TB-Profiler result

Run: ERR4815957
Summary

Run ID: ERR4815957

Sample name:

Date: 01-04-2023 14:09:36

Number of reads: 918582

Percentage reads mapped: 99.01

Strain: lineage4.2.1

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
lineage4.2 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
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 0.29 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
katG 2155193 p.Gly307Arg missense_variant 0.11 isoniazid
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 5331 p.Gly31Asp missense_variant 0.14
gyrB 5414 p.Ala59Thr missense_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8087 c.786T>C synonymous_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 620108 p.Asp73Gly missense_variant 0.15
rpoB 760624 p.Arg273His missense_variant 0.12
rpoB 761667 p.Gly621Cys missense_variant 0.12
rpoC 765732 p.Ala788Glu missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776049 p.Ser811Leu missense_variant 0.12
mmpL5 776355 p.Leu709Arg missense_variant 0.15
mmpL5 776533 p.Ala650Thr missense_variant 0.15
mmpS5 778530 p.Arg126Trp missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801378 c.570C>A synonymous_variant 0.13
Rv1258c 1406600 c.741C>T synonymous_variant 0.16
Rv1258c 1406683 p.Trp220Arg missense_variant 0.12
Rv1258c 1407446 c.-106G>T upstream_gene_variant 0.13
embR 1417454 c.-107C>A upstream_gene_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.8
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.8
rrs 1472623 n.778A>C non_coding_transcript_exon_variant 0.67
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.75
rrs 1472954 n.1110delC non_coding_transcript_exon_variant 0.75
rrs 1472958 n.1113_1114insC non_coding_transcript_exon_variant 0.75
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.5
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.5
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.5
rrs 1473288 n.1443C>G non_coding_transcript_exon_variant 0.29
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.29
rrs 1473292 n.1447G>T non_coding_transcript_exon_variant 0.29
rrs 1473294 n.1449A>G non_coding_transcript_exon_variant 0.29
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.29
rrs 1473315 n.1470T>C non_coding_transcript_exon_variant 0.33
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.29
rrs 1473319 n.1474C>T non_coding_transcript_exon_variant 0.29
rrs 1473324 n.1479G>A non_coding_transcript_exon_variant 0.29
rrl 1474853 n.1196A>G non_coding_transcript_exon_variant 1.0
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 1.0
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.5
rrl 1476363 n.2706A>G non_coding_transcript_exon_variant 0.5
rrl 1476366 n.2709A>C non_coding_transcript_exon_variant 0.5
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.5
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.5
rrl 1476374 n.2717T>G non_coding_transcript_exon_variant 0.6
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.75
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.5
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.5
fabG1 1673462 p.Gly8Glu missense_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102443 c.600A>G synonymous_variant 1.0
ndh 2102723 p.Thr107Ser missense_variant 1.0
ndh 2103043 c.-1C>T upstream_gene_variant 0.12
katG 2155249 p.Pro288Leu missense_variant 0.13
katG 2156338 c.-227C>A upstream_gene_variant 0.11
PPE35 2169179 c.1434C>A synonymous_variant 0.22
PPE35 2169593 c.1020C>T synonymous_variant 0.14
PPE35 2169879 p.Phe245Cys missense_variant 1.0
Rv1979c 2222494 c.670delG frameshift_variant 0.12
Rv1979c 2223214 c.-50A>G upstream_gene_variant 0.1
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289700 c.-459T>C upstream_gene_variant 0.12
folC 2747795 c.-197G>A upstream_gene_variant 0.15
thyX 3067433 c.513C>A synonymous_variant 0.15
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087803 c.984C>T synonymous_variant 0.11
ald 3087864 p.Ala349Thr missense_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3640924 p.Ile128Val missense_variant 0.1
rpoA 3877617 c.891G>A synonymous_variant 0.13
rpoA 3877803 c.705G>C synonymous_variant 0.12
ddn 3987091 p.Glu83Ala missense_variant 1.0
clpC1 4038304 p.Thr801Ala missense_variant 0.1
clpC1 4038933 p.Ala591Val missense_variant 0.11
clpC1 4039017 p.Ser563Phe missense_variant 0.11
clpC1 4039159 p.Lys516Gln missense_variant 0.11
clpC1 4040293 p.Val138Leu missense_variant 0.12
clpC1 4040319 p.Ala129Gly missense_variant 0.11
embC 4242110 p.Gly750Trp missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4245584 c.-930C>T upstream_gene_variant 0.11
aftB 4267410 p.Gly476Asp missense_variant 0.11
ethA 4326379 c.1095G>T synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0