TB-Profiler result

Run: ERR4814497
Summary

Run ID: ERR4814497

Sample name:

Date: 01-04-2023 13:19:57

Number of reads: 3352756

Percentage reads mapped: 91.47

Strain: lineage4.6.2.2

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
lineage4.6 Euro-American T;LAM None 1.0
lineage4.6.2 Euro-American T;LAM RD726 1.0
lineage4.6.2.2 Euro-American (Cameroon) LAM10-CAM RD726 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 1472733 n.888G>A non_coding_transcript_exon_variant 0.68 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
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
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 778298 c.-692C>T upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.14
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.22
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.1
rrs 1472487 n.643dupT non_coding_transcript_exon_variant 0.96
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.3
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.48
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.47
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.56
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.62
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.67
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.67
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.72
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.72
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.69
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.72
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.73
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.73
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.18
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.38
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.31
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.32
rrs 1472670 n.825G>T non_coding_transcript_exon_variant 0.28
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.21
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.28
rrs 1472677 n.832C>T non_coding_transcript_exon_variant 0.29
rrs 1472681 n.837_838delTT non_coding_transcript_exon_variant 0.33
rrs 1472687 n.843dupT non_coding_transcript_exon_variant 0.24
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.34
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.44
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.51
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.52
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.68
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.68
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.64
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.56
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.55
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.3
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.14
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.14
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.14
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.14
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.13
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.14
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.11
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.12
rrl 1474634 n.977T>G non_coding_transcript_exon_variant 0.1
rrl 1474636 n.979A>C non_coding_transcript_exon_variant 0.1
rrl 1474658 n.1001A>G non_coding_transcript_exon_variant 0.12
rrl 1474663 n.1006C>T non_coding_transcript_exon_variant 0.12
rrl 1474673 n.1016T>C non_coding_transcript_exon_variant 0.13
rrl 1474676 n.1019T>A non_coding_transcript_exon_variant 0.13
rrl 1474677 n.1020A>G non_coding_transcript_exon_variant 0.13
rrl 1474692 n.1035G>A non_coding_transcript_exon_variant 0.14
rrl 1474734 n.1077G>C non_coding_transcript_exon_variant 0.14
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.17
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.17
rrl 1474824 n.1167A>G non_coding_transcript_exon_variant 0.11
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.11
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.1
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.16
rrl 1474867 n.1210T>A non_coding_transcript_exon_variant 0.11
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.14
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.1
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.12
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155389 c.723C>G synonymous_variant 1.0
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 0.98
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyX 3067474 p.Pro158Ala missense_variant 1.0
Rv3083 3448567 p.His22Asp missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612571 c.546C>T synonymous_variant 1.0
Rv3236c 3612910 p.Leu69Phe missense_variant 1.0
embA 4242550 c.-683C>G upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4267272 p.Lys522Arg missense_variant 1.0
ethR 4326739 c.-810G>C upstream_gene_variant 1.0
ethA 4328004 c.-531C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0