TB-Profiler result

Run: ERR2514142

Summary

Run ID: ERR2514142

Sample name:

Date: 31-03-2023 20:08:39

Number of reads: 769327

Percentage reads mapped: 98.62

Strain: lineage1.2.2.2

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 0.98
lineage1.2.2 Indo-Oceanic EAI1 RD239 1.0
lineage1.2.2.2 Indo-Oceanic NA 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
gid 4408100 c.102delG frameshift_variant 1.0 streptomycin
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 5075 c.-165C>T upstream_gene_variant 1.0
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrA 7268 c.-34C>T upstream_gene_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
gyrA 9681 p.Ala794Thr missense_variant 0.13
gyrA 9704 c.2403T>A synonymous_variant 0.12
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576646 c.1299C>T synonymous_variant 0.12
mshA 576670 p.Tyr441* stop_gained 0.12
rpoB 759620 c.-187A>C upstream_gene_variant 0.15
rpoB 762236 c.2430G>A synonymous_variant 0.14
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 766367 p.Ala1000Thr missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 778210 p.Ala91Thr missense_variant 0.14
mmpS5 779625 c.-720G>A upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800691 c.-118A>G upstream_gene_variant 0.11
Rv1258c 1406504 c.837C>G synonymous_variant 0.11
Rv1258c 1407198 p.Ala48Asp missense_variant 0.17
Rv1258c 1407200 c.141G>T synonymous_variant 0.17
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472766 n.921G>A non_coding_transcript_exon_variant 0.4
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.75
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.5
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.5
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.5
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.2
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.2
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.18
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.18
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.18
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.15
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.15
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.15
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.13
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.13
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.12
rrl 1474469 n.812T>A non_coding_transcript_exon_variant 0.29
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 0.4
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.38
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.27
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.27
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.27
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.23
inhA 1674609 c.408G>T synonymous_variant 0.18
rpsA 1834669 c.1128G>C synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102240 p.Arg268His missense_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168742 p.Gly624Asp missense_variant 1.0
PPE35 2169971 c.642T>C synonymous_variant 0.13
PPE35 2170066 p.Ala183Thr missense_variant 0.29
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289464 c.-223A>T upstream_gene_variant 0.12
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2519107 c.993T>C synonymous_variant 0.15
kasA 2519108 p.Asp332Gln missense_variant 0.15
kasA 2519116 c.1002C>G synonymous_variant 0.18
kasA 2519122 c.1008G>C synonymous_variant 0.14
kasA 2519137 c.1023T>G synonymous_variant 0.14
kasA 2519158 c.1044C>T synonymous_variant 0.14
kasA 2519167 c.1053T>G synonymous_variant 0.12
kasA 2519170 c.1056G>T synonymous_variant 0.12
kasA 2519221 c.1107G>C synonymous_variant 0.11
kasA 2519230 c.1116C>T synonymous_variant 0.11
eis 2714307 c.1025dupC frameshift_variant 0.11
eis 2715468 c.-136C>T upstream_gene_variant 0.17
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2747458 c.141G>T synonymous_variant 0.12
ribD 2986684 c.-155T>C upstream_gene_variant 0.12
thyX 3067589 c.357G>A synonymous_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339580 p.Gly155Ser missense_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449797 p.Asp432Asn missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474143 p.Trp46Tyr missense_variant 0.17
fprA 3474165 c.159C>G synonymous_variant 0.13
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
fbiB 3641517 c.-18C>T upstream_gene_variant 0.11
fbiB 3641994 p.Arg154Cys missense_variant 0.11
fbiB 3642636 p.Ala368Ser missense_variant 0.15
rpoA 3877776 c.732T>C synonymous_variant 0.1
rpoA 3877782 c.726T>C synonymous_variant 0.11
rpoA 3877785 c.723C>G synonymous_variant 0.12
rpoA 3877797 c.711G>A synonymous_variant 0.11
rpoA 3877818 c.690A>G synonymous_variant 0.12
rpoA 3877824 c.684G>A synonymous_variant 0.12
rpoA 3877839 c.669G>C synonymous_variant 0.12
rpoA 3878508 c.-1C>T upstream_gene_variant 0.17
ddn 3986853 p.Ser4Thr missense_variant 0.11
clpC1 4038173 p.Glu844Asp missense_variant 0.4
clpC1 4038755 c.1950G>T synonymous_variant 0.11
clpC1 4038773 c.1932T>C synonymous_variant 0.12
clpC1 4038782 c.1923G>T synonymous_variant 0.12
clpC1 4038790 c.1915C>T synonymous_variant 0.12
clpC1 4038812 c.1893T>C synonymous_variant 0.11
clpC1 4038838 c.1867C>T synonymous_variant 0.12
clpC1 4038949 p.His586Tyr missense_variant 0.17
clpC1 4040517 p.Val63Ala missense_variant 1.0
clpC1 4040719 c.-15A>G upstream_gene_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241552 p.Pro564Ser missense_variant 0.11
embC 4241617 c.1755G>A synonymous_variant 0.12
embA 4242415 c.-818G>A upstream_gene_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244184 p.Ser318Arg missense_variant 0.11
embA 4244340 p.Ser370Thr missense_variant 0.11
embA 4245183 p.Leu651Met missense_variant 0.11
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4249323 p.Ala937Glu missense_variant 0.2
aftB 4267954 p.Ala295Pro missense_variant 0.15
aftB 4267960 p.Val293Met missense_variant 1.0
aftB 4268548 p.Leu97Met missense_variant 0.13
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326148 c.1326G>T synonymous_variant 1.0
ethA 4326439 p.Asn345Lys missense_variant 1.0
ethR 4327579 p.Leu11Met missense_variant 0.18
whiB6 4338203 p.Arg107Cys missense_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 4407848 p.Ala119Thr missense_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0