TB-Profiler result

Run: ERR2245355
Summary

Run ID: ERR2245355

Sample name:

Date: 31-03-2023 17:39:17

Number of reads: 1135767

Percentage reads mapped: 99.53

Strain: lineage3.1.1

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 0.99
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 1.0
lineage3.1.1 East-African-Indian CAS1-Kili RD750 0.99
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 5599 c.360G>A synonymous_variant 0.15
gyrB 6182 p.Thr315Ala missense_variant 0.25
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7393 p.Tyr31Phe missense_variant 0.5
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8414 c.1113C>T synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491107 p.Glu109* stop_gained 0.14
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.29
rpoB 759724 c.-83A>T upstream_gene_variant 0.5
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 761197 p.Leu464Arg missense_variant 0.13
rpoC 762434 c.-936T>G upstream_gene_variant 0.91
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764313 p.Asp315Ala missense_variant 0.4
rpoC 765724 c.2355C>T synonymous_variant 0.33
rpoC 766811 p.Ser1148Ala missense_variant 0.29
rpoC 767118 p.Glu1250Gly missense_variant 0.18
mmpL5 775636 p.Pro949Thr missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776586 p.Pro632His missense_variant 0.15
mmpL5 777963 p.Val173Gly missense_variant 0.29
mmpS5 778602 c.303delC frameshift_variant 0.21
mmpL5 778741 c.-261G>T upstream_gene_variant 0.18
mmpS5 779543 c.-638A>C upstream_gene_variant 0.25
mmpS5 779583 c.-678T>C upstream_gene_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304938 p.Glu670* stop_gained 0.29
fbiC 1305079 p.Arg717Trp missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673412 c.-28G>A upstream_gene_variant 0.13
inhA 1673791 c.-411C>T upstream_gene_variant 0.25
inhA 1674212 p.Leu4Pro missense_variant 0.2
rpsA 1833452 c.-90C>T upstream_gene_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154312 p.Lys600Asn missense_variant 0.22
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155218 p.Leu298Phe missense_variant 0.25
katG 2155546 p.Asp189Val missense_variant 0.15
katG 2155813 p.Pro100Gln missense_variant 0.18
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169144 p.Val490Glu missense_variant 0.3
PPE35 2170048 p.Leu189Val missense_variant 0.2
PPE35 2170053 p.Thr187Ser missense_variant 0.22
PPE35 2170461 p.Gly51Glu missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289360 c.-119G>T upstream_gene_variant 0.29
pncA 2289365 c.-125delC upstream_gene_variant 1.0
pncA 2289969 c.-728G>A upstream_gene_variant 0.2
pncA 2290173 c.-932C>T upstream_gene_variant 0.67
kasA 2519055 p.Ala314Glu missense_variant 0.12
kasA 2519102 p.Gly330Ser missense_variant 0.14
eis 2714196 c.1137T>C synonymous_variant 0.25
eis 2715433 c.-101T>C upstream_gene_variant 0.14
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
folC 2746178 p.Thr474Asn missense_variant 1.0
ribD 2986766 c.-73G>T upstream_gene_variant 0.15
ribD 2987575 p.Asp246Gly missense_variant 0.15
Rv2752c 3066072 c.120G>T synonymous_variant 0.2
Rv2752c 3066360 c.-169T>G upstream_gene_variant 0.22
thyX 3067253 c.692delA frameshift_variant 0.13
thyA 3074462 p.Tyr4Asn missense_variant 0.18
thyA 3074467 p.Thr2Lys missense_variant 0.22
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474861 p.Glu285Asp missense_variant 0.2
whiB7 3568828 c.-149C>A upstream_gene_variant 0.15
fbiA 3640814 p.Glu91Gly missense_variant 0.17
fbiB 3642250 p.Asp239Val missense_variant 0.12
alr 3840387 p.Gln345Leu missense_variant 0.4
alr 3840828 p.Val198Ala missense_variant 0.33
rpoA 3878091 c.417C>T synonymous_variant 0.17
rpoA 3878490 c.18C>G synonymous_variant 0.67
ddn 3986898 p.Lys19* stop_gained 0.29
clpC1 4038781 p.Leu642Ile missense_variant 0.25
clpC1 4039694 c.1011G>A synonymous_variant 0.12
clpC1 4040063 c.642G>T synonymous_variant 0.14
clpC1 4040194 p.Leu171Ile missense_variant 0.17
clpC1 4040760 c.-56C>A upstream_gene_variant 0.13
embC 4240059 p.Thr66Met missense_variant 0.12
embC 4240089 p.Gly76Val missense_variant 0.14
embC 4240172 p.Val104Met missense_variant 1.0
embC 4241280 p.Val473Glu missense_variant 0.14
embC 4241292 p.Leu477Arg missense_variant 0.14
embC 4241562 p.Arg567His missense_variant 1.0
embC 4241961 p.Leu700Gln missense_variant 0.33
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244640 p.Val470Leu missense_variant 0.2
embA 4244716 p.Trp495Leu missense_variant 0.15
embA 4246394 p.Trp1054Cys missense_variant 0.22
embB 4247028 p.Leu172Gln missense_variant 0.33
embB 4247972 p.Thr487Pro missense_variant 0.29
embB 4248007 c.1494C>A synonymous_variant 0.29
embB 4249565 p.Tyr1018Asp missense_variant 0.17
aftB 4268627 c.210C>T synonymous_variant 0.29
aftB 4268826 p.Val4Gly missense_variant 0.17
ethA 4326273 p.Phe401Val missense_variant 0.4
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0