TB-Profiler result

Run: ERR4596937
Summary

Run ID: ERR4596937

Sample name:

Date: 01-04-2023 06:30:05

Number of reads: 681933

Percentage reads mapped: 16.11

Strain: lineage1.1.2

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
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
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
mshA 576108 p.Ala254Gly missense_variant 0.33
mshA 576113 p.Arg256Gly missense_variant 0.25
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 764623 c.1254C>G synonymous_variant 0.12
rpoC 764632 c.1263T>C synonymous_variant 0.12
rpoC 764635 c.1266C>G synonymous_variant 0.12
rpoC 764665 c.1296C>G synonymous_variant 0.15
rpoC 764672 p.Gln435Thr missense_variant 0.16
rpoC 764677 c.1308C>G synonymous_variant 0.15
rpoC 764686 c.1317C>T synonymous_variant 0.14
rpoC 764695 c.1326T>C synonymous_variant 0.14
rpoC 764716 c.1347G>C synonymous_variant 0.14
rpoC 765171 p.Pro601Leu missense_variant 1.0
rpoC 767317 c.3948C>T synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776445 p.Ala679Val missense_variant 0.12
mmpL5 776802 p.Met560Lys missense_variant 0.12
mmpL5 777436 p.Ala349Thr missense_variant 0.15
mmpL5 778155 c.325delT frameshift_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406698 p.Gly215Trp missense_variant 0.15
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.13
rrs 1472210 n.365A>T non_coding_transcript_exon_variant 0.14
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.14
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.15
rrs 1472786 n.941C>G non_coding_transcript_exon_variant 0.12
rrs 1472887 n.1042G>C non_coding_transcript_exon_variant 0.27
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.64
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.63
rrs 1472972 n.1127T>A non_coding_transcript_exon_variant 0.65
rrs 1472974 n.1130_1133delTGGT non_coding_transcript_exon_variant 0.63
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.64
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.64
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.64
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.64
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.64
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.64
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.64
rrs 1473038 n.1193A>C non_coding_transcript_exon_variant 0.65
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.63
rrs 1473053 n.1208T>G non_coding_transcript_exon_variant 0.38
rrs 1473054 n.1209C>G non_coding_transcript_exon_variant 0.35
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.35
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.25
rrs 1473070 n.1225G>C non_coding_transcript_exon_variant 0.18
rrs 1473071 n.1226C>A non_coding_transcript_exon_variant 0.18
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.12
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.13
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.15
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.59
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.6
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.7
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.7
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.7
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.7
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.68
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.68
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.68
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.68
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.69
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.66
rrl 1476411 n.2754G>T non_coding_transcript_exon_variant 0.66
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.66
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.65
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.58
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.59
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.54
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.52
rrl 1476463 n.2806C>A non_coding_transcript_exon_variant 0.52
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.49
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.49
rrl 1476483 n.2826G>A non_coding_transcript_exon_variant 0.41
rrl 1476501 n.2844C>T non_coding_transcript_exon_variant 0.17
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.14
fabG1 1673283 c.-157A>C upstream_gene_variant 1.0
inhA 1674933 c.732G>T synonymous_variant 0.17
tlyA 1917777 c.-163A>G upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918106 p.Thr56Ile missense_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155557 c.555C>T synonymous_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 0.94
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2170378 p.Ala79Thr missense_variant 1.0
Rv1979c 2221783 p.Ala461Glu missense_variant 1.0
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
kasA 2519005 c.891G>A synonymous_variant 0.12
eis 2714199 p.Lys378Asn missense_variant 1.0
eis 2714874 c.459A>C synonymous_variant 0.11
ahpC 2725931 c.-262_-261insG upstream_gene_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726672 c.480G>A synonymous_variant 1.0
pepQ 2859968 p.Asp151Asn missense_variant 0.13
pepQ 2860504 c.-86A>T upstream_gene_variant 0.14
ribD 2986711 c.-128G>A upstream_gene_variant 0.14
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086963 c.144G>A synonymous_variant 0.17
ald 3087033 p.Leu72Phe missense_variant 0.14
ald 3087872 c.1053G>A synonymous_variant 0.14
Rv3083 3448442 c.-62A>C upstream_gene_variant 1.0
Rv3083 3448649 p.Arg49His missense_variant 0.13
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449567 p.Gly355Val missense_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474176 c.174dupC frameshift_variant 0.17
fprA 3474502 p.Leu166Met missense_variant 0.13
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3612297 p.Phe274Leu missense_variant 0.11
Rv3236c 3613012 c.105G>A synonymous_variant 1.0
Rv3236c 3613116 p.Val1Leu missense_variant 0.17
fbiA 3640636 p.Ser32Thr missense_variant 0.18
fbiB 3640758 c.-777G>T upstream_gene_variant 0.18
alr 3840262 p.His387Tyr missense_variant 1.0
clpC1 4038558 p.Ile716Thr missense_variant 0.25
clpC1 4039330 p.Ala459Thr missense_variant 0.14
clpC1 4039935 p.Ala257Val missense_variant 0.17
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240186 c.324G>A synonymous_variant 0.2
embC 4240569 p.Leu236Arg missense_variant 0.12
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4240794 p.Ala311Asp missense_variant 0.18
embC 4241011 c.1149C>T synonymous_variant 0.17
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4242073 c.2211C>T synonymous_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242898 c.-335G>A upstream_gene_variant 0.13
embA 4243848 p.Val206Met missense_variant 1.0
embA 4244799 p.Val523Leu missense_variant 0.18
embA 4244982 c.1750T>C synonymous_variant 0.12
embA 4245166 p.Pro645Gln missense_variant 1.0
embA 4245907 p.Leu892Pro missense_variant 0.12
embA 4245969 p.Pro913Ser missense_variant 1.0
embA 4246095 p.Ala955Thr missense_variant 0.15
embB 4246584 p.Arg24Pro missense_variant 0.29
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4267886 c.951C>T synonymous_variant 0.18
ubiA 4269025 p.Leu270Pro missense_variant 0.15
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ubiA 4269876 c.-43C>T upstream_gene_variant 0.2
ubiA 4269890 c.-57G>A upstream_gene_variant 0.15
whiB6 4338386 p.Asp46Asn missense_variant 0.12
whiB6 4338503 p.Ala7Thr missense_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
whiB6 4338617 c.-96C>T upstream_gene_variant 0.14
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0