TB-Profiler result

Run: ERR6140806

Summary

Run ID: ERR6140806

Sample name:

Date: 02-04-2023 01:44:24

Number of reads: 929098

Percentage reads mapped: 37.93

Strain: La1.8.2

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
La1 M.bovis None None 1.0
La1.8 M.bovis None None 1.0
La1.8.2 M.bovis None None 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
pncA 2289073 p.His57Asp missense_variant 1.0 pyrazinamide
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 5752 c.513G>A synonymous_variant 1.0
gyrA 6406 c.-896C>T upstream_gene_variant 1.0
gyrB 6446 p.Ala403Ser missense_variant 1.0
gyrB 6969 p.Asp577Val missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8285 c.984C>T synonymous_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9217 p.Asp639Ala missense_variant 0.97
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9647 c.2346C>G synonymous_variant 0.18
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576113 p.Arg256Gly missense_variant 0.4
rpoB 759912 p.Ala36Thr missense_variant 0.12
rpoB 762141 p.Asp779Tyr missense_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764367 p.Gly333Ala missense_variant 0.33
rpoC 764537 p.Pro390Ala missense_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776063 c.2418C>T synonymous_variant 0.2
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776197 p.Ala762Thr missense_variant 0.12
mmpL5 779193 c.-713G>A upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
fbiC 1303535 p.Ser202Leu missense_variant 0.15
embR 1416390 c.958C>T synonymous_variant 1.0
atpE 1460986 c.-59A>C upstream_gene_variant 0.12
atpE 1461173 c.129C>T synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476101 n.2444C>T non_coding_transcript_exon_variant 1.0
inhA 1674141 c.-61T>C upstream_gene_variant 0.14
inhA 1674627 c.426T>C synonymous_variant 0.11
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102991 p.Val18Met missense_variant 1.0
ndh 2103173 c.-132delG upstream_gene_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154935 p.Ile393Val missense_variant 0.1
katG 2155503 c.609C>T synonymous_variant 1.0
katG 2156025 c.87C>A synonymous_variant 0.97
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168011 p.Ser868Arg missense_variant 1.0
PPE35 2168216 c.2397C>T synonymous_variant 0.2
PPE35 2168319 p.Thr765Ile missense_variant 1.0
PPE35 2168814 c.1798dupA frameshift_variant 1.0
PPE35 2169565 p.Gly350Ser missense_variant 0.14
PPE35 2170159 p.Ala152Ser missense_variant 0.14
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289948 c.-707C>A upstream_gene_variant 0.13
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2519071 p.Asp319Glu missense_variant 0.33
eis 2715125 p.Thr70Ala missense_variant 1.0
folC 2747380 c.219C>T synonymous_variant 0.16
folC 2747631 c.-33C>T upstream_gene_variant 1.0
thyX 3067420 p.Pro176Ser missense_variant 0.13
ald 3086728 c.-92C>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087029 p.Leu70Phe missense_variant 0.15
ald 3087084 c.266delA frameshift_variant 1.0
Rv3083 3448783 p.Val94Ile missense_variant 1.0
Rv3083 3448946 p.Gly148Asp missense_variant 0.17
fprA 3473824 c.-183C>T upstream_gene_variant 0.12
fprA 3473825 c.-181delC upstream_gene_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474427 p.Val141Ile missense_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3612849 c.268C>T synonymous_variant 0.14
fbiA 3640427 c.-116T>C upstream_gene_variant 0.18
fbiB 3642815 c.1281A>G synonymous_variant 0.11
rpoA 3878630 c.-124delC upstream_gene_variant 1.0
clpC1 4038403 c.2302T>C synonymous_variant 1.0
embC 4240411 c.549G>C synonymous_variant 0.25
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241696 p.Ala612Thr missense_variant 0.17
embC 4242029 p.Leu723Val missense_variant 1.0
embA 4242337 c.-896C>T upstream_gene_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242970 c.-263C>T upstream_gene_variant 1.0
embA 4244220 c.988C>T synonymous_variant 1.0
embA 4244329 p.Ala366Gly missense_variant 0.14
embB 4246551 p.Asn13Ser missense_variant 1.0
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248319 c.1806A>C synonymous_variant 0.17
embB 4248328 c.1815G>C synonymous_variant 0.2
embB 4249175 p.Val888Leu missense_variant 0.11
aftB 4267858 p.Ile327Val missense_variant 1.0
aftB 4269351 c.-515C>T upstream_gene_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326585 p.Pro297Thr missense_variant 0.12
ethA 4327385 p.Lys30Arg missense_variant 0.1
whiB6 4338205 p.Val106Gly missense_variant 0.4
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
embR 1416583 c.-2382_764del frameshift_variant&start_lost 1.0