TB-Profiler result

Run: ERR2513853

Summary

Run ID: ERR2513853

Sample name:

Date: 31-03-2023 19:56:55

Number of reads: 1293988

Percentage reads mapped: 99.47

Strain: lineage3

Drug-resistance: Other


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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
pncA 2289091 p.His51Tyr missense_variant 0.25 pyrazinamide
embB 4247856 p.Gly448Val missense_variant 0.15 ethambutol
gid 4408087 c.115delC frameshift_variant 1.0 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 6205 c.966C>T synonymous_variant 0.25
gyrB 6211 c.972G>A synonymous_variant 0.22
gyrA 6415 c.-887G>T upstream_gene_variant 0.22
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7662 p.Asn121Asp missense_variant 0.15
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491372 p.Gly197Asp missense_variant 0.33
fgd1 491569 p.Asp263Asn missense_variant 0.14
fgd1 491734 p.Arg318Gly missense_variant 0.25
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575514 p.Pro56Gln missense_variant 0.15
mshA 575891 p.Ala182Ser missense_variant 0.12
mshA 576418 c.1071G>T synonymous_variant 0.12
ccsA 620656 p.Gly256Ser missense_variant 0.22
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766326 p.Gly986Asp missense_variant 0.18
rpoC 766576 p.Asp1069Glu missense_variant 0.15
rpoC 766650 p.Gly1094Asp missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777069 p.Ala471Asp missense_variant 0.29
mmpS5 778490 p.Val139Glu missense_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303326 c.396C>T synonymous_variant 0.33
Rv1258c 1406838 p.Val168Asp missense_variant 0.22
embR 1416197 p.Thr384Met missense_variant 0.17
embR 1417083 p.Asp89Tyr missense_variant 0.14
rrl 1474317 n.660G>T non_coding_transcript_exon_variant 0.67
fabG1 1673623 p.Val62Ile missense_variant 0.29
fabG1 1673635 p.Asp66Asn missense_variant 0.33
inhA 1674653 p.Pro151Gln missense_variant 0.15
inhA 1674753 c.552G>C synonymous_variant 0.33
rpsA 1833475 c.-67G>T upstream_gene_variant 0.18
rpsA 1834379 p.Gln280Lys missense_variant 0.22
rpsA 1834983 p.Ala481Val missense_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102311 c.732G>A synonymous_variant 0.4
ndh 2102633 p.Gly137Asp missense_variant 0.2
ndh 2102655 p.His130Tyr missense_variant 0.18
ndh 2102681 p.Ala121Val missense_variant 0.17
ndh 2102914 c.129C>T synonymous_variant 0.25
ndh 2103098 c.-56C>T upstream_gene_variant 0.33
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154899 p.Ala405Thr missense_variant 0.2
katG 2155110 p.Glu334Asp missense_variant 0.22
katG 2155718 p.Leu132Ile missense_variant 0.33
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170450 p.Gly55Trp missense_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288899 p.Pro115Thr missense_variant 0.33
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
folC 2746229 p.Ala457Val missense_variant 0.67
folC 2747548 c.51C>T synonymous_variant 0.33
Rv2752c 3064739 p.Gln485Lys missense_variant 0.25
Rv2752c 3066126 c.66C>T synonymous_variant 0.22
thyA 3074546 c.-75G>T upstream_gene_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087366 p.Ala183Ser missense_variant 0.2
ald 3087635 c.816C>A synonymous_variant 0.17
fbiD 3338966 c.-152C>A upstream_gene_variant 0.25
Rv3083 3448804 p.Gly101Cys missense_variant 0.13
Rv3083 3449937 c.1434C>T synonymous_variant 0.18
fprA 3473939 c.-68G>A upstream_gene_variant 0.4
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474615 c.609G>A synonymous_variant 0.14
whiB7 3568451 p.Val77Met missense_variant 0.14
fbiA 3641063 p.Val174Ala missense_variant 0.22
fbiB 3641791 p.Leu86Ser missense_variant 0.33
fbiB 3641798 c.264C>A synonymous_variant 0.33
fbiB 3642149 c.615C>A synonymous_variant 0.14
fbiB 3642730 p.Gly399Asp missense_variant 0.17
alr 3841473 c.-53G>A upstream_gene_variant 1.0
rpoA 3878377 p.Ser44Leu missense_variant 0.33
rpoA 3878471 p.Val13Ile missense_variant 0.22
ddn 3987217 p.Gln125Arg missense_variant 0.25
clpC1 4039271 p.Glu478Asp missense_variant 0.25
clpC1 4039294 p.Gly471Cys missense_variant 0.22
clpC1 4039944 p.Ser254Leu missense_variant 0.2
clpC1 4040701 p.Phe2Leu missense_variant 0.17
clpC1 4040810 c.-106A>G upstream_gene_variant 0.2
panD 4044074 p.Gly70Cys missense_variant 0.25
embC 4240616 p.Asp252Tyr missense_variant 0.22
embC 4240628 p.Gly256Cys missense_variant 0.22
embC 4241263 p.Phe467Leu missense_variant 0.18
embC 4241633 p.Gly591Trp missense_variant 0.25
embC 4242075 p.Arg738Gln missense_variant 1.0
embC 4242451 p.Met863Ile missense_variant 0.2
embA 4242505 c.-728G>A upstream_gene_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243671 p.Gly147Ser missense_variant 0.22
embA 4243802 p.Asp190Glu missense_variant 0.4
embA 4244026 p.His265Arg missense_variant 0.25
embA 4244375 c.1143C>T synonymous_variant 0.17
embA 4246338 p.Leu1036Val missense_variant 0.17
embB 4248688 c.2175G>A synonymous_variant 0.67
embB 4249068 p.Ala852Val missense_variant 0.14
embB 4249503 p.Gln997Arg missense_variant 0.13
aftB 4268772 p.Trp22Leu missense_variant 0.29
aftB 4269333 c.-497C>T upstream_gene_variant 0.12
ubiA 4269566 p.Arg90Trp missense_variant 0.12
ethR 4327318 c.-231T>C upstream_gene_variant 0.2
ethR 4327734 p.Tyr62* stop_gained 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0