TB-Profiler result

Run: ERR2513574

Summary

Run ID: ERR2513574

Sample name:

Date: 31-03-2023 19:46:15

Number of reads: 524488

Percentage reads mapped: 99.31

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 5803 c.564A>G synonymous_variant 0.11
gyrA 6952 c.-350C>A upstream_gene_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7954 p.Ala218Glu missense_variant 0.14
gyrA 8790 p.Arg497Trp missense_variant 0.15
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491321 p.Ala180Val missense_variant 0.4
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575306 c.-42T>C upstream_gene_variant 0.17
mshA 576459 p.Ala371Val missense_variant 0.18
ccsA 620203 p.Val105Met missense_variant 0.2
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 759985 p.Gly60Asp missense_variant 0.12
rpoB 760918 p.Arg371Leu missense_variant 0.25
rpoB 761275 p.Leu490Pro missense_variant 0.14
rpoB 761519 c.1713C>T synonymous_variant 0.13
rpoB 761936 c.2130C>A synonymous_variant 0.15
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoB 762629 p.Asp941Glu missense_variant 0.22
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763205 c.-165G>A upstream_gene_variant 0.15
rpoC 764377 c.1008C>T synonymous_variant 0.13
rpoC 764625 p.Gly419Asp missense_variant 0.13
rpoC 766350 p.Ala994Asp missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777820 c.661C>T synonymous_variant 1.0
mmpR5 778181 c.-809C>A upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406822 c.519A>G synonymous_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673726 p.Phe96Tyr missense_variant 0.15
fabG1 1674037 p.Gln200Lys missense_variant 0.11
inhA 1674454 p.Gly85Cys missense_variant 0.17
rpsA 1833914 p.Ala125Ser missense_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168651 p.Leu654Phe missense_variant 1.0
PPE35 2169566 c.1047T>C synonymous_variant 0.1
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 2289667 c.-426C>A upstream_gene_variant 0.13
kasA 2519152 c.1038G>T synonymous_variant 0.29
eis 2715546 c.-214C>T upstream_gene_variant 0.5
ahpC 2726105 c.-88G>A upstream_gene_variant 0.94
ahpC 2726338 p.Val49Gly missense_variant 0.21
ahpC 2726341 p.Val50Gly missense_variant 0.25
ahpC 2726664 p.Val158Ile missense_variant 0.12
pepQ 2860190 p.Arg77Cys missense_variant 0.25
pepQ 2860399 p.Arg7Gln missense_variant 1.0
ribD 2986767 c.-72T>C upstream_gene_variant 0.11
Rv2752c 3065405 p.Gly263Cys missense_variant 0.13
Rv2752c 3065412 c.780G>A synonymous_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339470 p.Pro118Leu missense_variant 0.14
Rv3083 3448355 c.-149C>T upstream_gene_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475349 p.Ala448Val missense_variant 0.2
whiB7 3568784 c.-105C>A upstream_gene_variant 0.2
Rv3236c 3612157 c.960G>A synonymous_variant 0.12
fbiB 3641193 c.-342G>A upstream_gene_variant 0.22
alr 3840670 p.Val251Met missense_variant 0.13
alr 3841473 c.-53G>A upstream_gene_variant 1.0
rpoA 3878633 c.-126C>A upstream_gene_variant 1.0
clpC1 4039469 c.1236T>C synonymous_variant 0.14
clpC1 4040492 p.Gln71His missense_variant 0.11
clpC1 4040556 p.Glu50Gly missense_variant 0.11
panD 4044056 p.Ala76Ser missense_variant 0.14
embC 4240290 p.Pro143Gln missense_variant 0.12
embC 4241767 c.1905C>T synonymous_variant 0.12
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242993 p.Thr1044Lys missense_variant 0.13
embA 4245163 c.1934delC frameshift_variant 0.14
embA 4245761 p.Tyr843* stop_gained 0.2
embB 4246008 c.-506C>A upstream_gene_variant 0.18
embB 4246799 p.Gly96Trp missense_variant 0.14
embB 4247174 p.Ala221Ser missense_variant 0.2
embB 4247888 p.Gly459Ser missense_variant 0.17
embB 4247926 c.1413C>A synonymous_variant 0.14
embB 4248445 p.Asn644Lys missense_variant 0.18
embB 4249579 c.3066G>A synonymous_variant 0.12
aftB 4267198 p.Tyr547His missense_variant 0.13
aftB 4267311 p.Gly509Val missense_variant 0.12
aftB 4267720 p.Gly373Cys missense_variant 0.17
ubiA 4269532 p.Leu101Pro missense_variant 0.12
ethR 4326922 c.-627G>A upstream_gene_variant 0.12
ethA 4327061 p.Ser138Ile missense_variant 0.14
whiB6 4338335 p.Ala63Ser missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408468 c.-266G>T upstream_gene_variant 0.2