TB-Profiler result

Run: SRR6511600
Summary

Run ID: SRR6511600

Sample name:

Date: 04-04-2023 15:14:40

Number of reads: 1134366

Percentage reads mapped: 72.46

Strain: lineage4.3.4.2

Drug-resistance: MDR-TB

Download CSV Download TXT Download PDF Download JSON
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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 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 761110 p.Asp435Val missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.55 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
inhA 1674481 p.Ser94Ala missense_variant 1.0 isoniazid, ethionamide
pncA 2288992 c.249dupC frameshift_variant 1.0 pyrazinamide, pyrazinamide
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 6817 c.-485G>A upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305494 c.2565_*55delGGCCTAGCCCCGGCGACGATGCCGGGTCGCGGGATGCGGCCCGTTGAGGAGCGGGGCAATCT frameshift_variant&stop_lost&splice_region_variant 0.31
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.23
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.27
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.27
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.33
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.35
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.4
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.4
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.51
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.5
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.48
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.49
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.49
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.52
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.52
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.53
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.55
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.55
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.55
rrs 1472668 n.825_829delGGGTT non_coding_transcript_exon_variant 0.54
rrs 1472675 n.830_831insAGAC non_coding_transcript_exon_variant 0.55
rrs 1472680 n.835C>T non_coding_transcript_exon_variant 0.54
rrs 1472682 n.837T>C non_coding_transcript_exon_variant 0.54
rrs 1472683 n.838T>G non_coding_transcript_exon_variant 0.53
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.54
rrs 1472689 n.844C>T non_coding_transcript_exon_variant 0.53
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.55
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.58
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.57
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.55
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.55
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.41
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.36
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.29
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.15
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.14
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.14
rrs 1472836 n.991G>C non_coding_transcript_exon_variant 0.14
rrs 1472846 n.1002delG non_coding_transcript_exon_variant 0.13
rrs 1472859 n.1014G>A non_coding_transcript_exon_variant 0.14
rrs 1472860 n.1015C>G non_coding_transcript_exon_variant 0.14
rrs 1472861 n.1016G>T non_coding_transcript_exon_variant 0.14
rrs 1472864 n.1019C>T non_coding_transcript_exon_variant 0.14
rrs 1472869 n.1024G>C non_coding_transcript_exon_variant 0.13
rrs 1472870 n.1025T>G non_coding_transcript_exon_variant 0.13
rrs 1472873 n.1028C>A non_coding_transcript_exon_variant 0.14
rrs 1472875 n.1030T>A non_coding_transcript_exon_variant 0.14
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.12
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.12
rrs 1473248 n.1403G>A non_coding_transcript_exon_variant 0.15
rrs 1473249 n.1404T>C non_coding_transcript_exon_variant 0.15
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.15
rrs 1473255 n.1410A>G non_coding_transcript_exon_variant 0.14
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.14
rrs 1473260 n.1415G>T non_coding_transcript_exon_variant 0.14
rrs 1473274 n.1429C>T non_coding_transcript_exon_variant 0.12
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.13
rrs 1473280 n.1435G>A non_coding_transcript_exon_variant 0.12
rrs 1473281 n.1436C>G non_coding_transcript_exon_variant 0.12
rrs 1473282 n.1437C>G non_coding_transcript_exon_variant 0.12
rrs 1473288 n.1443C>A non_coding_transcript_exon_variant 0.12
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.12
rrs 1473291 n.1446G>T non_coding_transcript_exon_variant 0.12
rrs 1473296 n.1451G>C non_coding_transcript_exon_variant 0.11
rrs 1473297 n.1452G>C non_coding_transcript_exon_variant 0.11
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.11
rrs 1473303 n.1458T>C non_coding_transcript_exon_variant 0.11
rrs 1473318 n.1473G>A non_coding_transcript_exon_variant 0.11
rrs 1473327 n.1482A>G non_coding_transcript_exon_variant 0.11
rrl 1476126 n.2469C>T non_coding_transcript_exon_variant 0.11
rrl 1476130 n.2473G>A non_coding_transcript_exon_variant 0.13
rrl 1476135 n.2478T>C non_coding_transcript_exon_variant 0.18
rrl 1476141 n.2484A>G non_coding_transcript_exon_variant 0.24
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.35
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.44
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.39
rrl 1476195 n.2538C>A non_coding_transcript_exon_variant 0.39
rrl 1476196 n.2539C>A non_coding_transcript_exon_variant 0.39
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.38
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.38
rrl 1476204 n.2547C>A non_coding_transcript_exon_variant 0.38
rrl 1476210 n.2553G>T non_coding_transcript_exon_variant 0.38
rrl 1476211 n.2554G>T non_coding_transcript_exon_variant 0.38
rrl 1476212 n.2555T>C non_coding_transcript_exon_variant 0.38
rrl 1476214 n.2557G>C non_coding_transcript_exon_variant 0.39
rrl 1476215 n.2558C>A non_coding_transcript_exon_variant 0.38
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.49
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 0.49
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.49
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.57
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.57
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.57
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.57
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.56
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.55
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.54
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.54
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.54
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.54
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.54
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.54
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.56
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.57
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.57
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.57
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.58
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.56
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.55
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.54
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.53
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.53
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.53
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.48
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.46
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.48
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.25
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4239763 c.-100C>T upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0
fbiC 1305494 c.2565_*56delCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN frameshift_variant&stop_lost&splice_region_variant 1.0