TB-Profiler result

Run: SRR6045846
Summary

Run ID: SRR6045846

Sample name:

Date: 04-04-2023 12:06:27

Number of reads: 963346

Percentage reads mapped: 98.45

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 1.0 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
gyrB 5476 p.Asp79Glu missense_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8763 p.Asp488Asn missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 762596 c.-774G>T upstream_gene_variant 0.17
rpoC 764322 p.Pro318Leu missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303935 c.1005G>A synonymous_variant 0.12
Rv1258c 1407371 c.-31C>T upstream_gene_variant 0.11
atpE 1461046 c.2T>A start_lost 0.13
rrs 1471659 n.-187C>T upstream_gene_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 1472670 n.825G>T non_coding_transcript_exon_variant 1.0
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 1.0
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 1.0
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 1.0
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 1.0
rrl 1473726 n.69C>T non_coding_transcript_exon_variant 0.22
rrl 1475704 n.2047C>T non_coding_transcript_exon_variant 1.0
rrl 1475713 n.2056C>G non_coding_transcript_exon_variant 1.0
rrl 1475716 n.2059A>G non_coding_transcript_exon_variant 1.0
rrl 1475717 n.2060C>G non_coding_transcript_exon_variant 1.0
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.67
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.67
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.67
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.67
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.67
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.67
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.67
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.67
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.67
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.67
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.67
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.67
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.67
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.67
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.67
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.67
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 1.0
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 1.0
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 1.0
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 1.0
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 1.0
rpsA 1834869 p.Arg443His missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102506 c.537C>A synonymous_variant 0.12
ndh 2102990 p.Val18Ala missense_variant 1.0
PPE35 2169840 p.Gly258Asp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518151 p.Ser13Arg missense_variant 0.19
kasA 2518332 p.Gly73Asp missense_variant 0.12
folC 2746923 p.Gly226Ser missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 1.0
Rv3083 3448969 p.Val156Met missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
clpC1 4038234 p.Arg824His missense_variant 0.13
clpC1 4038396 c.2308delG frameshift_variant 0.12
clpC1 4039547 c.1158C>A synonymous_variant 0.11
clpC1 4039945 p.Ser254Pro missense_variant 0.11
embC 4240731 p.Asn290Ser missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243692 p.Gly154Ser missense_variant 1.0
embB 4246904 p.Val131Met missense_variant 1.0
aftB 4267887 p.Gly317Val missense_variant 0.1
ethA 4328252 c.-779T>G upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0