TB-Profiler result

Run: SRR10315640
Summary

Run ID: SRR10315640

Sample name:

Date: 02-04-2023 17:13:19

Number of reads: 4348718

Percentage reads mapped: 94.4

Strain: lineage4.8

Drug-resistance: MDR-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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.37 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289067 p.Ser59Pro missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
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 6815 p.Lys526Gln missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.34
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 0.2
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.33
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.33
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.27
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.25
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.17
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.22
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.44
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.22
rrs 1472575 n.730C>T non_coding_transcript_exon_variant 0.22
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.38
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.4
rrs 1472591 n.746G>A non_coding_transcript_exon_variant 0.2
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.4
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.2
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.31
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.5
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.41
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.44
rrs 1472680 n.835C>T non_coding_transcript_exon_variant 0.18
rrs 1472687 n.843dupT non_coding_transcript_exon_variant 0.23
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.38
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.24
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.37
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.37
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.33
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.33
rrs 1472966 n.1121A>G non_coding_transcript_exon_variant 0.11
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.13
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.18
rrs 1473276 n.1431A>C non_coding_transcript_exon_variant 0.13
rrs 1473277 n.1432G>A non_coding_transcript_exon_variant 0.12
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474389 n.732G>T non_coding_transcript_exon_variant 0.33
rrl 1474467 n.810A>G non_coding_transcript_exon_variant 0.5
rrl 1474483 n.826C>T non_coding_transcript_exon_variant 0.4
rrl 1474488 n.831G>T non_coding_transcript_exon_variant 0.4
rrl 1474495 n.838G>A non_coding_transcript_exon_variant 0.5
rrl 1474496 n.839C>G non_coding_transcript_exon_variant 0.5
rrl 1474497 n.840G>A non_coding_transcript_exon_variant 0.5
rrl 1474506 n.849C>T non_coding_transcript_exon_variant 0.67
rrl 1474508 n.851C>T non_coding_transcript_exon_variant 0.67
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.67
rrl 1474527 n.870T>C non_coding_transcript_exon_variant 0.67
rrl 1474528 n.871T>A non_coding_transcript_exon_variant 0.67
rrl 1474529 n.872A>G non_coding_transcript_exon_variant 0.67
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.67
rrl 1474540 n.883T>C non_coding_transcript_exon_variant 0.67
rrl 1474541 n.884G>T non_coding_transcript_exon_variant 0.67
rrl 1474542 n.885A>G non_coding_transcript_exon_variant 0.67
rrl 1474551 n.894G>A non_coding_transcript_exon_variant 0.67
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.5
rrl 1475683 n.2026G>T non_coding_transcript_exon_variant 0.29
rrl 1475699 n.2042C>T non_coding_transcript_exon_variant 0.29
rrl 1475722 n.2065G>T non_coding_transcript_exon_variant 0.29
rrl 1475751 n.2094C>T non_coding_transcript_exon_variant 0.29
rrl 1475752 n.2095C>T non_coding_transcript_exon_variant 0.29
rrl 1475753 n.2096C>G non_coding_transcript_exon_variant 0.29
rrl 1475758 n.2101A>G non_coding_transcript_exon_variant 0.29
rrl 1475760 n.2103C>T non_coding_transcript_exon_variant 0.29
rrl 1475762 n.2105G>T non_coding_transcript_exon_variant 0.29
rrl 1475763 n.2106C>T non_coding_transcript_exon_variant 0.25
rrl 1475764 n.2107A>T non_coding_transcript_exon_variant 0.25
rrl 1475765 n.2108A>T non_coding_transcript_exon_variant 0.25
rrl 1475769 n.2112T>C non_coding_transcript_exon_variant 0.25
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.29
rrl 1475783 n.2126T>G non_coding_transcript_exon_variant 0.25
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.13
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.13
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.12
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.12
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.15
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.17
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 0.13
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.14
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.14
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.14
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.14
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.19
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.29
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.18
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.18
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.18
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.18
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.18
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.18
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.18
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.19
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.19
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.19
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.2
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.24
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.38
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.39
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.3
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.31
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.37
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.37
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.36
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.41
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.36
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.15
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.39
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.32
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.24
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.19
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154769 p.Asp448Ala missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.45
fbiD 3339749 p.Val211Gly missense_variant 0.29
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
whiB7 3568428 c.252A>G synonymous_variant 0.22
alr 3840764 c.657G>C synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.23
embB 4247028 p.Leu172Arg missense_variant 0.24
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0