA 1918219 p.Gly94Ser missense_variant 0.12
ndh 2102937 p.Ala36Pro missense_variant 0.11
katG 2155605 c.507C>T synonymous_variant 0.13
PPE35 2170197 p.Ala139Glu missense_variant 0.2
Rv1979c 2223044 p.Gly41Trp missense_variant 0.15
Rv1979c 2223229 c.-65T>C upstream_gene_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289006 p.Ala79Val missense_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518545 p.Met144Thr missense_variant 0.13
kasA 2518739 p.Ala209Thr missense_variant 0.13
eis 2714276 p.Arg353Trp missense_variant 0.12
folC 2746153 c.1446C>T synonymous_variant 0.2
folC 2746400 p.Ser400Tyr missense_variant 0.12
Rv2752c 3065413 p.Ser260Trp missense_variant 0.18
Rv2752c 3065744 p.Thr150Ala missense_variant 0.15
thyA 3074453 p.Leu7Met missense_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448891 p.Thr130Ala missense_variant 0.25
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474075 c.69G>A synonymous_variant 0.2
fprA 3474143 p.Trp46Tyr missense_variant 0.15
fprA 3474165 c.159C>G synonymous_variant 0.12
fprA 3474747 p.Gln247His missense_variant 0.18
whiB7 3568713 c.-34C>T upstream_gene_variant 0.15
Rv3236c 3612248 p.Met290Thr missense_variant 0.11
fbiA 3641422 p.Asp294Asn missense_variant 0.11
alr 3840964 p.Thr153Ser missense_variant 0.13
alr 3841173 p.Gly83Glu missense_variant 0.22
rpoA 3878002 p.Ser169* stop_gained 0.14
ddn 3986647 c.-197T>G upstream_gene_variant 0.14
clpC1 4039180 p.Arg509Gly missense_variant 0.15
clpC1 4039293 p.Gly471Asp missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4244893 p.Gly554Asp missense_variant 0.17
embB 4246205 c.-309A>G upstream_gene_variant 0.1
embB 4247011 c.498C>T synonymous_variant 0.13
embB 4247516 p.Asn335Asp missense_variant 0.12
embB 4249166 p.Gly885Ser missense_variant 0.13
embB 4249721 p.Leu1070Met missense_variant 0.11
aftB 4266961 p.Arg626Trp missense_variant 0.11
aftB 4267016 c.1821C>G synonymous_variant 0.12
aftB 4268251 p.Ala196Ser missense_variant 0.2
ethA 4327104 p.Gly124Arg missense_variant 0.12
ethR 4327864 p.Gly106Arg missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0