TB-Profiler result

Run: ERR702399

Summary

Run ID: ERR702399

Sample name:

Date: 19-10-2023 20:24:35

Number of reads: 3249341

Percentage reads mapped: 91.09

Strain: lineage5.1.1

Drug-resistance: Sensitive


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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
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
lineage5 West-Africa 1 AFRI_2;AFRI_3 RD711 1.0
lineage5.1 West-Africa 1 AFRI_2;AFRI_3 RD711 0.84
lineage5.1.1 West-Africa 1 AFRI_2;AFRI_3 RD711 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
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 6446 p.Ala403Ser missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9566 c.2265C>T synonymous_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763280 c.-90C>T upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
Rv1258c 1406511 p.Gly277Val missense_variant 1.0
Rv1258c 1407273 p.Asp23Val missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.24
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.23
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.25
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.26
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.23
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.34
rrs 1472518 n.673G>C non_coding_transcript_exon_variant 0.34
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.37
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.36
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.36
rrs 1472544 n.699C>G non_coding_transcript_exon_variant 0.36
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.36
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.47
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.49
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.48
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.5
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.49
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.23
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.27
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.39
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.38
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.41
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.36
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.33
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.26
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.19
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.18
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.19
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.2
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.2
rrs 1473080 n.1235C>A non_coding_transcript_exon_variant 0.2
rrs 1473082 n.1237G>A non_coding_transcript_exon_variant 0.2
rrs 1473084 n.1239T>A non_coding_transcript_exon_variant 0.2
rrs 1473094 n.1249T>A non_coding_transcript_exon_variant 0.19
rrs 1473099 n.1254T>A non_coding_transcript_exon_variant 0.21
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.21
rrs 1473147 n.1302G>C non_coding_transcript_exon_variant 0.18
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.17
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.21
rrs 1473164 n.1319C>G non_coding_transcript_exon_variant 0.21
rrs 1473172 n.1327T>C non_coding_transcript_exon_variant 0.22
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.21
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.22
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.26
rrs 1473201 n.1356_1357delACinsT non_coding_transcript_exon_variant 0.25
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.25
rrl 1474289 n.632C>G non_coding_transcript_exon_variant 1.0
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.5
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.53
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.53
rrl 1474830 n.1173A>T non_coding_transcript_exon_variant 0.53
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.54
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.59
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.55
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.55
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.54
rrl 1474902 n.1245T>C non_coding_transcript_exon_variant 0.45
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.43
rrl 1474913 n.1256T>A non_coding_transcript_exon_variant 0.33
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.24
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.25
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.28
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.28
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.38
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.35
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.33
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.31
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.32
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.33
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.33
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.33
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.32
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.31
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.31
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.47
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.54
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.54
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.55
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.62
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.63
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.65
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.6
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.59
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.6
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.47
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.39
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.29
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.23
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.17
inhA 1673338 c.-864G>A upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101921 c.1122G>A synonymous_variant 1.0
ndh 2103112 c.-70G>T upstream_gene_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 2290062 c.-821G>A upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
ald 3087084 c.266delA frameshift_variant 1.0
ald 3087184 c.368_373delCCGACG disruptive_inframe_deletion 1.0
Rv3083 3449644 p.Ala381Thr missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
alr 3840932 c.489C>T synonymous_variant 1.0
rpoA 3878493 c.15G>A synonymous_variant 1.0
ddn 3986987 c.144G>T synonymous_variant 1.0
ddn 3987180 p.Asp113Asn missense_variant 1.0
clpC1 4040824 c.-120C>T upstream_gene_variant 1.0
embC 4239843 c.-20A>C upstream_gene_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244220 c.988C>T synonymous_variant 1.0
embA 4244635 p.Val468Ala missense_variant 1.0
embA 4245147 p.Pro639Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethR 4326928 c.-621G>A upstream_gene_variant 1.0
ethA 4327103 p.Gly124Asp missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0