TB-Profiler result

Run: SRR19303776
Summary

Run ID: SRR19303776

Sample name:

Date: 03-04-2023 21:06:12

Number of reads: 700577

Percentage reads mapped: 24.85

Strain: lineage4.1.2.1

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
lineage4.1 Euro-American T;X;H None 0.99
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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
ethA 4324975 c.-673_*1028del transcript_ablation 1.0 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
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 576613 c.1266A>C synonymous_variant 0.38
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 764500 c.1131C>T synonymous_variant 0.15
rpoC 764521 c.1152T>C synonymous_variant 0.18
rpoC 764536 c.1167G>C synonymous_variant 0.18
rpoC 764537 p.Pro390Val missense_variant 0.25
rpoC 764540 p.Val391Ile missense_variant 0.29
rpoC 764548 c.1179G>C synonymous_variant 0.29
rpoC 764549 p.Pro394Ala missense_variant 0.29
rpoC 764552 p.Gly395Asn missense_variant 0.29
rpoC 764557 p.Asn396Lys missense_variant 0.25
rpoC 764575 c.1206T>C synonymous_variant 0.2
rpoC 764576 p.Ser403Ala missense_variant 0.2
rpoC 764581 c.1212T>C synonymous_variant 0.18
rpoC 764582 p.Leu405Met missense_variant 0.18
rpoC 764605 c.1236G>C synonymous_variant 0.21
rpoC 764611 c.1242G>C synonymous_variant 0.21
rpoC 764620 c.1251G>C synonymous_variant 0.15
rpoC 764621 c.1252_1254delCTCinsTTG synonymous_variant 0.15
rpoC 764632 c.1263T>C synonymous_variant 0.14
rpoC 764641 c.1272C>T synonymous_variant 0.15
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765871 c.2502T>C synonymous_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775917 p.Val855Ala missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.33
rrl 1476356 n.2699C>G non_coding_transcript_exon_variant 0.33
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.33
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.33
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.3
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.33
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.33
rrl 1476384 n.2727G>C non_coding_transcript_exon_variant 0.31
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.27
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.21
rrl 1476428 n.2771C>A non_coding_transcript_exon_variant 0.19
rrl 1476443 n.2786G>C non_coding_transcript_exon_variant 0.18
rrl 1476455 n.2798C>G non_coding_transcript_exon_variant 0.16
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.16
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.14
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.14
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.13
rpsA 1834375 c.834G>C synonymous_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2519071 p.Asp319Glu missense_variant 0.19
folC 2746524 p.Ala359Thr missense_variant 0.12
pepQ 2860159 p.Ala87Gly missense_variant 0.21
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087816 p.Cys333Gly missense_variant 0.19
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475019 p.Ser338Asn missense_variant 1.0
fbiA 3641455 p.Ser305Ala missense_variant 0.2
embC 4240409 p.Pro183Ala missense_variant 0.19
embC 4240413 p.Leu184Arg missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4246527 p.Ala5Gly missense_variant 0.3
embB 4248319 c.1806A>T synonymous_variant 0.19
embB 4248324 p.Ala604Gly missense_variant 0.26
aftB 4268634 p.Tyr68Phe missense_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0