TB-Profiler result

Run: ERR036224

Summary

Run ID: ERR036224

Sample name:

Date: 31-03-2023 08:30:38

Number of reads: 1096221

Percentage reads mapped: 95.69

Strain: lineage4.3.4.2.1;lineage1.1.3

Drug-resistance: HR-TB


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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 0.72
lineage1 Indo-Oceanic EAI RD239 0.16
lineage4.3 Euro-American (LAM) mainly-LAM None 0.64
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.23
lineage1.1.3 Indo-Oceanic EAI6 RD239 0.08
lineage4.3.4 Euro-American (LAM) LAM RD174 0.38
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 0.39
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 1472733 n.888G>A non_coding_transcript_exon_variant 0.15 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.33 isoniazid, ethionamide
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 0.17
gyrB 6140 p.Val301Leu missense_variant 0.38
gyrA 6445 c.-857C>T upstream_gene_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7493 c.192C>T synonymous_variant 0.21
gyrA 7585 p.Ser95Thr missense_variant 0.89
gyrA 8040 p.Gly247Ser missense_variant 0.12
gyrA 8188 p.Leu296Pro missense_variant 0.17
gyrA 8377 p.Asp359Gly missense_variant 0.29
gyrA 8452 p.Ala384Val missense_variant 0.15
gyrA 9143 c.1842T>C synonymous_variant 0.16
gyrA 9304 p.Gly668Asp missense_variant 0.76
fgd1 491742 c.960T>C synonymous_variant 0.23
ccsA 619695 c.-196G>A upstream_gene_variant 0.24
ccsA 620029 c.139C>T synonymous_variant 0.18
ccsA 620407 p.Pro173Ala missense_variant 0.37
ccsA 620625 p.Ile245Met missense_variant 0.12
rpoB 759608 c.-199C>T upstream_gene_variant 0.13
rpoB 762249 p.Leu815Val missense_variant 0.14
rpoC 762836 c.-534C>G upstream_gene_variant 0.25
rpoC 763031 c.-339T>C upstream_gene_variant 0.3
rpoC 764995 c.1626C>G synonymous_variant 0.42
rpoC 765171 p.Pro601Leu missense_variant 0.11
rpoC 765230 p.Ala621Thr missense_variant 0.2
rpoC 767305 p.Tyr1312* stop_gained 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777745 p.Gly246Ser missense_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800997 p.Asn63Lys missense_variant 0.36
rplC 801166 p.Gly120Ser missense_variant 0.25
Rv1258c 1407055 c.285delG frameshift_variant 0.15
Rv1258c 1407240 p.Val34Gly missense_variant 0.38
embR 1417019 p.Cys110Tyr missense_variant 0.15
embR 1417501 c.-154A>C upstream_gene_variant 0.43
atpE 1461019 c.-26C>A upstream_gene_variant 0.28
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.13
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.1
rrs 1472378 n.533G>T non_coding_transcript_exon_variant 0.19
rrs 1472379 n.534T>G non_coding_transcript_exon_variant 0.19
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.19
rrs 1472389 n.544G>A non_coding_transcript_exon_variant 0.18
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 0.18
rrs 1472412 n.567A>C non_coding_transcript_exon_variant 0.19
rrs 1472415 n.570T>G non_coding_transcript_exon_variant 0.16
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.1
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.15
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.24
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.24
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.19
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.11
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.11
rrs 1473343 n.1498G>T non_coding_transcript_exon_variant 0.27
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 0.24
rrl 1474380 n.723G>T non_coding_transcript_exon_variant 0.23
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.25
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.15
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.15
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.15
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.14
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.13
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.17
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.23
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.29
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.42
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.3
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.34
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.3
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.26
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.21
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.12
inhA 1674892 p.Asn231Asp missense_variant 0.4
rpsA 1834177 c.636A>C synonymous_variant 0.23
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918106 p.Thr56Ile missense_variant 0.15
ndh 2102891 p.Phe51Ser missense_variant 0.35
katG 2154724 p.Arg463Leu missense_variant 0.36
PPE35 2167926 p.Leu896Ser missense_variant 0.36
PPE35 2167983 p.Gly877Asp missense_variant 0.33
PPE35 2169320 p.Leu431Phe missense_variant 0.13
PPE35 2169866 c.747G>C synonymous_variant 0.31
Rv1979c 2222308 p.Asp286Gly missense_variant 0.3
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.21
kasA 2518144 c.29dupG frameshift_variant 0.17
kasA 2518919 p.Gly269Ser missense_variant 0.2
eis 2714366 p.Val323Leu missense_variant 0.2
ahpC 2726051 c.-142G>A upstream_gene_variant 0.21
ahpC 2726756 c.564C>G synonymous_variant 0.35
pepQ 2859381 c.1038C>G synonymous_variant 0.18
ribD 2987307 p.Ala157Pro missense_variant 0.3
Rv2752c 3064552 p.Arg547Pro missense_variant 0.23
Rv2752c 3064632 c.1560C>T synonymous_variant 0.28
Rv2752c 3064741 p.Gly484Ala missense_variant 0.4
thyA 3073868 p.Thr202Ala missense_variant 0.46
thyA 3074654 c.-183T>G upstream_gene_variant 0.5
ald 3086788 c.-32T>C upstream_gene_variant 0.86
Rv3083 3448714 p.Asp71His missense_variant 0.17
Rv3083 3448929 p.Tyr142* stop_gained 0.24
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474601 p.Arg199Gly missense_variant 0.17
fprA 3475159 p.Asn385Asp missense_variant 0.11
Rv3236c 3612009 p.Ala370Thr missense_variant 0.33
fbiB 3642734 c.1200G>C synonymous_variant 0.4
fbiB 3642772 p.Asp413Ala missense_variant 0.33
alr 3840719 c.702A>G synonymous_variant 0.52
rpoA 3878238 p.Asp90Glu missense_variant 0.15
clpC1 4038287 c.2418C>T synonymous_variant 0.63
clpC1 4039363 p.Ala448Pro missense_variant 0.4
clpC1 4039932 p.Gly258Val missense_variant 0.18
clpC1 4040517 p.Val63Ala missense_variant 0.24
embC 4241042 p.Asn394Asp missense_variant 0.22
embC 4241429 p.Phe523Val missense_variant 0.71
embC 4242425 p.Arg855Gly missense_variant 0.29
embC 4242476 p.Pro872Ala missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.23
embA 4243460 c.228C>T synonymous_variant 0.23
embA 4244263 p.Leu344Arg missense_variant 0.22
embA 4245025 p.His598Arg missense_variant 0.12
embA 4245969 p.Pro913Ser missense_variant 0.18
embB 4247603 p.Leu364Val missense_variant 0.31
embB 4247646 p.Glu378Ala missense_variant 0.2
embB 4249732 c.3219C>G synonymous_variant 0.12
ubiA 4269387 p.Glu149Asp missense_variant 0.29
aftB 4269606 c.-770T>C upstream_gene_variant 0.38
ethA 4327672 c.-199G>A upstream_gene_variant 0.29
whiB6 4338371 p.Thr51Pro missense_variant 0.29
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.36
gid 4407873 c.330G>T synonymous_variant 0.18
gid 4407927 p.Glu92Asp missense_variant 0.17
gid 4408156 p.Leu16Arg missense_variant 0.64