TB-Profiler result

Run: SRR5709926
Summary

Run ID: SRR5709926

Sample name:

Date: 25-01-2024 13:08:56

Number of reads: 4218165

Percentage reads mapped: 79.35

Strain: lineage2.2.1

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
Rifampicin R rpoB p.His445Tyr (0.95)
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Val (0.94)
Pyrazinamide
Streptomycin R rrs n.514A>C (1.00)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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 761139 p.His445Tyr missense_variant 0.95 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247429 p.Met306Val missense_variant 0.94 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620526 c.636G>T synonymous_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761441 p.Asp545Glu missense_variant 1.0
rpoC 762995 c.-375G>T upstream_gene_variant 0.13
rpoC 763022 c.-348C>G upstream_gene_variant 0.11
rpoC 763028 c.-342T>C upstream_gene_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 0.99
rpoB 763038 p.Thr1078Ala missense_variant 0.11
rpoC 763088 c.-282C>G upstream_gene_variant 0.1
rpoC 763618 c.249C>G synonymous_variant 0.14
rpoC 763621 c.252C>G synonymous_variant 0.14
rpoC 763633 c.264T>C synonymous_variant 0.14
rpoC 763636 c.267T>C synonymous_variant 0.14
rpoC 763660 c.291T>C synonymous_variant 0.12
rpoC 763663 c.294C>T synonymous_variant 0.12
rpoC 763666 c.297G>A synonymous_variant 0.12
rpoC 763669 c.300C>G synonymous_variant 0.12
rpoC 763672 c.303C>G synonymous_variant 0.12
rpoC 763696 c.327T>C synonymous_variant 0.12
rpoC 763702 c.333C>G synonymous_variant 0.1
rpoC 764405 c.1036_1038delAGGinsCGC synonymous_variant 0.1
rpoC 764419 c.1050C>G synonymous_variant 0.11
rpoC 764431 c.1062G>C synonymous_variant 0.11
rpoC 764434 c.1065A>G synonymous_variant 0.11
rpoC 764435 c.1066_1068delAGGinsCGC synonymous_variant 0.11
rpoC 764446 c.1077T>C synonymous_variant 0.12
rpoC 764452 c.1083T>C synonymous_variant 0.13
rpoC 764458 c.1089G>C synonymous_variant 0.13
rpoC 764461 c.1092A>G synonymous_variant 0.13
rpoC 764497 c.1128A>G synonymous_variant 0.15
rpoC 764498 p.Ser377Ala missense_variant 0.15
rpoC 764503 c.1134G>C synonymous_variant 0.15
rpoC 764521 c.1152T>C synonymous_variant 0.17
rpoC 764539 c.1170C>G synonymous_variant 0.16
rpoC 764542 c.1173C>G synonymous_variant 0.16
rpoC 764548 c.1179G>A synonymous_variant 0.16
rpoC 764560 c.1191T>C synonymous_variant 0.15
rpoC 764575 c.1206T>C synonymous_variant 0.16
rpoC 764581 c.1212T>C synonymous_variant 0.16
rpoC 764582 p.Leu405Met missense_variant 0.17
rpoC 764623 c.1254C>G synonymous_variant 0.16
rpoC 764632 c.1263T>C synonymous_variant 0.15
rpoC 764644 c.1275G>C synonymous_variant 0.17
rpoC 764650 c.1281G>T synonymous_variant 0.17
rpoC 764695 c.1326T>C synonymous_variant 0.15
rpoC 764706 p.Leu446Gln missense_variant 0.16
rpoC 764752 c.1383G>C synonymous_variant 0.15
rpoC 764764 c.1395T>C synonymous_variant 0.14
rpoC 764780 c.1411_1412delAGinsTC synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472148 n.303T>C non_coding_transcript_exon_variant 0.17
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.17
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.17
rrs 1472225 n.380C>G non_coding_transcript_exon_variant 0.15
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.13
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.12
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.12
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.11
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.11
rrs 1472957 n.1112C>G non_coding_transcript_exon_variant 0.11
rrs 1472968 n.1124_1130delACGTAAT non_coding_transcript_exon_variant 0.12
rrs 1472978 n.1133_1134insTCGGCC non_coding_transcript_exon_variant 0.12
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.1
rrs 1472989 n.1144G>C non_coding_transcript_exon_variant 0.1
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.1
rrs 1472991 n.1146G>A non_coding_transcript_exon_variant 0.1
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.15
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.18
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.2
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.2
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.21
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.21
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.2
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.21
rrs 1473262 n.1417T>C non_coding_transcript_exon_variant 0.2
rrs 1473276 n.1431A>C non_coding_transcript_exon_variant 0.2
rrs 1473277 n.1432G>A non_coding_transcript_exon_variant 0.19
rrs 1473289 n.1444_1445delTCinsCTTTTTG non_coding_transcript_exon_variant 0.15
rrs 1473300 n.1455C>T non_coding_transcript_exon_variant 0.15
rrs 1473301 n.1456T>G non_coding_transcript_exon_variant 0.15
rrs 1473314 n.1469A>G non_coding_transcript_exon_variant 0.16
rrs 1473315 n.1470T>C non_coding_transcript_exon_variant 0.17
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.17
rrl 1474483 n.826C>G non_coding_transcript_exon_variant 0.11
rrl 1474488 n.831G>C non_coding_transcript_exon_variant 0.11
