TB-Profiler result

Run: ERR4817551
Summary

Run ID: ERR4817551

Sample name:

Date: 01-04-2023 15:03:31

Number of reads: 1178293

Percentage reads mapped: 95.6

Strain: lineage4.9

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
lineage4.9 Euro-American (H37Rv-like) T1 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
mmpR5 779191 p.Ser68Gly missense_variant 0.1 clofazimine, bedaquiline
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.78 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 6760 c.-542G>T upstream_gene_variant 0.1
gyrA 7362 p.Glu21Gln missense_variant 1.0
mshA 576751 p.Lys468Asn missense_variant 0.27
rpoC 764375 p.Ala336Thr missense_variant 0.11
rpoC 766956 p.Glu1196Ala missense_variant 0.12
rpoC 766970 p.Ala1201Ser missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471914 n.69A>G non_coding_transcript_exon_variant 0.15
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.25
rrs 1472210 n.365A>T non_coding_transcript_exon_variant 0.25
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.25
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 1.0
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 1.0
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 1.0
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 1.0
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 1.0
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 1.0
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 1472668 n.825_829delGGGTT non_coding_transcript_exon_variant 0.75
rrs 1472675 n.830_831insAGAC non_coding_transcript_exon_variant 0.75
rrs 1472680 n.835C>T non_coding_transcript_exon_variant 0.75
rrs 1472682 n.837T>C non_coding_transcript_exon_variant 0.75
rrs 1472683 n.838T>G non_coding_transcript_exon_variant 0.75
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.75
rrs 1472689 n.844C>T non_coding_transcript_exon_variant 0.6
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.6
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.6
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.71
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.71
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.78
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.78
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.6
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.6
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.6
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.5
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.6
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.5
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.13
rrs 1473201 n.1356delA non_coding_transcript_exon_variant 0.17
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.14
rrl 1474228 n.571T>C non_coding_transcript_exon_variant 1.0
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.67
rrl 1474252 n.595T>A non_coding_transcript_exon_variant 0.67
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.22
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 0.25
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.29
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.33
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.33
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.33
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.33
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.33
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156045 p.Val23Leu missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2715535 c.-203T>C upstream_gene_variant 0.13
folC 2746834 c.765G>T synonymous_variant 0.11
pepQ 2859588 c.831G>A synonymous_variant 0.13
thyX 3067318 p.Arg210* stop_gained 0.17
fbiA 3641129 p.Ala196Val missense_variant 1.0
alr 3841093 p.Leu110Met missense_variant 0.12
embC 4241692 c.1830C>A synonymous_variant 0.15
embA 4245500 p.Gln756His missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0