TB-Profiler result

Run: ERR9119082
Summary

Run ID: ERR9119082

Sample name:

Date: 02-04-2023 09:34:59

Number of reads: 410911

Percentage reads mapped: 99.6

Strain: lineage4.2.1

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
lineage4.2 Euro-American H;T;LAM None 1.0
lineage4.2.1 Euro-American (TUR) H3;H4 None 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 5639 c.400C>A synonymous_variant 0.17
gyrB 5893 c.654C>A synonymous_variant 0.14
gyrB 6374 p.Glu379* stop_gained 0.25
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 491285 p.Gly168Glu missense_variant 0.17
fgd1 491312 p.Gly177Asp missense_variant 0.2
rpoC 763477 c.108C>T synonymous_variant 0.12
rpoC 763628 p.Val87Met missense_variant 0.13
rpoC 764473 c.1104C>T synonymous_variant 0.15
rpoC 766073 p.Ala902Ser missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776478 p.Ala668Glu missense_variant 0.25
mmpL5 778092 p.Trp130Leu missense_variant 0.12
mmpL5 778762 c.-282G>T upstream_gene_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781502 c.-58G>T upstream_gene_variant 0.17
fbiC 1303856 p.Ala309Asp missense_variant 0.22
embR 1416203 p.Ala382Val missense_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472519 n.674G>T non_coding_transcript_exon_variant 1.0
rrs 1473128 n.1283C>A non_coding_transcript_exon_variant 0.25
rrs 1473179 n.1334C>A non_coding_transcript_exon_variant 0.29
rrl 1473848 n.191G>A non_coding_transcript_exon_variant 0.67
rrl 1473853 n.196G>A non_coding_transcript_exon_variant 0.67
rrl 1474132 n.475G>A non_coding_transcript_exon_variant 0.5
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102047 c.996G>A synonymous_variant 0.14
katG 2154594 p.Glu506Asp missense_variant 0.13
katG 2155933 p.Ala60Val missense_variant 0.13
katG 2156039 p.His25Asn missense_variant 0.12
PPE35 2169879 p.Phe245Cys missense_variant 1.0
PPE35 2169985 p.Ala210Thr missense_variant 0.25
PPE35 2170512 p.Leu34Pro missense_variant 0.4
Rv1979c 2221987 p.Leu393His missense_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518174 c.60A>G synonymous_variant 0.12
eis 2714314 p.Cys340Phe missense_variant 0.13
eis 2714940 c.393C>T synonymous_variant 0.2
ahpC 2725978 c.-215G>T upstream_gene_variant 0.17
folC 2746446 p.Lys385Glu missense_variant 0.13
pepQ 2859607 p.Arg271Leu missense_variant 0.13
pepQ 2860511 c.-93C>A upstream_gene_variant 0.12
thyX 3067333 p.Asp205Tyr missense_variant 0.4
thyX 3067527 p.Arg140Leu missense_variant 0.15
thyA 3073925 p.Leu183Val missense_variant 0.22
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448513 p.His4Asn missense_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568835 c.-156A>G upstream_gene_variant 0.17
fbiA 3640553 p.Thr4Asn missense_variant 0.22
alr 3840447 p.Arg325Leu missense_variant 0.2
alr 3841001 c.417_419delCGA disruptive_inframe_deletion 0.12
alr 3841497 c.-77C>T upstream_gene_variant 0.14
rpoA 3878244 p.Glu88Asp missense_variant 0.12
ddn 3986859 p.Pro6Ser missense_variant 0.2
ddn 3986954 c.111G>T synonymous_variant 0.12
clpC1 4040351 c.354C>T synonymous_variant 0.12
panD 4044118 p.Leu55Arg missense_variant 0.13
embC 4240131 p.Ala90Val missense_variant 0.11
embC 4242572 p.Glu904Gln missense_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246310 c.-204C>T upstream_gene_variant 1.0
embB 4246815 p.Thr101Ile missense_variant 0.17
embB 4247770 c.1257C>T synonymous_variant 0.13
embB 4248387 p.Arg625Gln missense_variant 0.18
embB 4249594 c.3081G>A synonymous_variant 1.0
aftB 4268443 p.Arg132Ser missense_variant 0.12
ubiA 4269367 p.Ala156Val missense_variant 0.17
ethA 4328376 c.-903G>C upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408101 c.102G>T synonymous_variant 0.12