TB-Profiler result

Run: ERR164021
Summary

Run ID: ERR164021

Sample name:

Date: 31-03-2023 14:53:23

Number of reads: 8921572

Percentage reads mapped: 94.99

Strain: lineage4.3.4.2.1;lineage1.2.2.2

Drug-resistance: MDR-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 0.69
lineage1 Indo-Oceanic EAI RD239 0.32
lineage4.3 Euro-American (LAM) mainly-LAM None 0.68
lineage1.2.2 Indo-Oceanic EAI1 RD239 0.29
lineage4.3.4 Euro-American (LAM) LAM RD174 0.69
lineage1.2.2.2 Indo-Oceanic NA RD239 0.31
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 0.7
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 0.7
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.His445Asn missense_variant 0.27 rifampicin
rrs 1472359 n.514A>T non_coding_transcript_exon_variant 0.23 streptomycin
inhA 1674481 p.Ser94Ala missense_variant 0.28 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 5075 c.-165C>T upstream_gene_variant 0.27
gyrB 6112 p.Met291Ile missense_variant 0.24
gyrB 6140 p.Val301Leu missense_variant 0.77
gyrA 7268 c.-34C>T upstream_gene_variant 0.27
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.27
gyrA 9143 c.1842T>C synonymous_variant 0.27
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.25
rpoC 763031 c.-339T>C upstream_gene_variant 0.3
rpoC 763552 c.183C>T synonymous_variant 0.28
rpoC 763884 p.Ala172Val missense_variant 0.27
rpoC 763886 c.517C>A synonymous_variant 0.28
rpoC 764995 c.1626C>G synonymous_variant 0.73
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.25
mmpL5 777017 c.1464C>T synonymous_variant 0.65
mmpS5 779625 c.-720G>A upstream_gene_variant 0.27
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.1
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 1473053 n.1208T>A non_coding_transcript_exon_variant 0.14
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.14
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.14
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.14
rrs 1473070 n.1225G>A non_coding_transcript_exon_variant 0.14
rrs 1473089 n.1244A>C non_coding_transcript_exon_variant 0.13
rrs 1473094 n.1249T>A non_coding_transcript_exon_variant 0.12
rrs 1473097 n.1252G>A non_coding_transcript_exon_variant 0.12
rrs 1473099 n.1254T>A non_coding_transcript_exon_variant 0.11
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.1
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.11
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.11
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.13
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.12
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.12
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.16
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.17
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.19
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.21
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.24
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.25
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.25
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.3
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.25
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.23
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.18
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102240 p.Arg268His missense_variant 0.29
katG 2154724 p.Arg463Leu missense_variant 0.26
PPE35 2167926 p.Leu896Ser missense_variant 0.29
PPE35 2168742 p.Gly624Asp missense_variant 0.32
Rv1979c 2222308 p.Asp286Gly missense_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.28
ahpC 2726051 c.-142G>A upstream_gene_variant 0.29
thyA 3073868 p.Thr202Ala missense_variant 0.74
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.24
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.35
fprA 3475159 p.Asn385Asp missense_variant 0.37
Rv3236c 3612009 p.Ala370Thr missense_variant 0.66
alr 3840719 c.702A>G synonymous_variant 0.67
clpC1 4038287 c.2418C>T synonymous_variant 0.76
clpC1 4038328 p.Glu793Gln missense_variant 0.26
clpC1 4038857 c.1848C>A synonymous_variant 0.27
clpC1 4040517 p.Val63Ala missense_variant 0.3
clpC1 4040719 c.-15A>G upstream_gene_variant 0.3
embC 4240671 p.Thr270Ile missense_variant 0.3
embC 4241042 p.Asn394Asp missense_variant 0.27
embA 4242559 c.-674G>A upstream_gene_variant 0.4
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245670 p.Ala813Gly missense_variant 0.28
embA 4245969 p.Pro913Ser missense_variant 0.34
embB 4246979 p.Gly156Cys missense_variant 0.35
embB 4247646 p.Glu378Ala missense_variant 0.32
aftB 4267960 p.Val293Met missense_variant 0.2
ubiA 4269162 p.Leu224Phe missense_variant 0.29
ubiA 4269387 p.Glu149Asp missense_variant 0.36
aftB 4269606 c.-770T>C upstream_gene_variant 0.3
ethA 4326148 c.1326G>T synonymous_variant 0.27
ethA 4326439 p.Asn345Lys missense_variant 0.33
whiB6 4338203 p.Arg107Cys missense_variant 0.32
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.27
gid 4407588 c.615A>G synonymous_variant 0.25
gid 4407848 p.Ala119Thr missense_variant 0.29
gid 4407873 c.330G>T synonymous_variant 0.26
gid 4408156 p.Leu16Arg missense_variant 0.72