TB-Profiler result

Run: ERR181708

Summary

Run ID: ERR181708

Sample name:

Date: 24-01-2024 12:25:35

Number of reads: 5522065

Percentage reads mapped: 87.06

Strain: lineage4;lineage1.1.2

Drug-resistance: RR-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.Leu430Pro (0.92)
Isoniazid
Ethambutol
Pyrazinamide
Streptomycin
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
lineage4 Euro-American LAM;T;S;X;H None 0.08
lineage1 Indo-Oceanic EAI RD239 0.92
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.95
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 0.94
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 761095 p.Leu430Pro missense_variant 0.92 rifampicin
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 6112 p.Met291Ile missense_variant 0.95
gyrB 6124 c.885C>T synonymous_variant 0.94
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.93
gyrA 9143 c.1842T>C synonymous_variant 0.94
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.92
rpoC 763031 c.-339T>C upstream_gene_variant 0.92
rpoC 763884 p.Ala172Val missense_variant 0.94
rpoC 763886 c.517C>A synonymous_variant 0.94
rpoC 765171 p.Pro601Leu missense_variant 0.92
rpoC 765988 c.2619G>A synonymous_variant 0.95
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.94
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 0.94
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.13
rrs 1472117 n.272A>T non_coding_transcript_exon_variant 0.22
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 0.22
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.23
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.23
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.24
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.26
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.29
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.29
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.29
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.29
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.29
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.26
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.12
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.1
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.14
rrs 1472733 n.888G>C non_coding_transcript_exon_variant 0.22
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.22
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.21
rrs 1472742 n.897C>G non_coding_transcript_exon_variant 0.22
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.22
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.23
rrs 1472779 n.934G>A non_coding_transcript_exon_variant 0.23
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.23
rrs 1472786 n.941C>T non_coding_transcript_exon_variant 0.23
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.21
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.19
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.18
rrs 1473147 n.1302G>C non_coding_transcript_exon_variant 0.17
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.17
rrs 1473150 n.1305T>G non_coding_transcript_exon_variant 0.18
rrs 1473161 n.1316A>C non_coding_transcript_exon_variant 0.17
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.17
rrs 1473164 n.1319C>G non_coding_transcript_exon_variant 0.17
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.18
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.18
rrs 1473179 n.1334C>T non_coding_transcript_exon_variant 0.18
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.16
rrs 1473201 n.1356_1357delACinsT non_coding_transcript_exon_variant 0.17
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.16
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.16
rrl 1474780 n.1123C>T non_coding_transcript_exon_variant 0.15
rrl 1474790 n.1133C>T non_coding_transcript_exon_variant 0.26
rrl 1474798 n.1141C>T non_coding_transcript_exon_variant 0.31
rrl 1474800 n.1143T>C non_coding_transcript_exon_variant 0.32
rrl 1474804 n.1147C>T non_coding_transcript_exon_variant 0.34
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.38
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.38
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.4
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.41
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.39
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.21
rrl 1474902 n.1245T>C non_coding_transcript_exon_variant 0.19
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.18
rrl 1474913 n.1256T>A non_coding_transcript_exon_variant 0.15
rrl 1476113 n.2456T>A non_coding_transcript_exon_variant 0.12
rrl 1476122 n.2465A>C non_coding_transcript_exon_variant 0.13
rrl 1476126 n.2469C>T non_coding_transcript_exon_variant 0.13
rrl 1476128 n.2471T>A non_coding_transcript_exon_variant 0.13
rrl 1476135 n.2478T>C non_coding_transcript_exon_variant 0.14
rrl 1476141 n.2484A>G non_coding_transcript_exon_variant 0.15
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.15
rrl 1476164 n.2507A>G non_coding_transcript_exon_variant 0.13
rrl 1476165 n.2508T>A non_coding_transcript_exon_variant 0.14
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.3
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.37
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.47
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.5
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.56
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.58
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.59
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.73
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.72
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.74
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.54
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.43
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.17
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.2
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.2
rrl 1476577 n.2920T>G non_coding_transcript_exon_variant 0.2
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.21
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.21
rrl 1476603 n.2946G>A non_coding_transcript_exon_variant 0.22
rrl 1476608 n.2951C>A non_coding_transcript_exon_variant 0.22
rrl 1476614 n.2957A>G non_coding_transcript_exon_variant 0.22
rrl 1476619 n.2962C>T non_coding_transcript_exon_variant 0.21
rrl 1476621 n.2964C>A non_coding_transcript_exon_variant 0.21
rrl 1476624 n.2967T>A non_coding_transcript_exon_variant 0.21
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.21
rrl 1476630 n.2973A>G non_coding_transcript_exon_variant 0.2
rrl 1476637 n.2980C>G non_coding_transcript_exon_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.94
PPE35 2167926 p.Leu896Ser missense_variant 0.91
PPE35 2167983 p.Gly877Asp missense_variant 0.92
Rv1979c 2222308 p.Asp286Gly missense_variant 0.94
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.96
ahpC 2726051 c.-142G>A upstream_gene_variant 0.89
ahpC 2726468 c.276G>A synonymous_variant 0.95
Rv2752c 3064632 c.1560C>T synonymous_variant 0.9
thyX 3067491 p.Ala152Val missense_variant 0.9
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086823 p.Arg2Gly missense_variant 0.12
Rv3083 3448714 p.Asp71His missense_variant 0.94
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.95
fprA 3475023 c.1017G>A synonymous_variant 0.91
fprA 3475159 p.Asn385Asp missense_variant 0.91
fbiA 3640446 c.-97A>T upstream_gene_variant 0.93
clpC1 4040517 p.Val63Ala missense_variant 0.96
embC 4240671 p.Thr270Ile missense_variant 0.93
embC 4241042 p.Asn394Asp missense_variant 0.91
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 0.93
embA 4245969 p.Pro913Ser missense_variant 0.95
embB 4247646 p.Glu378Ala missense_variant 0.89
ubiA 4269387 p.Glu149Asp missense_variant 0.91
aftB 4269606 c.-770T>C upstream_gene_variant 0.92
ethA 4326851 p.Ser208Leu missense_variant 0.92
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.9
gid 4407588 c.615A>G synonymous_variant 0.97
gid 4407873 c.330G>T synonymous_variant 0.91