TB-Profiler result

Run: ERR036185

Summary

Run ID: ERR036185

Sample name:

Date: 31-03-2023 08:28:25

Number of reads: 1334475

Percentage reads mapped: 93.97

Strain: lineage4.9;lineage4.3.4.2.1;lineage4.3.4.1;lineage3;lineage2.2.1

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
lineage3 East-African-Indian CAS RD750 0.14
lineage2 East-Asian Beijing RD105 0.06
lineage4 Euro-American LAM;T;S;X;H None 0.74
lineage4.3 Euro-American (LAM) mainly-LAM None 0.59
lineage4.9 Euro-American (H37Rv-like) T1 None 0.06
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.07
lineage4.3.4 Euro-American (LAM) LAM RD174 0.6
lineage4.3.4.1 Euro-American (LAM) LAM1;LAM2 RD174 0.11
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 0.38
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 761155 p.Ser450Leu missense_variant 0.12 rifampicin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.15 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.11 isoniazid
pncA 2288820 p.Gln141Pro missense_variant 0.28 pyrazinamide
embA 4243217 c.-16C>T upstream_gene_variant 0.41 ethambutol
gid 4407816 c.386delG frameshift_variant 0.1 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 6140 p.Val301Leu missense_variant 0.36
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 0.81
fgd1 491604 c.822G>C synonymous_variant 0.17
fgd1 491742 c.960T>C synonymous_variant 0.21
rpoB 759746 c.-61C>T upstream_gene_variant 0.2
rpoB 759831 p.Thr9Pro missense_variant 0.31
rpoB 762249 p.Leu815Val missense_variant 0.24
rpoC 762434 c.-936T>G upstream_gene_variant 0.17
rpoB 762714 p.Val970Met missense_variant 0.18
rpoC 762836 c.-534C>G upstream_gene_variant 0.62
rpoC 763031 c.-339T>C upstream_gene_variant 0.27
rpoC 764995 c.1626C>G synonymous_variant 0.54
rpoC 767305 p.Tyr1312* stop_gained 0.24
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.53
mmpL5 776182 p.Asp767Asn missense_variant 0.15
mmpR5 779371 p.Ala128Pro missense_variant 0.33
mmpS5 779615 c.-710C>G upstream_gene_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.12
atpE 1461019 c.-26C>A upstream_gene_variant 0.27
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.12
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.21
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.16
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.1
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.1
rrs 1472378 n.533G>T non_coding_transcript_exon_variant 0.14
rrs 1472379 n.534T>G non_coding_transcript_exon_variant 0.15
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.15
rrs 1472389 n.544G>A non_coding_transcript_exon_variant 0.15
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 0.17
rrs 1472412 n.567A>C non_coding_transcript_exon_variant 0.14
rrs 1472415 n.570T>G non_coding_transcript_exon_variant 0.15
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.12
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.15
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.2
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.26
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.25
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.27
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.19
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.12
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.11
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.12
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.13
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.15
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.18
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.18
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.21
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.36
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.5
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.45
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.45
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.22
rpsA 1834177 c.636A>C synonymous_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102540 p.Ala168Gly missense_variant 0.36
katG 2154724 p.Arg463Leu missense_variant 0.34
PPE35 2167926 p.Leu896Ser missense_variant 0.24
PPE35 2169320 p.Leu431Phe missense_variant 0.14
PPE35 2169866 c.747G>C synonymous_variant 0.37
PPE35 2170461 p.Gly51Glu missense_variant 0.25
Rv1979c 2223145 p.Arg7Lys missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289138 p.Leu35Arg missense_variant 0.12
pncA 2289365 c.-125delC upstream_gene_variant 0.14
pncA 2289448 c.-207G>A upstream_gene_variant 0.15
eis 2714225 p.Ala370Pro missense_variant 0.25
eis 2714366 p.Val323Leu missense_variant 0.29
eis 2715586 c.-254G>C upstream_gene_variant 0.44
ahpC 2726105 c.-88G>A upstream_gene_variant 0.23
Rv2752c 3064741 p.Gly484Ala missense_variant 0.3
Rv2752c 3065008 p.Pro395Arg missense_variant 0.22
Rv2752c 3067191 c.-1000G>A upstream_gene_variant 0.33
thyA 3073868 p.Thr202Ala missense_variant 0.56
ald 3086788 c.-32T>C upstream_gene_variant 0.96
fbiD 3339153 p.Leu12Phe missense_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.85
Rv3236c 3612009 p.Ala370Thr missense_variant 0.42
Rv3236c 3612813 p.Thr102Ala missense_variant 0.18
fbiB 3642734 c.1200G>C synonymous_variant 0.25
alr 3840268 p.Thr385Pro missense_variant 0.3
alr 3840719 c.702A>G synonymous_variant 0.4
rpoA 3878238 p.Asp90Glu missense_variant 0.33
ddn 3987013 p.Gly57Ala missense_variant 0.3
clpC1 4038287 c.2418C>T synonymous_variant 0.75
clpC1 4038857 c.1848C>A synonymous_variant 0.13
clpC1 4039293 p.Gly471Asp missense_variant 0.11
clpC1 4039363 p.Ala448Pro missense_variant 0.28
embC 4239842 c.-21C>A upstream_gene_variant 0.23
embC 4241429 p.Phe523Val missense_variant 0.45
embC 4241539 c.1677T>C synonymous_variant 0.25
embC 4242075 p.Arg738Gln missense_variant 0.17
embC 4242425 p.Arg855Gly missense_variant 0.27
embC 4242476 p.Pro872Ala missense_variant 0.21
embA 4242643 c.-590C>T upstream_gene_variant 0.94
embC 4242822 p.Val987Gly missense_variant 0.47
embC 4242827 p.Leu989Val missense_variant 0.25
embA 4243460 c.228C>T synonymous_variant 0.2
embB 4248730 c.2217C>T synonymous_variant 0.18
aftB 4267647 p.Asp397Gly missense_variant 0.12
aftB 4268812 p.Ser9Ala missense_variant 0.5
ubiA 4269529 p.Ala102Gly missense_variant 0.13
ethA 4327229 p.Leu82Pro missense_variant 0.11
ethA 4327672 c.-199G>A upstream_gene_variant 0.56
ethA 4328212 c.-740delC upstream_gene_variant 0.24
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.22
gid 4408156 p.Leu16Arg missense_variant 0.69