TB-Profiler result

Run: ERR1063888
Summary

Run ID: ERR1063888

Sample name:

Date: 31-03-2023 10:32:32

Number of reads: 2990054

Percentage reads mapped: 89.75

Strain: lineage1.1.2

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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 1.0
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
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 1.0
gyrB 6124 c.885C>T synonymous_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 765171 p.Pro601Leu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 0.98
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.11
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.12
rrs 1472803 n.958T>C non_coding_transcript_exon_variant 0.12
rrs 1472953 n.1108G>A non_coding_transcript_exon_variant 0.11
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.11
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 0.11
rrs 1472970 n.1125C>A non_coding_transcript_exon_variant 0.11
rrs 1472975 n.1130T>A non_coding_transcript_exon_variant 0.12
rrs 1472977 n.1132G>T non_coding_transcript_exon_variant 0.12
rrs 1472978 n.1133T>C non_coding_transcript_exon_variant 0.12
rrs 1472982 n.1137G>A non_coding_transcript_exon_variant 0.12
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.12
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.11
rrs 1473001 n.1156G>C non_coding_transcript_exon_variant 0.12
rrs 1473002 n.1157G>A non_coding_transcript_exon_variant 0.12
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.12
rrs 1473008 n.1163C>T non_coding_transcript_exon_variant 0.11
rrs 1473009 n.1164T>G non_coding_transcript_exon_variant 0.11
rrs 1473020 n.1175T>C non_coding_transcript_exon_variant 0.11
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.16
rrl 1476229 n.2572C>G non_coding_transcript_exon_variant 0.17
rrl 1476251 n.2594T>G non_coding_transcript_exon_variant 0.25
rrl 1476256 n.2599A>T non_coding_transcript_exon_variant 0.26
rrl 1476260 n.2603A>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 0.39
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.4
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.39
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.39
rrl 1476297 n.2640C>A non_coding_transcript_exon_variant 0.41
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.4
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.4
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.41
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.44
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.44
rrl 1476353 n.2696G>A non_coding_transcript_exon_variant 0.42
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.37
rrl 1476359 n.2702C>T non_coding_transcript_exon_variant 0.37
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.44
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.43
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.39
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.39
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.36
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.35
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.26
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.25
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.23
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.21
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
PPE35 2167983 p.Gly877Asp missense_variant 0.98
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339741 c.624G>A synonymous_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.98
fprA 3474700 p.Gly232Ser missense_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4249673 p.Ser1054Pro missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4328209 c.-736C>A upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0
gid 4407935 p.Leu90Val missense_variant 1.0
gid 4407944 p.Gln87Glu missense_variant 1.0
gid 4408070 p.Trp45Arg missense_variant 1.0