TB-Profiler result

Run: SRR21239878

Summary

Run ID: SRR21239878

Sample name:

Date: 03-04-2023 23:59:42

Number of reads: 2767917

Percentage reads mapped: 85.37

Strain: lineage4.4.1.1

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
lineage4.4 Euro-American S;T None 0.99
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 0.22 streptomycin
ahpC 2726119 c.-74G>A upstream_gene_variant 1.0 isoniazid
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
mshA 576108 p.Ala254Gly missense_variant 0.15
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 1472507 n.662C>G non_coding_transcript_exon_variant 0.19
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.21
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.21
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.29
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.29
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.29
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.29
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.29
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.29
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.28
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.28
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.29
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.3
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.3
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.31
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.32
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.27
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.26
rrs 1472668 n.825_829delGGGTT non_coding_transcript_exon_variant 0.19
rrs 1472675 n.830_831insAGAC non_coding_transcript_exon_variant 0.19
rrs 1472680 n.835C>T non_coding_transcript_exon_variant 0.19
rrs 1472682 n.837T>C non_coding_transcript_exon_variant 0.18
rrs 1472683 n.838T>G non_coding_transcript_exon_variant 0.18
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.16
rrs 1472689 n.844C>T non_coding_transcript_exon_variant 0.17
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.17
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.23
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.22
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.22
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.2
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.2
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.38
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 0.37
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.38
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.57
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.58
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.57
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.6
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.61
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.58
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.57
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.57
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.57
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.56
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.51
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.52
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.52
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.52
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.52
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.58
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.62
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.65
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.66
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.59
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.59
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.57
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.56
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.53
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.53
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.54
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.49
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.31
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 1.0
PPE35 2169840 p.Gly258Asp missense_variant 0.98
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.23
thyA 3073880 p.Glu198Lys missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.64
Rv3083 3448608 c.105G>A synonymous_variant 0.99
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568428 c.252A>G synonymous_variant 0.19
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
rpoA 3877919 p.Glu197Lys missense_variant 1.0
rpoA 3878641 c.-134C>G upstream_gene_variant 0.27
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245461 c.2229C>T synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0