TB-Profiler result

Run: ERR2514869
Summary

Run ID: ERR2514869

Sample name:

Date: 31-03-2023 20:36:47

Number of reads: 877615

Percentage reads mapped: 99.62

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
gid 4408100 c.102delG 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 5319 p.Arg27His missense_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9596 c.2295G>T synonymous_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575639 p.Pro98Ser missense_variant 0.12
rpoB 759615 c.-192A>C upstream_gene_variant 0.21
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 760011 p.Ala69Thr missense_variant 0.14
rpoB 761119 p.Asn438Ser missense_variant 0.14
rpoB 762155 c.2349C>T synonymous_variant 0.11
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764047 p.Phe226Leu missense_variant 0.12
rpoC 764181 p.Asp271Gly missense_variant 1.0
rpoC 765309 p.Glu647Gly missense_variant 0.12
rpoC 766349 p.Ala994Thr missense_variant 0.11
rpoC 767096 p.Asp1243Asn missense_variant 0.14
mmpL5 775615 p.Ala956Thr missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775684 p.Leu933Ile missense_variant 0.11
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302990 c.60G>A synonymous_variant 0.12
Rv1258c 1406774 c.567C>A synonymous_variant 0.12
Rv1258c 1406985 p.Ala119Val missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475195 n.1538G>T non_coding_transcript_exon_variant 1.0
inhA 1674366 c.165G>A synonymous_variant 0.14
rpsA 1833877 c.336C>T synonymous_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918549 p.Arg204Cys missense_variant 0.29
ndh 2102602 p.Leu147Phe missense_variant 0.12
ndh 2103225 c.-183A>C upstream_gene_variant 0.29
katG 2153994 c.2118G>A synonymous_variant 0.14
katG 2154000 c.2112G>A synonymous_variant 0.14
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155234 p.Leu293Pro missense_variant 0.25
katG 2155746 c.366C>T synonymous_variant 0.2
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170464 p.Ala50Val missense_variant 0.12
PPE35 2170769 c.-157C>T upstream_gene_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288741 c.501C>T synonymous_variant 0.12
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
kasA 2518209 p.Thr32Met missense_variant 0.13
kasA 2518319 p.Asp69Asn missense_variant 0.18
kasA 2518473 p.Glu120Val missense_variant 0.12
kasA 2518864 c.750G>C synonymous_variant 0.17
kasA 2519052 p.Thr313Met missense_variant 0.13
kasA 2519171 p.Leu353Ile missense_variant 0.11
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726338 p.Val49Gly missense_variant 0.22
folC 2747555 p.Thr15Ile missense_variant 0.13
folC 2747786 c.-188G>A upstream_gene_variant 0.13
pepQ 2859320 c.1098delC frameshift_variant 0.18
Rv2752c 3067185 c.-994T>C upstream_gene_variant 0.12
thyX 3067928 c.18G>A synonymous_variant 0.12
thyX 3068004 c.-59C>T upstream_gene_variant 0.11
thyA 3073906 p.Ala189Val missense_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339266 p.Ala50Val missense_variant 0.15
fbiD 3339750 c.633C>T synonymous_variant 0.14
Rv3083 3448354 c.-150C>T upstream_gene_variant 0.33
Rv3083 3448499 c.-5G>C upstream_gene_variant 0.12
Rv3083 3448548 c.45C>T synonymous_variant 0.11
Rv3083 3448749 c.246G>A synonymous_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612159 p.Arg320Gly missense_variant 0.15
Rv3236c 3612287 p.Gly277Glu missense_variant 0.11
Rv3236c 3613302 c.-186G>A upstream_gene_variant 0.12
fbiA 3641525 p.Gly328Glu missense_variant 0.12
alr 3840512 c.909C>T synonymous_variant 0.25
rpoA 3877981 p.Tyr176Cys missense_variant 0.11
rpoA 3878421 c.87A>G synonymous_variant 0.11
clpC1 4038469 p.Asp746Asn missense_variant 0.12
clpC1 4039104 p.Arg534His missense_variant 0.11
clpC1 4039691 c.1014G>C synonymous_variant 0.12
embC 4240635 p.Arg258Gln missense_variant 0.18
embC 4240988 p.Ala376Thr missense_variant 0.14
embC 4241964 p.Ala701Val missense_variant 0.12
embC 4242075 p.Arg738Gln missense_variant 1.0
embC 4242174 p.Ala771Val missense_variant 0.14
embC 4242402 p.Arg847His missense_variant 0.15
embA 4242511 c.-722G>A upstream_gene_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244303 p.Asn357Lys missense_variant 0.15
embA 4244847 p.Gly539Ser missense_variant 0.11
embB 4249686 p.Ala1058Val missense_variant 0.11
ubiA 4268971 p.Ala288Glu missense_variant 0.11
ethA 4328469 c.-996G>T upstream_gene_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0