TB-Profiler result

Run: ERR4814442
Summary

Run ID: ERR4814442

Sample name:

Date: 01-04-2023 13:17:45

Number of reads: 564590

Percentage reads mapped: 85.85

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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.94 streptomycin
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 8020 p.Thr240Asn missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491168 p.Phe129Ser missense_variant 0.14
ccsA 619831 c.-60T>G upstream_gene_variant 0.33
rpoC 763265 c.-105G>A upstream_gene_variant 0.11
rpoC 764818 c.1449G>T synonymous_variant 0.1
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303016 p.Val29Gly missense_variant 0.23
fbiC 1303688 p.Ile253Thr missense_variant 0.18
atpE 1460938 c.-107C>T upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.64
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.64
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.64
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.81
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.81
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.86
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.86
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.89
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.89
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.9
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.13
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.91
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.96
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.96
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.85
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.95
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 1.0
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 1.0
rrs 1472670 n.825G>T non_coding_transcript_exon_variant 0.94
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 1.0
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 1.0
rrs 1472677 n.832C>T non_coding_transcript_exon_variant 1.0
rrs 1472681 n.837_838delTT non_coding_transcript_exon_variant 1.0
rrs 1472687 n.842_843insC non_coding_transcript_exon_variant 1.0
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 1.0
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 1.0
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.94
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.94
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.94
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.94
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.86
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.8
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.75
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.6
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.5
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.5
rrs 1472951 n.1106T>C non_coding_transcript_exon_variant 0.4
rrs 1472953 n.1108G>A non_coding_transcript_exon_variant 0.4
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.4
rrs 1472971 n.1126G>T non_coding_transcript_exon_variant 0.33
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.4
rrs 1473001 n.1156G>C non_coding_transcript_exon_variant 0.4
rrs 1473002 n.1157G>A non_coding_transcript_exon_variant 0.4
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.4
rrs 1473008 n.1163C>T non_coding_transcript_exon_variant 0.4
rrs 1473009 n.1164T>G non_coding_transcript_exon_variant 0.4
rrs 1473020 n.1175T>C non_coding_transcript_exon_variant 0.4
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.4
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.25
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.25
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.5
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.5
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.5
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.5
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.5
rpsA 1833817 c.276C>A synonymous_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 1.0
ndh 2103225 c.-183A>C upstream_gene_variant 0.24
PPE35 2167906 p.Ile903Val missense_variant 0.11
PPE35 2168853 p.Pro587Leu missense_variant 1.0
PPE35 2169725 c.888T>C synonymous_variant 0.12
PPE35 2169840 p.Gly258Asp missense_variant 1.0
PPE35 2170392 p.Gly74Ala missense_variant 0.13
PPE35 2170400 c.213G>C synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519058 p.Thr315Lys missense_variant 0.29
ahpC 2726350 p.Trp53Leu missense_variant 0.25
Rv2752c 3065756 p.Val146Ile missense_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474164 p.Val53Ala missense_variant 0.12
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
clpC1 4039018 p.Ser563Ala missense_variant 0.15
clpC1 4039022 c.1683A>G synonymous_variant 0.14
clpC1 4040522 c.183T>C synonymous_variant 1.0
embC 4239778 c.-85C>T upstream_gene_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244164 c.933_953delTGCCCAGCTGGCGGCGGTGAG disruptive_inframe_deletion 0.13
ethR 4326961 c.-588G>C upstream_gene_variant 0.11
ethR 4326964 c.-585G>A upstream_gene_variant 0.11
ethR 4326970 c.-579G>T upstream_gene_variant 0.12
ethR 4326982 c.-567C>G upstream_gene_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0