TB-Profiler result

Run: SRR1173866
Summary

Run ID: SRR1173866

Sample name:

Date: 03-04-2023 03:33:17

Number of reads: 1210238

Percentage reads mapped: 87.76

Strain: lineage4.6.1;lineage2.2.1.1

Drug-resistance: MDR-TB

Download CSV Download TXT Download PDF Download JSON
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 0.71
lineage4 Euro-American LAM;T;S;X;H None 0.22
lineage4.6 Euro-American T;LAM None 0.17
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.74
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.77
lineage4.6.1 Euro-American (Uganda) T2 RD724 0.29
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 0.76
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 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.7 streptomycin
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.2 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288826 p.Val139Ala missense_variant 0.81 pyrazinamide
embA 4243217 c.-16C>T upstream_gene_variant 0.36 ethambutol
embB 4247728 p.Glu405Asp missense_variant 0.3 ethambutol
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 5081 c.-159_-158insA upstream_gene_variant 0.29
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7539 p.Thr80Ala missense_variant 0.3
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.82
mshA 575425 c.78C>A synonymous_variant 0.11
mshA 575907 p.Ala187Val missense_variant 0.56
mshA 576770 p.Arg475Ser missense_variant 0.11
ccsA 620625 p.Ile245Met missense_variant 0.91
rpoB 760011 p.Ala69Ser missense_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 0.64
rpoC 766699 p.Gln1110His missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.88
mmpL5 776182 p.Asp767Asn missense_variant 0.88
mmpS5 779615 c.-710C>G upstream_gene_variant 0.7
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.74
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.11
rrs 1472422 n.577T>C non_coding_transcript_exon_variant 0.1
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.14
rrs 1472770 n.925C>T non_coding_transcript_exon_variant 0.16
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.17
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.17
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.12
rrs 1472812 n.967A>C non_coding_transcript_exon_variant 0.1
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.16
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.2
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.19
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.16
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.15
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.15
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.15
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.15
rrl 1476491 n.2834T>C non_coding_transcript_exon_variant 0.12
rpsA 1834177 c.636A>C synonymous_variant 0.84
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918198 p.Leu87Val missense_variant 0.4
katG 2154724 p.Arg463Leu missense_variant 0.67
PPE35 2167926 p.Leu896Ser missense_variant 0.74
PPE35 2169320 p.Leu431Phe missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714846 p.Val163Ile missense_variant 0.81
folC 2747195 p.Asp135Gly missense_variant 0.85
Rv2752c 3064985 p.Leu403Met missense_variant 0.39
ald 3086750 c.-70A>C upstream_gene_variant 0.39
ald 3086788 c.-32T>C upstream_gene_variant 0.69
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568874 c.-195C>T upstream_gene_variant 0.72
Rv3236c 3612813 p.Thr102Ala missense_variant 0.62
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243190 c.-43G>C upstream_gene_variant 0.72
embA 4243216 c.-17G>A upstream_gene_variant 0.62
embA 4243460 c.228C>T synonymous_variant 0.81
embA 4243557 p.Ala109Thr missense_variant 0.25
embB 4247873 p.Ala454Thr missense_variant 0.35
embB 4248115 c.1602C>T synonymous_variant 0.91
aftB 4267647 p.Asp397Gly missense_variant 0.72
ethA 4327373 p.Ile34Thr missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.64
gid 4407927 p.Glu92Asp missense_variant 0.7