TB-Profiler result

Run: ERR4820586
Summary

Run ID: ERR4820586

Sample name:

Date: 20-10-2023 09:23:59

Number of reads: 2474317

Percentage reads mapped: 90.78

Strain: lineage3

Drug-resistance: Other

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid
Ethambutol
Pyrazinamide
Streptomycin
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides R rrs n.1402C>A (0.16), rrs n.1484G>T (0.15)
Amikacin R rrs n.1402C>A (0.16), rrs n.1484G>T (0.15)
Capreomycin R rrs n.1402C>A (0.16), rrs n.1484G>T (0.15)
Kanamycin R rrs n.1402C>A (0.16), rrs n.1484G>T (0.15)
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
lineage3 East-African-Indian CAS RD750 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 1473247 n.1402C>A non_coding_transcript_exon_variant 0.16 kanamycin, capreomycin, aminoglycosides, amikacin
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 0.15 kanamycin, capreomycin, aminoglycosides, amikacin
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 5075 c.-165C>T 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
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 762101 c.2295C>G synonymous_variant 0.14
rpoB 762114 p.Ile770Val missense_variant 0.16
rpoB 762122 p.Asp772Glu missense_variant 0.15
rpoB 762125 p.Glu773Asp missense_variant 0.13
rpoB 762132 p.Ala776Ser missense_variant 0.14
rpoB 762136 p.Asp777Ala missense_variant 0.14
rpoB 762143 c.2337T>C synonymous_variant 0.14
rpoB 762149 c.2343G>C synonymous_variant 0.15
rpoB 762156 p.Val784Ile missense_variant 0.15
rpoB 762160 p.Arg785His missense_variant 0.15
rpoB 762167 c.2361T>C synonymous_variant 0.14
rpoB 762175 c.2370_2372delTCG disruptive_inframe_deletion 0.14
rpoB 762181 c.2375_2376insGGC disruptive_inframe_insertion 0.14
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763570 c.201G>C synonymous_variant 0.12
rpoC 763660 c.291T>G synonymous_variant 0.1
rpoC 763675 c.306C>G synonymous_variant 0.12
rpoC 763696 c.327T>C synonymous_variant 0.15
rpoC 763705 c.336G>C synonymous_variant 0.15
rpoC 763708 c.339G>C synonymous_variant 0.15
rpoC 763714 c.345G>C synonymous_variant 0.15
rpoC 763717 c.348T>C synonymous_variant 0.15
rpoC 763726 c.357C>T synonymous_variant 0.15
rpoC 763732 c.363C>G synonymous_variant 0.15
rpoC 763741 c.372C>T synonymous_variant 0.12
rpoC 763765 c.396T>C synonymous_variant 0.17
rpoC 763772 p.Val135Met missense_variant 0.16
rpoC 764405 c.1036A>C synonymous_variant 0.15
rpoC 764410 c.1041G>C synonymous_variant 0.18
rpoC 764428 c.1059G>C synonymous_variant 0.17
rpoC 764434 c.1065A>G synonymous_variant 0.17
rpoC 764435 c.1066_1068delAGGinsCGC synonymous_variant 0.16
rpoC 764441 p.Ile358Leu missense_variant 0.16
rpoC 764449 c.1080G>C synonymous_variant 0.19
rpoC 764458 c.1089G>C synonymous_variant 0.2
rpoC 764461 c.1092A>G synonymous_variant 0.2
rpoC 764470 c.1101C>G synonymous_variant 0.22
rpoC 764497 c.1128A>G synonymous_variant 0.25
rpoC 764498 p.Ser377Ala missense_variant 0.24
rpoC 764507 p.Ala380Ser missense_variant 0.23
rpoC 764521 c.1152T>C synonymous_variant 0.25
rpoC 764524 c.1155C>T synonymous_variant 0.25
rpoC 764527 c.1158C>G synonymous_variant 0.26
rpoC 764536 c.1167G>T synonymous_variant 0.24
rpoC 764539 c.1170C>G synonymous_variant 0.23
rpoC 764560 c.1191T>C synonymous_variant 0.2
rpoC 764566 c.1197C>G synonymous_variant 0.2
rpoC 764572 c.1203G>C synonymous_variant 0.21
rpoC 764575 c.1206T>G synonymous_variant 0.21
rpoC 764578 c.1209C>G synonymous_variant 0.2
rpoC 764581 c.1212T>C synonymous_variant 0.2
rpoC 764582 p.Leu405Met missense_variant 0.2
rpoC 764611 c.1242G>C synonymous_variant 0.18
rpoC 764623 c.1254C>G synonymous_variant 0.16
rpoC 764632 c.1263T>C synonymous_variant 0.15
rpoC 764635 c.1266C>G synonymous_variant 0.18
rpoC 764650 c.1281G>C synonymous_variant 0.15
rpoC 764665 c.1296C>G synonymous_variant 0.14
rpoC 764677 c.1308C>G synonymous_variant 0.11
rpoC 764681 p.Leu438Met missense_variant 0.12
rpoC 764706 p.Leu446Gln missense_variant 0.12
rpoC 764713 c.1344G>C synonymous_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776445 p.Ala679Asp missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302758 c.-173A>G upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 0.99
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.23
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.25
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.42
