TB-Profiler result

Run: ERR2514377
Summary

Run ID: ERR2514377

Sample name:

Date: 31-03-2023 20:17:59

Number of reads: 1395128

Percentage reads mapped: 99.28

Strain: lineage4.5

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
lineage4.5 Euro-American H;T RD122 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7376 c.75G>A synonymous_variant 0.13
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7892 c.591G>A synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575879 p.His178Asn missense_variant 0.11
mshA 576695 p.Ala450Thr missense_variant 0.25
ccsA 619952 p.Ala21Val missense_variant 0.12
ccsA 620029 c.139C>T synonymous_variant 1.0
rpoC 766851 p.Met1161Thr missense_variant 0.12
mmpL5 775620 p.Ser954* stop_gained 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777245 c.1236G>C synonymous_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305423 c.2493T>C synonymous_variant 0.12
Rv1258c 1406101 p.Pro414Ser missense_variant 1.0
Rv1258c 1406491 p.Arg284Cys missense_variant 0.12
atpE 1461112 p.Gly23Val missense_variant 0.4
atpE 1461155 c.111C>T synonymous_variant 0.13
atpE 1461157 p.Gly38Val missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 1.0
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.5
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.5
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 1.0
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 1.0
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 1.0
rrs 1473101 n.1256C>T non_coding_transcript_exon_variant 0.5
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.5
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 1.0
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 1.0
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 1.0
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.5
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 1.0
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.5
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.5
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 1.0
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 1.0
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.67
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.67
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 1.0
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 1.0
rrs 1473262 n.1417T>C non_coding_transcript_exon_variant 1.0
rrs 1473270 n.1425G>C non_coding_transcript_exon_variant 1.0
rrs 1473276 n.1431A>C non_coding_transcript_exon_variant 1.0
rrl 1473633 n.-25C>A upstream_gene_variant 0.18
rrl 1476100 n.2443A>T non_coding_transcript_exon_variant 0.5
fabG1 1673431 c.-9G>T upstream_gene_variant 0.11
rpsA 1834287 p.Ser249Phe missense_variant 1.0
rpsA 1834869 p.Arg443His missense_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918047 c.108G>A synonymous_variant 0.13
tlyA 1918369 p.Ile144Val missense_variant 0.11
ndh 2101681 c.1362C>A synonymous_variant 0.22
katG 2155269 c.843C>A synonymous_variant 0.15
katG 2155740 c.372C>A synonymous_variant 0.11
PPE35 2170568 p.Ile15Met missense_variant 1.0
Rv1979c 2221965 c.1200G>A synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518879 c.765A>G synonymous_variant 0.1
kasA 2519221 c.1107G>T synonymous_variant 0.15
ahpC 2726131 c.-62C>T upstream_gene_variant 1.0
folC 2747631 c.-33C>T upstream_gene_variant 0.12
Rv2752c 3065289 c.903G>A synonymous_variant 0.11
thyX 3068104 c.-159C>T upstream_gene_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475020 p.Ser338Arg missense_variant 0.13
Rv3236c 3612094 c.1023C>T synonymous_variant 0.12
rpoA 3878492 p.Arg6Cys missense_variant 0.11
rpoA 3878575 c.-68C>T upstream_gene_variant 1.0
clpC1 4038318 p.Pro796Leu missense_variant 1.0
clpC1 4039091 c.1614G>C synonymous_variant 0.11
clpC1 4039641 p.Thr355Ile missense_variant 0.11
panD 4044004 p.Met93Arg missense_variant 0.11
embC 4241329 c.1467T>G synonymous_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243637 c.405C>G synonymous_variant 0.1
embA 4244266 p.Arg345Leu missense_variant 0.11
embA 4245680 p.Lys816Asn missense_variant 0.12
aftB 4267409 c.1428C>G synonymous_variant 0.11
ethA 4328118 c.-645T>C upstream_gene_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0