TB-Profiler result

Run: ERR2516776
Summary

Run ID: ERR2516776

Sample name:

Date: 31-03-2023 21:43:58

Number of reads: 1035785

Percentage reads mapped: 99.65

Strain: lineage3

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
lineage3 East-African-Indian CAS RD750 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 2155700 p.Asn138His missense_variant 0.83 isoniazid
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 6518 p.Val427Leu missense_variant 0.2
gyrB 6999 p.Arg587Leu missense_variant 0.15
gyrB 7105 p.Trp622Cys missense_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7707 p.Pro136Thr missense_variant 0.16
gyrA 8409 p.Leu370Ile missense_variant 0.15
gyrA 8445 p.Arg382Ser missense_variant 0.2
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491238 c.456C>A synonymous_variant 0.15
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 759861 p.Gln19Lys missense_variant 0.15
rpoB 760039 p.Gly78Val missense_variant 0.2
rpoB 760047 p.Glu81* stop_gained 0.2
rpoB 760639 p.Gly278Asp missense_variant 0.18
rpoB 761152 p.Leu449Gln missense_variant 0.17
rpoB 761465 c.1659G>T synonymous_variant 0.18
rpoB 762314 c.2508C>A synonymous_variant 0.22
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764551 c.1182G>T synonymous_variant 0.18
rpoC 764612 p.Gln415Lys missense_variant 0.2
rpoC 765549 p.Ser727Ile missense_variant 0.17
rpoC 766142 p.Leu925Met missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777122 c.1359C>T synonymous_variant 0.17
mmpL5 777125 p.Ser452Arg missense_variant 0.17
mmpL5 777622 p.Glu287* stop_gained 0.2
mmpR5 778088 c.-902C>A upstream_gene_variant 0.22
mmpR5 778184 c.-806C>A upstream_gene_variant 0.14
mmpL5 778795 c.-315C>A upstream_gene_variant 0.25
mmpL5 779089 c.-609G>T upstream_gene_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801165 p.Lys119Asn missense_variant 0.17
embR 1417038 p.Ser104Arg missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472360 n.515G>T non_coding_transcript_exon_variant 0.22
rrs 1472372 n.527C>A non_coding_transcript_exon_variant 0.17
rrl 1473797 n.140G>T non_coding_transcript_exon_variant 0.2
rrl 1474289 n.632C>A non_coding_transcript_exon_variant 0.16
rrl 1474660 n.1003G>T non_coding_transcript_exon_variant 0.15
rrl 1474693 n.1036C>A non_coding_transcript_exon_variant 0.2
rrl 1474770 n.1113G>T non_coding_transcript_exon_variant 0.17
rrl 1474959 n.1302C>T non_coding_transcript_exon_variant 1.0
rrl 1475033 n.1376G>T non_coding_transcript_exon_variant 0.15
rrl 1475317 n.1660G>T non_coding_transcript_exon_variant 0.29
rrl 1476309 n.2652G>T non_coding_transcript_exon_variant 0.21
fabG1 1673413 c.-27G>T upstream_gene_variant 0.13
inhA 1674012 c.-190C>A upstream_gene_variant 0.17
inhA 1674653 p.Pro151Gln missense_variant 0.17
rpsA 1834227 p.Gly229Val missense_variant 0.2
rpsA 1834718 p.Pro393Thr missense_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154511 p.Gly534Val missense_variant 0.29
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154735 p.Lys459Asn missense_variant 0.15
katG 2155004 p.Gly370Trp missense_variant 0.17
katG 2155197 c.915C>A synonymous_variant 0.18
katG 2155229 p.Gln295Lys missense_variant 0.18
katG 2155238 p.Pro292Thr missense_variant 0.2
katG 2156395 c.-284G>T upstream_gene_variant 0.19
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168102 c.2511C>A synonymous_variant 0.15
PPE35 2168205 p.Pro803Gln missense_variant 0.25
PPE35 2168861 c.1752G>T synonymous_variant 0.18
PPE35 2170048 p.Leu189Val missense_variant 0.24
PPE35 2170053 p.Thr187Ser missense_variant 0.2
Rv1979c 2221883 p.Leu428Met missense_variant 0.15
Rv1979c 2222555 p.Pro204Thr missense_variant 0.2
Rv1979c 2222694 c.471G>T synonymous_variant 0.16
Rv1979c 2223056 p.Gly37Cys missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289191 c.51C>A synonymous_variant 0.14
pncA 2289365 c.-125delC upstream_gene_variant 1.0
pncA 2289505 c.-264G>T upstream_gene_variant 0.22
pncA 2290177 c.-936G>C upstream_gene_variant 0.12
kasA 2518159 c.45G>T synonymous_variant 0.15
ahpC 2725984 c.-209C>A upstream_gene_variant 0.15
ahpC 2726030 c.-163C>A upstream_gene_variant 0.17
ahpC 2726054 c.-139C>A upstream_gene_variant 0.17
ahpC 2726071 c.-122C>A upstream_gene_variant 0.14
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726139 c.-54C>A upstream_gene_variant 0.16
ahpC 2726513 c.321C>A synonymous_variant 0.14
folC 2746517 p.Ala361Asp missense_variant 0.2
folC 2746546 p.Asp351Glu missense_variant 0.25
folC 2747685 c.-87C>A upstream_gene_variant 0.22
pepQ 2859736 p.Gly228Val missense_variant 0.18
ribD 2987151 p.His105Asn missense_variant 0.2
Rv2752c 3064917 c.1275C>T synonymous_variant 1.0
Rv2752c 3065931 c.261C>A synonymous_variant 0.4
Rv2752c 3065948 p.Gly82Trp missense_variant 0.25
Rv2752c 3066081 c.111G>T synonymous_variant 0.18
thyX 3068014 c.-69G>T upstream_gene_variant 0.16
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474644 p.Arg213Leu missense_variant 0.18
whiB7 3568695 c.-16G>T upstream_gene_variant 0.14
whiB7 3568734 c.-55G>T upstream_gene_variant 0.15
whiB7 3568746 c.-67G>T upstream_gene_variant 0.15
fbiA 3640856 p.Gly105Val missense_variant 0.15
fbiA 3641152 p.Ala204Ser missense_variant 0.2
rpoA 3878181 p.Asp109Glu missense_variant 0.17
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242672 p.Pro937Gln missense_variant 0.17
embA 4244867 c.1635C>A synonymous_variant 0.17
embA 4244884 p.Arg551Leu missense_variant 0.17
embA 4245461 c.2229C>A synonymous_variant 0.21
embA 4245752 p.Met840Ile missense_variant 0.15
embB 4247243 p.Gly244Trp missense_variant 0.17
aftB 4266996 p.Gly614Val missense_variant 0.15
aftB 4267364 p.Met491Ile missense_variant 0.2
aftB 4267566 p.Leu424Pro missense_variant 0.12
aftB 4267947 p.Asp297Val missense_variant 0.2
aftB 4268009 c.828G>T synonymous_variant 0.18
aftB 4268340 p.Pro166Gln missense_variant 0.17
aftB 4268946 c.-110G>T upstream_gene_variant 0.17
aftB 4269576 c.-740C>A upstream_gene_variant 0.17
ethA 4326223 c.1251G>T synonymous_variant 0.18
ethA 4326304 c.1170C>A synonymous_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0