TB-Profiler result

Run: ERR2517058
Summary

Run ID: ERR2517058

Sample name:

Date: 31-03-2023 21:54:49

Number of reads: 1178940

Percentage reads mapped: 99.73

Strain: lineage3

Drug-resistance: Sensitive

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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
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 5704 c.465C>A synonymous_variant 0.25
gyrB 5813 p.Arg192Ser missense_variant 0.31
gyrB 6653 p.Asp472His missense_variant 0.14
gyrA 7275 c.-27C>A upstream_gene_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491576 p.Pro265Gln missense_variant 0.15
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 761193 p.Gly463Trp missense_variant 0.2
rpoB 761457 p.Pro551Thr missense_variant 0.14
rpoB 762432 p.Gly876Trp missense_variant 0.29
rpoB 762464 p.Lys886Asn missense_variant 0.25
rpoC 762617 c.-753C>A upstream_gene_variant 0.15
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763669 c.300C>A synonymous_variant 0.18
rpoC 764260 p.Lys297Asn missense_variant 0.15
rpoC 764292 p.Ser308* stop_gained 0.25
rpoC 766141 c.2772C>A synonymous_variant 0.16
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776399 p.Glu694Asp missense_variant 0.11
mmpR5 779254 p.Arg89Trp missense_variant 0.21
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416944 p.Ser135Ile missense_variant 0.15
embR 1417038 p.Ser104Arg missense_variant 1.0
atpE 1461212 c.168C>A synonymous_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471843 n.-3G>T upstream_gene_variant 0.18
rrs 1473152 n.1307T>C non_coding_transcript_exon_variant 0.11
rrl 1473837 n.180G>T non_coding_transcript_exon_variant 0.22
rrl 1474792 n.1135C>A non_coding_transcript_exon_variant 0.18
rrl 1474959 n.1302C>T non_coding_transcript_exon_variant 1.0
rrl 1475360 n.1703G>T non_coding_transcript_exon_variant 0.14
rrl 1475639 n.1982C>A non_coding_transcript_exon_variant 0.18
rrl 1476049 n.2392C>T non_coding_transcript_exon_variant 0.17
rrl 1476720 n.3063G>T non_coding_transcript_exon_variant 0.25
fabG1 1673380 c.-60C>G upstream_gene_variant 0.23
fabG1 1673513 p.Arg25Leu missense_variant 0.2
rpsA 1834204 p.Asn221Lys missense_variant 0.2
rpsA 1834227 p.Gly229Asp missense_variant 0.18
rpsA 1834241 p.Leu234Met missense_variant 0.18
rpsA 1834284 p.Pro248Gln missense_variant 0.17
rpsA 1834756 p.Glu405Asp missense_variant 0.23
rpsA 1834799 p.Glu420* stop_gained 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154263 p.Leu617Ile missense_variant 0.13
katG 2154299 p.Pro605Thr missense_variant 0.17
katG 2154414 c.1698C>A synonymous_variant 0.25
katG 2154545 p.Glu523* stop_gained 0.25
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155938 p.Met58Ile missense_variant 0.18
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168238 p.Pro792Gln missense_variant 0.2
PPE35 2168904 p.Ile570Thr missense_variant 0.2
PPE35 2169269 c.1344A>G synonymous_variant 0.12
PPE35 2169272 c.1341C>G synonymous_variant 0.11
PPE35 2169278 c.1335T>C synonymous_variant 0.12
PPE35 2169281 c.1332T>G synonymous_variant 0.12
PPE35 2169287 c.1326T>C synonymous_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 0.13
PPE35 2170053 p.Thr187Ser missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
pncA 2290033 c.-792C>A upstream_gene_variant 0.4
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726285 c.93C>A synonymous_variant 0.21
Rv2752c 3064917 c.1275C>T synonymous_variant 1.0
Rv2752c 3065439 c.753C>A synonymous_variant 0.15
Rv2752c 3066138 c.54C>A synonymous_variant 0.16
thyX 3067971 c.-26T>A upstream_gene_variant 0.12
thyA 3074294 p.Leu60Met missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449105 p.Pro201His missense_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475021 p.Gly339Trp missense_variant 0.15
fprA 3475296 p.Glu430Asp missense_variant 0.13
fprA 3475331 p.Val442Ala missense_variant 0.13
fprA 3475371 c.1365C>A synonymous_variant 0.25
Rv3236c 3613280 c.-164G>T upstream_gene_variant 0.2
alr 3840625 p.Leu266Ile missense_variant 0.18
rpoA 3877502 p.Tyr336His missense_variant 0.14
rpoA 3877737 c.771G>T synonymous_variant 0.15
rpoA 3877963 p.Arg182Leu missense_variant 0.18
rpoA 3878207 p.Gly101Cys missense_variant 0.17
embC 4241654 p.Gly598Trp missense_variant 0.18
embC 4241663 p.Gly601Trp missense_variant 0.18
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4267105 p.Val578Leu missense_variant 0.13
aftB 4267252 p.Asp529His missense_variant 0.11
aftB 4267981 c.856C>A synonymous_variant 0.33
aftB 4268014 p.Pro275Thr missense_variant 0.22
aftB 4268080 p.Gly253Cys missense_variant 0.18
ubiA 4269056 p.Leu260Met missense_variant 0.19
ubiA 4269714 p.Leu40Phe missense_variant 0.22
ethR 4327573 p.Ala9Ser missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407603 c.600G>T synonymous_variant 0.24