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.46
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.56
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.59
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.48
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.33
rrs 1472825 n.980G>A non_coding_transcript_exon_variant 0.33
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.37
rrs 1472836 n.991G>A non_coding_transcript_exon_variant 0.37
rrs 1472840 n.995A>C non_coding_transcript_exon_variant 0.33
rrs 1472844 n.999C>T non_coding_transcript_exon_variant 0.33
rrs 1472845 n.1000G>C non_coding_transcript_exon_variant 0.33
rrs 1472846 n.1001C>G non_coding_transcript_exon_variant 0.33
rrs 1472847 n.1002G>T non_coding_transcript_exon_variant 0.33
rrs 1472850 n.1005T>C non_coding_transcript_exon_variant 0.32
rrs 1472857 n.1012A>G non_coding_transcript_exon_variant 0.38
rrs 1472859 n.1014G>T non_coding_transcript_exon_variant 0.38
rrs 1472860 n.1015C>T non_coding_transcript_exon_variant 0.38
rrs 1472861 n.1016G>C non_coding_transcript_exon_variant 0.38
rrs 1472869 n.1024G>T non_coding_transcript_exon_variant 0.35
rrs 1472873 n.1028C>G non_coding_transcript_exon_variant 0.33
rrs 1472875 n.1031dupG non_coding_transcript_exon_variant 0.33
rrs 1472880 n.1035G>A non_coding_transcript_exon_variant 0.43
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.43
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.48
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.52
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.65
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.63
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.62
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.62
rrs 1473089 n.1244A>T non_coding_transcript_exon_variant 0.52
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.44
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.38
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.3
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.3
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.27
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.27
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.27
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.26
rrs 1473122 n.1277T>A non_coding_transcript_exon_variant 0.26
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.23
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.16
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.16
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.17
rrs 1473277 n.1432G>A non_coding_transcript_exon_variant 0.17
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.18
rrs 1473292 n.1447_1455delGGAGGGAGCinsTGGAGGGAGT non_coding_transcript_exon_variant 0.2
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.17
rrs 1473315 n.1470T>C non_coding_transcript_exon_variant 0.14
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.15
rrl 1473577 n.-81A>C upstream_gene_variant 1.0
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.71
rrl 1474275 n.618T>G non_coding_transcript_exon_variant 0.75
rrl 1474284 n.631_633delCCT non_coding_transcript_exon_variant 0.62
rrl 1474293 n.637_651delCCTCTCCGGAGGAGG non_coding_transcript_exon_variant 0.57
rrl 1474310 n.653T>G non_coding_transcript_exon_variant 0.57
rrl 1474348 n.691C>T non_coding_transcript_exon_variant 0.5
rrl 1474351 n.694G>T non_coding_transcript_exon_variant 0.5
rrl 1474353 n.696A>T non_coding_transcript_exon_variant 0.5
rrl 1474354 n.697C>T non_coding_transcript_exon_variant 0.6
rrl 1474355 n.698A>C non_coding_transcript_exon_variant 0.6
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.6
rrl 1475722 n.2065G>T non_coding_transcript_exon_variant 0.53
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 0.45
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.59
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.71
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.59
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.61
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.49
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.46
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A 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
alr 3841473 c.-53G>A upstream_gene_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0