TB-Profiler result

Run: ERR6139638
Summary

Run ID: ERR6139638

Sample name:

Date: 02-04-2023 01:42:55

Number of reads: 1066249

Percentage reads mapped: 99.29

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
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 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.27
mshA 576442 p.Cys365Trp missense_variant 0.17
mshA 576447 p.Thr367Lys missense_variant 0.13
mshA 576489 p.Val381Gly missense_variant 0.22
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764367 p.Gly333Ala missense_variant 0.17
rpoC 764459 c.1093delA frameshift_variant 0.13
rpoC 766966 p.Glu1199Asp missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
fbiC 1303977 c.1047C>G synonymous_variant 0.2
fbiC 1304951 p.Asp674Ala missense_variant 0.15
embR 1416390 c.958C>T synonymous_variant 1.0
atpE 1461173 c.129C>T synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473749 n.92A>T non_coding_transcript_exon_variant 0.12
rrl 1476101 n.2444C>T non_coding_transcript_exon_variant 1.0
fabG1 1673553 p.Asp38Glu missense_variant 0.24
rpsA 1834131 p.Glu197Val missense_variant 0.12
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917906 c.-34G>C upstream_gene_variant 0.13
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 2154753 c.1359C>T synonymous_variant 0.13
katG 2155503 c.609C>T synonymous_variant 1.0
katG 2156025 c.87C>A synonymous_variant 1.0
PPE35 2167791 p.Ser941Tyr missense_variant 0.18
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168011 p.Ser868Arg missense_variant 1.0
PPE35 2168319 p.Thr765Ile missense_variant 1.0
PPE35 2168386 p.Glu743Gln missense_variant 0.29
PPE35 2168814 c.1798dupA frameshift_variant 1.0
PPE35 2170344 p.Ala90Val missense_variant 0.17
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289956 c.-715C>T upstream_gene_variant 0.12
pncA 2289964 c.-723C>T upstream_gene_variant 0.12
kasA 2518132 c.18C>T synonymous_variant 1.0
eis 2715125 p.Thr70Ala missense_variant 1.0
folC 2747631 c.-33C>T upstream_gene_variant 0.93
pepQ 2860149 c.270C>A synonymous_variant 0.22
pepQ 2860159 p.Ala87Gly missense_variant 0.25
pepQ 2860183 p.Val79Gly missense_variant 0.21
ribD 2987501 c.663C>G synonymous_variant 0.17
Rv2752c 3064830 c.1362C>G synonymous_variant 0.2
thyX 3067990 c.-45C>A upstream_gene_variant 0.25
ald 3086728 c.-92C>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087084 c.266delA frameshift_variant 1.0
Rv3083 3448783 p.Val94Ile missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474213 p.Lys69Asn missense_variant 0.25
fprA 3474427 p.Val141Ile missense_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3612880 c.237G>A synonymous_variant 0.18
rpoA 3878630 c.-124delC upstream_gene_variant 1.0
clpC1 4038167 p.Ala846Pro missense_variant 0.29
clpC1 4038403 c.2302T>C synonymous_variant 1.0
embC 4240427 p.Ser189Cys missense_variant 0.4
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241580 p.Ile573Thr missense_variant 0.25
embC 4242029 p.Leu723Val missense_variant 1.0
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 4244603 c.1371G>A synonymous_variant 0.12
embA 4245829 p.Arg866Pro missense_variant 0.23
embB 4246551 p.Asn13Ser missense_variant 1.0
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4247028 p.Leu172Arg missense_variant 0.29
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248328 c.1815G>C synonymous_variant 0.17
aftB 4267314 c.1522dupA frameshift_variant 0.12
aftB 4267858 p.Ile327Val missense_variant 1.0
aftB 4267899 p.Ala313Gly missense_variant 0.22
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
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