TB-Profiler result

Run: ERR2660518
Summary

Run ID: ERR2660518

Sample name:

Date: 31-03-2023 22:53:47

Number of reads: 275994

Percentage reads mapped: 99.41

Strain:

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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.2.2.2 Indo-Oceanic NA 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
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 5075 c.-165C>T upstream_gene_variant 1.0
gyrB 5541 p.Thr101Ile missense_variant 0.4
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrA 6745 c.-557T>C upstream_gene_variant 1.0
gyrA 7268 c.-34C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575482 c.135C>A synonymous_variant 0.18
mshA 575549 p.Met68Leu missense_variant 0.15
rpoB 760832 c.1026G>A synonymous_variant 0.5
rpoB 761643 p.Val613Ile missense_variant 0.22
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763552 c.183C>T synonymous_variant 1.0
rpoC 766259 p.Ser964Pro missense_variant 0.33
rpoC 766558 p.Lys1063Asn missense_variant 0.13
rpoC 766916 p.Arg1183Ser missense_variant 0.12
rpoC 766974 p.Ala1202Asp missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777447 p.Ile345Asn missense_variant 0.14
mmpS5 779625 c.-720G>A upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781848 p.Ile97Phe missense_variant 0.18
rpsL 781860 p.Ser101Thr missense_variant 0.18
rplC 801007 p.Thr67Ala missense_variant 0.2
rplC 801019 p.Thr71Pro missense_variant 0.17
rplC 801159 c.351C>T synonymous_variant 0.15
fbiC 1305248 p.Ala773Val missense_variant 0.22
Rv1258c 1407102 p.Ala80Val missense_variant 0.17
embR 1417019 p.Cys110Tyr missense_variant 1.0
atpE 1461055 p.Thr4Asn missense_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473858 n.201A>G non_coding_transcript_exon_variant 0.22
inhA 1674905 p.Ala235Val missense_variant 0.4
rpsA 1833349 c.-193C>A upstream_gene_variant 0.18
rpsA 1834085 p.Asn182His missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918084 p.Thr49Ala missense_variant 0.4
tlyA 1918120 p.Ala61Ser missense_variant 0.29
ndh 2101791 p.Thr418Ser missense_variant 0.13
ndh 2102240 p.Arg268His missense_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155346 p.Ala256Ser missense_variant 0.29
katG 2155924 p.Asp63Val missense_variant 0.25
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168449 p.Gln722Glu missense_variant 0.29
PPE35 2170772 c.-160C>A upstream_gene_variant 0.17
PPE35 2170809 c.-197C>T upstream_gene_variant 0.25
Rv1979c 2221771 p.Leu465Pro missense_variant 0.4
Rv1979c 2222098 p.Thr356Lys missense_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222623 p.Gly181Glu missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518240 c.126C>T synonymous_variant 0.25
kasA 2519057 p.Thr315Ser missense_variant 0.15
kasA 2519062 c.948T>G synonymous_variant 0.15
kasA 2519065 c.951C>A synonymous_variant 0.18
kasA 2519070 p.Asp319Val missense_variant 0.18
eis 2715003 c.330T>C synonymous_variant 0.22
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2747345 p.Leu85Arg missense_variant 0.15
folC 2747734 c.-136C>T upstream_gene_variant 0.14
ribD 2986678 c.-161C>T upstream_gene_variant 0.25
Rv2752c 3065515 p.Ile226Thr missense_variant 0.5
thyX 3067370 p.Trp192Cys missense_variant 0.2
thyX 3067535 c.411C>T synonymous_variant 0.33
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087210 p.Ala131Thr missense_variant 0.12
fbiD 3339465 c.348T>C synonymous_variant 0.2
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449600 p.Gln366Arg missense_variant 0.15
Rv3083 3449877 p.His458Gln missense_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474214 p.Thr70Pro missense_variant 0.18
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
whiB7 3568605 c.75C>G synonymous_variant 0.25
Rv3236c 3612317 p.Arg267His missense_variant 1.0
fbiA 3641461 p.Pro307Ala missense_variant 0.29
fbiB 3641748 c.214C>A synonymous_variant 0.33
alr 3841168 p.Gly85Ser missense_variant 0.2
rpoA 3877885 p.Leu208Pro missense_variant 0.15
rpoA 3878230 p.Val93Asp missense_variant 0.2
ddn 3986910 p.Arg23Trp missense_variant 0.14
clpC1 4039702 p.Asp335Asn missense_variant 0.15
clpC1 4040278 p.Ser143Pro missense_variant 0.11
clpC1 4040517 p.Val63Ala missense_variant 1.0
clpC1 4040719 c.-15A>G upstream_gene_variant 1.0
embC 4239698 c.-165T>A upstream_gene_variant 0.18
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241599 p.Met579Ile missense_variant 0.4
embC 4241909 p.Ala683Thr missense_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244508 p.Leu426Val missense_variant 0.12
embA 4244909 c.1677C>T synonymous_variant 0.25
embA 4245670 p.Ala813Gly missense_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246979 p.Gly156Cys missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4249787 p.Gly1092Ser missense_variant 0.29
aftB 4267201 p.Trp546Arg missense_variant 0.33
aftB 4267960 p.Val293Met missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326439 p.Asn345Lys missense_variant 1.0
whiB6 4338203 p.Arg107Cys missense_variant 1.0
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 4407848 p.Ala119Thr missense_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0
gid 4408132 p.Glu24Val missense_variant 0.29