TB-Profiler result

Run: ERR4815478
Summary

Run ID: ERR4815478

Sample name:

Date: 01-04-2023 13:53:06

Number of reads: 2215958

Percentage reads mapped: 95.25

Strain: lineage2.2.1;lineage1.1.1

Drug-resistance: RR-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
lineage2 East-Asian Beijing RD105 0.87
lineage1 Indo-Oceanic EAI RD239 0.1
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.09
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.88
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.89
lineage1.1.1 Indo-Oceanic EAI4;EAI5 RD239 0.09
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
rpoB 761139 p.His445Tyr missense_variant 0.83 rifampicin
rrs 1472644 n.799C>T non_coding_transcript_exon_variant 0.4 streptomycin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.33 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.2
gyrA 9121 p.Arg607His missense_variant 0.87
gyrA 9143 c.1842T>C synonymous_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.9
ccsA 620625 p.Ile245Met missense_variant 0.83
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.14
rpoC 763886 c.517C>A synonymous_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.87
mmpS5 779615 c.-710C>G upstream_gene_variant 0.96
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.82
embR 1417019 p.Cys110Tyr missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.2
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.2
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.2
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.3
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.27
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.25
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.2
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.38
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.43
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.5
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.5
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.5
rrs 1472527 n.682G>A non_coding_transcript_exon_variant 0.5
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.5
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.5
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.5
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.5
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.67
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.67
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.5
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.5
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.5
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.5
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.67
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.4
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.4
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.4
rrs 1472669 n.824_825insTGGA non_coding_transcript_exon_variant 0.5
rrs 1472678 n.833T>G non_coding_transcript_exon_variant 0.5
rrs 1472679 n.834T>C non_coding_transcript_exon_variant 0.5
rrs 1472682 n.839_843delGGGAT non_coding_transcript_exon_variant 0.5
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.4
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.4
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.4
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.29
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.29
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.38
rrs 1472896 n.1051T>C non_coding_transcript_exon_variant 0.25
rrs 1473144 n.1299T>C non_coding_transcript_exon_variant 0.12
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.25
rrs 1473147 n.1302G>C non_coding_transcript_exon_variant 0.12
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.12
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.11
rrs 1473164 n.1319C>G non_coding_transcript_exon_variant 0.11
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.19
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.17
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.19
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.19
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.17
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.33
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.41
rrs 1473276 n.1431A>C non_coding_transcript_exon_variant 0.33
rrs 1473277 n.1432G>A non_coding_transcript_exon_variant 0.33
rrs 1473288 n.1443C>G non_coding_transcript_exon_variant 0.24
rrs 1473289 n.1444_1445insTTTTG non_coding_transcript_exon_variant 0.21
rrs 1473293 n.1449delA non_coding_transcript_exon_variant 0.24
rrs 1473300 n.1455C>T non_coding_transcript_exon_variant 0.23
rrs 1473301 n.1456T>G non_coding_transcript_exon_variant 0.23
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.29
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 0.38
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.45
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.5
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.6
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.43
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.36
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.44
rpsA 1833879 p.Trp113Leu missense_variant 0.15
rpsA 1834177 c.636A>C synonymous_variant 0.85
rpsA 1834319 p.Val260Ile missense_variant 0.17
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 0.11
Rv1979c 2222308 p.Asp286Gly missense_variant 0.16
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 0.14
ahpC 2726070 c.-123G>A upstream_gene_variant 0.15
ahpC 2726338 p.Val49Gly missense_variant 0.26
Rv2752c 3064632 c.1560C>T synonymous_variant 0.19
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 0.12
fprA 3475302 c.1296C>T synonymous_variant 0.12
Rv3236c 3612813 p.Thr102Ala missense_variant 0.88
clpC1 4040517 p.Val63Ala missense_variant 0.1
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.89
embA 4244096 c.864C>T synonymous_variant 0.13
aftB 4267647 p.Asp397Gly missense_variant 0.88
ubiA 4269387 p.Glu149Asp missense_variant 0.13
ethA 4327483 c.-10G>A upstream_gene_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 0.18
gid 4407927 p.Glu92Asp missense_variant 0.9