TB-Profiler result

Run: ERR4815772
Summary

Run ID: ERR4815772

Sample name:

Date: 01-04-2023 14:03:13

Number of reads: 516786

Percentage reads mapped: 94.63

Strain: lineage4.4.1.1

Drug-resistance: Other

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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
lineage4.4 Euro-American S;T None 1.0
lineage4.4.1 Euro-American (S-type) S;T None 1.0
lineage4.4.1.1 Euro-American S;Orphans 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
gyrA 7582 p.Asp94Gly missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
thyA 3074095 p.Arg126Gln missense_variant 0.12 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 5107 c.-133C>A upstream_gene_variant 0.22
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9026 c.1725G>A synonymous_variant 0.33
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9635 c.2334T>C synonymous_variant 0.1
mshA 576142 c.795G>A synonymous_variant 0.12
rpoB 760537 p.Glu244Val missense_variant 0.29
rpoC 763802 p.His145Tyr missense_variant 0.4
rpoC 764632 c.1263T>C synonymous_variant 0.22
rpoC 764647 c.1278C>T synonymous_variant 0.18
rpoC 764650 c.1281G>T synonymous_variant 0.2
rpoC 764653 c.1284G>C synonymous_variant 0.2
rpoC 764656 c.1287C>T synonymous_variant 0.2
rpoC 764662 c.1293G>C synonymous_variant 0.2
rpoC 764668 c.1299C>A synonymous_variant 0.18
rpoC 764677 c.1308C>G synonymous_variant 0.18
rpoC 764706 p.Leu446Gln missense_variant 0.15
rpoC 766524 p.Arg1052Gln missense_variant 0.29
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777258 c.1222delC frameshift_variant 0.14
mmpR5 778025 c.-965T>C upstream_gene_variant 0.13
mmpL5 778357 p.Thr42Ser missense_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303065 c.135C>T synonymous_variant 0.17
fbiC 1304350 p.Glu474Gln missense_variant 0.2
fbiC 1305313 p.Arg795Gly missense_variant 0.14
embR 1416637 p.Asp237Glu missense_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.6
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.67
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.67
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.67
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.67
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.33
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.4
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.5
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 1.0
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 1.0
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 1.0
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 1.0
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 1.0
rrs 1472755 n.910G>A non_coding_transcript_exon_variant 0.4
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.6
rrs 1472841 n.996G>T non_coding_transcript_exon_variant 0.67
rrs 1472958 n.1113A>G non_coding_transcript_exon_variant 0.67
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.67
rrs 1472974 n.1129A>G non_coding_transcript_exon_variant 0.67
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.5
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.4
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.4
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.43
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.29
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.43
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.38
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.38
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.38
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.56
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.44
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.33
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.5
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.4
rrs 1473319 n.1474C>T non_coding_transcript_exon_variant 0.33
rrl 1473384 n.-274A>G upstream_gene_variant 0.67
rrl 1473724 n.67T>C non_coding_transcript_exon_variant 1.0
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 1.0
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 1.0
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 1.0
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 1.0
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 1.0
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 1.0
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 1.0
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 1.0
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.67
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.6
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.71
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.67
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.6
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.67
fabG1 1673947 p.Glu170Lys missense_variant 0.17
inhA 1674493 p.Met98Leu missense_variant 0.25
rpsA 1834034 p.Ile165Val missense_variant 0.25
rpsA 1834040 p.Lys167Gln missense_variant 0.29
rpsA 1834057 c.516G>A synonymous_variant 0.29
rpsA 1834069 c.528G>C synonymous_variant 0.4
rpsA 1834195 c.654G>C synonymous_variant 0.17
rpsA 1834213 c.672G>A synonymous_variant 0.15
rpsA 1834228 c.687C>T synonymous_variant 0.14
rpsA 1834246 c.705G>T synonymous_variant 0.17
rpsA 1834249 c.708T>C synonymous_variant 0.18
rpsA 1834261 c.720A>G synonymous_variant 0.16
rpsA 1834264 c.723G>C synonymous_variant 0.16
rpsA 1834327 c.786G>T synonymous_variant 0.15
rpsA 1834788 p.Ala416Asp missense_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102389 c.653delC frameshift_variant 0.14
ndh 2102550 p.Glu165Gln missense_variant 0.18
ndh 2102990 p.Val18Ala missense_variant 1.0
katG 2155455 c.657G>T synonymous_variant 0.22
katG 2156569 c.-458C>T upstream_gene_variant 0.4
PPE35 2169840 p.Gly258Asp missense_variant 1.0
PPE35 2170413 p.Ala67Val missense_variant 0.2
Rv1979c 2222532 c.633C>A synonymous_variant 0.22
Rv1979c 2222729 p.Gly146Ser missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289723 c.-482C>A upstream_gene_variant 0.2
eis 2714136 c.1197G>C synonymous_variant 0.12
ahpC 2726046 c.-147G>T upstream_gene_variant 0.18
folC 2746229 p.Ala457Val missense_variant 0.12
folC 2747228 c.370delT frameshift_variant 0.17
folC 2747625 c.-27C>T upstream_gene_variant 0.2
thyA 3074440 p.Val11Ala missense_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087491 c.672G>A synonymous_variant 0.15
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474417 p.His137Gln missense_variant 0.18
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
fbiB 3641037 c.-498G>A upstream_gene_variant 0.11
fbiB 3642006 p.Asn158Asp missense_variant 0.17
alr 3841459 c.-39C>T upstream_gene_variant 0.17
panD 4044443 c.-162G>A upstream_gene_variant 0.12
embC 4240803 p.Tyr314Phe missense_variant 0.11
embC 4242607 p.Met915Ile missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244681 c.1449A>G synonymous_variant 0.11
embA 4245389 c.2157C>A synonymous_variant 0.11
embB 4247584 c.1074delG frameshift_variant 0.17
embB 4248285 p.Lys591Met missense_variant 0.29
ubiA 4268963 p.Trp291Arg missense_variant 0.12
ubiA 4269429 p.Gln135His missense_variant 0.22
ethA 4326692 p.Arg261Gln missense_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408219 c.-17A>G upstream_gene_variant 0.12