TB-Profiler result

Run: ERR4815797
Summary

Run ID: ERR4815797

Sample name:

Date: 01-04-2023 14:04:12

Number of reads: 307607

Percentage reads mapped: 97.34

Strain: lineage1.1.2

Drug-resistance: HR-TB

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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
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 1.0
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 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
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
embB 4247730 p.Gly406Asp missense_variant 1.0 ethambutol
ethA 4326791 p.Trp228* stop_gained 1.0 ethionamide
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 6175 c.936G>A synonymous_variant 0.22
gyrB 6895 p.Met552Ile missense_variant 0.33
gyrB 6905 p.Ile556Val missense_variant 0.33
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7679 c.378G>A synonymous_variant 0.4
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9047 c.1746C>T synonymous_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575433 c.89delC frameshift_variant 0.2
mshA 575906 p.Ala187Thr missense_variant 0.2
mshA 576000 p.Asp218Ala missense_variant 1.0
rpoB 760490 c.684C>T synonymous_variant 1.0
rpoB 761218 p.Pro471Gln missense_variant 0.33
rpoB 761330 c.1524G>A synonymous_variant 0.29
rpoC 762524 c.-846G>A upstream_gene_variant 0.5
rpoC 763536 p.Arg56Leu missense_variant 0.25
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 764574 p.Leu402Pro missense_variant 0.33
rpoC 765990 p.Thr874Ile missense_variant 0.29
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776395 p.Phe696Leu missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800625 c.-184A>T upstream_gene_variant 1.0
fbiC 1304121 c.1192delT frameshift_variant 0.22
fbiC 1304260 c.1334delG frameshift_variant 0.4
Rv1258c 1406470 p.Met291Val missense_variant 0.18
Rv1258c 1406533 p.Gly270Ser missense_variant 0.13
Rv1258c 1406930 p.Trp137* stop_gained 0.29
embR 1416222 p.Phe376Leu missense_variant 0.5
embR 1416232 p.Cys372Gly missense_variant 0.5
embR 1416920 p.Arg143Lys missense_variant 0.22
embR 1417019 p.Cys110Tyr missense_variant 1.0
embR 1417060 c.288A>G synonymous_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1833414 c.-127delT upstream_gene_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102024 c.1018delG frameshift_variant 1.0
katG 2154217 p.Arg632Leu missense_variant 0.33
katG 2155737 c.375C>G synonymous_variant 0.25
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2170462 p.Gly51Arg missense_variant 0.25
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223243 c.-79G>A upstream_gene_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289585 c.-345dupT upstream_gene_variant 0.22
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518584 p.Gln157Arg missense_variant 0.22
ahpC 2725933 c.-260G>T upstream_gene_variant 0.18
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3066122 p.Ile24Val missense_variant 0.29
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086916 p.Val33Met missense_variant 0.33
fbiD 3339657 c.540A>G synonymous_variant 0.17
Rv3083 3448675 p.Asp58Asn missense_variant 0.67
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3448889 p.Arg129Gln missense_variant 0.25
Rv3083 3448950 c.447T>C synonymous_variant 0.2
Rv3083 3449982 c.1479G>A synonymous_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
fbiA 3640976 p.Ala145Val missense_variant 0.25
alr 3840896 p.Met175Ile missense_variant 0.33
alr 3841220 c.201C>T synonymous_variant 0.22
ddn 3986726 c.-118G>A upstream_gene_variant 0.25
ddn 3986807 c.-37G>A upstream_gene_variant 0.18
ddn 3986815 c.-29_-28insGC upstream_gene_variant 0.18
clpC1 4039694 c.1011G>C synonymous_variant 0.5
clpC1 4039724 c.981A>G synonymous_variant 1.0
clpC1 4040517 p.Val63Ala missense_variant 1.0
clpC1 4040706 c.-2C>T upstream_gene_variant 0.67
embC 4239755 c.-108C>T upstream_gene_variant 0.22
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243583 c.351G>T synonymous_variant 0.22
embA 4243848 p.Val206Met missense_variant 1.0
embA 4245819 p.Ser863Gly missense_variant 0.18
embA 4245969 p.Pro913Ser missense_variant 1.0
embA 4246312 p.Gly1027Asp missense_variant 0.2
embB 4246801 c.288G>T synonymous_variant 0.17
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248015 p.Thr501Met missense_variant 0.33
embB 4248055 c.1542G>A synonymous_variant 0.22
embB 4248835 p.Trp774* stop_gained 0.29
embB 4248853 c.2340G>T synonymous_variant 0.29
embB 4249149 p.Ala879Val missense_variant 0.29
embB 4249250 c.2739delC frameshift_variant 0.22
embB 4249440 p.Glu976Val missense_variant 0.2
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4327389 p.Thr29Ser missense_variant 0.33
ethR 4327906 p.Val120Ile missense_variant 0.25
ethA 4328324 c.-851A>G upstream_gene_variant 0.33
whiB6 4338270 c.252A>G synonymous_variant 0.4
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0