rrl 1474508 n.851C>T non_coding_transcript_exon_variant 0.12
rrl 1474516 n.859C>G non_coding_transcript_exon_variant 0.12
rrl 1474527 n.870T>C non_coding_transcript_exon_variant 0.12
rrl 1474528 n.871T>A non_coding_transcript_exon_variant 0.12
rrl 1474530 n.873G>C non_coding_transcript_exon_variant 0.12
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.12
rrl 1474539 n.882C>G non_coding_transcript_exon_variant 0.11
rrl 1474541 n.884G>T non_coding_transcript_exon_variant 0.12
rrl 1474542 n.885A>G non_coding_transcript_exon_variant 0.12
rrl 1474551 n.894G>C non_coding_transcript_exon_variant 0.13
rrl 1474558 n.901G>T non_coding_transcript_exon_variant 0.15
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.18
rrl 1474636 n.979A>T non_coding_transcript_exon_variant 0.15
rrl 1474637 n.980C>T non_coding_transcript_exon_variant 0.15
rrl 1474638 n.981C>G non_coding_transcript_exon_variant 0.15
rrl 1474639 n.982G>C non_coding_transcript_exon_variant 0.16
rrl 1474651 n.995delT non_coding_transcript_exon_variant 0.17
rrl 1474664 n.1007G>T non_coding_transcript_exon_variant 0.17
rrl 1474666 n.1009T>G non_coding_transcript_exon_variant 0.17
rrl 1474676 n.1019T>C non_coding_transcript_exon_variant 0.18
rrl 1474687 n.1030C>A non_coding_transcript_exon_variant 0.19
rrl 1474708 n.1053_1054delTG non_coding_transcript_exon_variant 0.14
rrl 1474713 n.1056_1057insAA non_coding_transcript_exon_variant 0.14
rrl 1474716 n.1059A>G non_coding_transcript_exon_variant 0.15
rrl 1474734 n.1077G>T non_coding_transcript_exon_variant 0.17
rrl 1474749 n.1092C>T non_coding_transcript_exon_variant 0.15
rrl 1474753 n.1097delC non_coding_transcript_exon_variant 0.17
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.18
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.18
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.18
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.15
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.14
rrl 1474824 n.1167A>G non_coding_transcript_exon_variant 0.14
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.14
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.15
rrl 1475713 n.2056C>T non_coding_transcript_exon_variant 0.11
rrl 1475740 n.2083G>C non_coding_transcript_exon_variant 0.12
rrl 1475747 n.2090A>G non_coding_transcript_exon_variant 0.11
rrl 1475753 n.2096C>T non_coding_transcript_exon_variant 0.11
rrl 1475758 n.2101A>G non_coding_transcript_exon_variant 0.11
rrl 1475760 n.2103C>T non_coding_transcript_exon_variant 0.11
rrl 1475769 n.2112T>C non_coding_transcript_exon_variant 0.11
rrl 1475781 n.2124T>C non_coding_transcript_exon_variant 0.13
rrl 1475788 n.2131C>G non_coding_transcript_exon_variant 0.15
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.12
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.12
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.12
rrl 1475900 n.2243A>G non_coding_transcript_exon_variant 0.12
rrl 1475902 n.2245T>C non_coding_transcript_exon_variant 0.12
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.12
rrl 1476164 n.2507A>G non_coding_transcript_exon_variant 0.12
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.12
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.17
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.18
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.18
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.19
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.19
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.18
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 0.19
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.18
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.23
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.21
rrl 1476255 n.2598A>G non_coding_transcript_exon_variant 0.2
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.2
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.21
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.24
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.18
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.17
rrl 1476298 n.2641C>G non_coding_transcript_exon_variant 0.17
rrl 1476299 n.2642C>T non_coding_transcript_exon_variant 0.17
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.17
rrl 1476309 n.2652G>C non_coding_transcript_exon_variant 0.18
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.24
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.27
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.21
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.17
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.18
rrl 1476528 n.2871A>G non_coding_transcript_exon_variant 0.18
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.18
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.18
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.18
rpsA 1833540 c.-2A>G upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156552 c.-441C>T upstream_gene_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4326676 p.Ser266Arg missense_variant 0.99
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0