TB-Profiler result

Run: SRR13861417
Summary

Run ID: SRR13861417

Sample name:

Date: 03-04-2023 09:31:18

Number of reads: 2748215

Percentage reads mapped: 68.77

Strain: lineage4.9

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
lineage4.9 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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.26 streptomycin
katG 2154798 c.1313_1314insT frameshift_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
gyrB 5906 p.Val223Leu missense_variant 1.0
gyrB 6011 p.Val258Met missense_variant 1.0
gyrB 6678 p.Pro480Arg missense_variant 1.0
fgd1 490676 c.-107G>C upstream_gene_variant 1.0
ccsA 620028 c.138G>C synonymous_variant 1.0
rpoB 759638 c.-169T>A upstream_gene_variant 1.0
rpoB 760454 c.650delG frameshift_variant 1.0
rpoC 765487 p.Met706Ile missense_variant 1.0
rpsL 781409 c.-151T>A upstream_gene_variant 1.0
fbiC 1302873 c.-58A>T upstream_gene_variant 1.0
rrs 1471874 n.29A>C non_coding_transcript_exon_variant 1.0
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.18
rrs 1472122 n.277G>A non_coding_transcript_exon_variant 0.12
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.21
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.21
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.23
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.23
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.22
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.22
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.22
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.22
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.22
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.22
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.22
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 0.22
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.21
rrs 1472234 n.389T>C non_coding_transcript_exon_variant 0.22
rrs 1472236 n.391C>G non_coding_transcript_exon_variant 0.21
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.22
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.16
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.15
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.11
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.16
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.17
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.17
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.18
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.18
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.18
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.17
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.19
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.19
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.19
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.2
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.18
rrs 1472596 n.751G>T non_coding_transcript_exon_variant 0.18
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.19
rrs 1472614 n.769G>T non_coding_transcript_exon_variant 0.28
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.31
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.33
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.29
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.28
rrs 1472665 n.820G>A non_coding_transcript_exon_variant 0.28
rrs 1472669 n.824_825insTAGG non_coding_transcript_exon_variant 0.27
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.25
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.24
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.25
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.25
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.25
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.25
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.26
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.3
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.34
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.34
rrl 1476268 n.2611A>T non_coding_transcript_exon_variant 0.35
rrl 1476275 n.2618T>A non_coding_transcript_exon_variant 0.36
rrl 1476279 n.2622G>A non_coding_transcript_exon_variant 0.35
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.35
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.34
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.35
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.34
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.34
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.34
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.34
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.34
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.35
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.35
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.37
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.52
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.63
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.65
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.65
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.63
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.64
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.51
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.64
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.63
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.63
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.64
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.68
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.65
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.48
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.4
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.36
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.37
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.37
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.37
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.36
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.36
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.37
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.37
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.37
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.38
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.33
rrl 1476572 n.2915G>A non_coding_transcript_exon_variant 0.34
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.35
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.29
katG 2154654 p.Ser486Arg missense_variant 1.0
katG 2154882 c.1230G>A synonymous_variant 1.0
katG 2155857 c.255C>A synonymous_variant 1.0
PPE35 2170198 p.Ala139Ser missense_variant 1.0
pncA 2290069 c.-828C>T upstream_gene_variant 1.0
eis 2714922 c.411G>A synonymous_variant 1.0
thyA 3074067 c.405C>G synonymous_variant 1.0
alr 3840223 c.1198A>C synonymous_variant 1.0
alr 3840711 p.Ser237Leu missense_variant 1.0
clpC1 4039648 p.Glu353Gln missense_variant 1.0
embC 4242023 p.Val721Leu missense_variant 1.0
embA 4245071 c.1839G>A synonymous_variant 0.99
ethA 4327364 p.Lys37Arg missense_variant 1.0