TB-Profiler result

Run: SRR21240202
Summary

Run ID: SRR21240202

Sample name:

Date: 04-04-2023 00:12:00

Number of reads: 869014

Percentage reads mapped: 88.9

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 0.23 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
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 1472530 n.685G>A non_coding_transcript_exon_variant 0.16
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.17
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.17
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.17
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.28
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.28
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.27
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.26
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.26
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.31
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.28
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.26
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.21
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.2
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.2
rrs 1472668 n.825_829delGGGTT non_coding_transcript_exon_variant 0.2
rrs 1472675 n.830_831insAGAC non_coding_transcript_exon_variant 0.2
rrs 1472680 n.835C>T non_coding_transcript_exon_variant 0.2
rrs 1472682 n.837T>C non_coding_transcript_exon_variant 0.19
rrs 1472683 n.838T>G non_coding_transcript_exon_variant 0.19
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.19
rrs 1472689 n.844C>T non_coding_transcript_exon_variant 0.19
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.2
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.19
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.2
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.19
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.26
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.26
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.21
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.18
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.12
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.1
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.23
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 0.23
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.26
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.34
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.34
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.35
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.35
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.36
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.33
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.33
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.32
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.32
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.32
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.31
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.31
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.3
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.3
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.3
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.35
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.36
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.36
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.35
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.34
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.34
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.33
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.33
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.21
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.21
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.21
tlyA 1917972 c.33A>G synonymous_variant 1.0
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
thyA 3073880 p.Glu198Lys missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473998 c.-9G>A upstream_gene_variant 1.0
fprA 3473998 c.-10_-9insA upstream_gene_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
rpoA 3877919 p.Glu197Lys missense_variant 1.0
embC 4240146 p.Ala95Val missense_variant 0.1
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