TB-Profiler result

Run: ERR3587591
Summary

Run ID: ERR3587591

Sample name:

Date: 01-04-2023 02:37:17

Number of reads: 454452

Percentage reads mapped: 98.02

Strain: La1.7.1

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
La1.7 M.bovis None None 1.0
La1.7.1 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
gyrA 9432 p.Leu711Val missense_variant 0.12
gyrA 9510 p.Ile737Val missense_variant 0.14
gyrA 9612 p.Asp771Tyr missense_variant 0.13
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 761457 p.Pro551Ser missense_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764758 c.1389C>A synonymous_variant 0.14
rpoC 766173 p.Asn935Ser missense_variant 0.1
rpoC 766455 p.Pro1029His missense_variant 0.12
rpoC 767150 p.Gly1261Ser missense_variant 0.27
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 779503 c.-598A>G upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800851 p.Gln15Lys missense_variant 0.16
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
fbiC 1304044 p.Pro372Ser missense_variant 0.14
fbiC 1305192 c.2262C>A synonymous_variant 0.22
Rv1258c 1407157 p.Ala62Pro missense_variant 0.14
Rv1258c 1407414 c.-75delT upstream_gene_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472177 n.332C>A non_coding_transcript_exon_variant 0.15
rrs 1472407 n.565delA non_coding_transcript_exon_variant 0.15
rrl 1474093 n.436G>A non_coding_transcript_exon_variant 0.12
rrl 1474156 n.499G>A non_coding_transcript_exon_variant 0.13
rrl 1474365 n.710delT non_coding_transcript_exon_variant 0.18
rpsA 1833924 p.Gly128Asp missense_variant 0.12
rpsA 1834859 p.Ala440Thr missense_variant 1.0
rpsA 1834904 p.Pro455Ser missense_variant 0.22
tlyA 1917940 p.Val1Met missense_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103173 c.-132delG upstream_gene_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154984 c.1128G>A synonymous_variant 1.0
katG 2155503 c.609C>T synonymous_variant 1.0
katG 2156025 c.87C>A synonymous_variant 1.0
katG 2156548 c.-437C>A upstream_gene_variant 0.2
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 2168814 c.1798dupA frameshift_variant 1.0
PPE35 2169973 p.Gly214Cys missense_variant 0.15
PPE35 2170442 p.Trp57Cys missense_variant 0.25
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289020 c.222C>T synonymous_variant 1.0
pncA 2289276 c.-35C>G upstream_gene_variant 0.15
pncA 2289496 c.-255G>T upstream_gene_variant 0.12
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518924 c.810C>A synonymous_variant 0.17
kasA 2519062 c.948T>G synonymous_variant 0.11
eis 2715293 c.39delG frameshift_variant 0.12
eis 2715409 c.-77C>T upstream_gene_variant 0.15
ahpC 2726104 c.-89T>G upstream_gene_variant 1.0
folC 2746660 c.938delT frameshift_variant 0.4
folC 2746927 c.672C>A synonymous_variant 0.12
pepQ 2859693 c.726C>T synonymous_variant 1.0
thyA 3074648 c.-177T>G upstream_gene_variant 0.31
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
fbiD 3339384 c.267C>G synonymous_variant 0.2
fbiD 3339526 p.Arg137Ser missense_variant 0.12
Rv3083 3448783 p.Val94Ile missense_variant 1.0
Rv3083 3449355 p.Ser284Arg missense_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474243 c.237C>T synonymous_variant 0.17
fprA 3474427 p.Val141Ile missense_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3611982 p.Ala379Thr missense_variant 0.17
Rv3236c 3612170 p.Glu316Gly missense_variant 0.25
Rv3236c 3612781 c.336G>T synonymous_variant 0.12
fbiA 3641172 p.Met210Ile missense_variant 0.12
fbiB 3641301 c.-234C>A upstream_gene_variant 0.11
fbiB 3642478 p.Asp315Ala missense_variant 0.75
rpoA 3878630 c.-124delC upstream_gene_variant 1.0
ddn 3986829 c.-15G>A upstream_gene_variant 0.2
ddn 3987187 p.Thr115Ile missense_variant 0.11
clpC1 4038187 p.Ala840Ser missense_variant 0.4
clpC1 4038403 c.2302T>C synonymous_variant 1.0
clpC1 4039643 p.His354Gln missense_variant 0.15
clpC1 4039793 c.912C>T synonymous_variant 0.12
clpC1 4040257 p.Ala150Pro missense_variant 0.11
embC 4240080 p.Pro73Gln missense_variant 1.0
embC 4240549 c.687G>A synonymous_variant 0.22
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4240865 p.Ala335Ser missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242850 c.-383G>T upstream_gene_variant 0.14
embA 4242970 c.-263C>T upstream_gene_variant 1.0
embA 4244220 c.988C>T synonymous_variant 1.0
embA 4244544 c.1314_1317delCATC frameshift_variant 0.13
embB 4246551 p.Asn13Ser missense_variant 1.0
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4247057 p.Arg182Ser missense_variant 0.13
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248904 c.2391G>T synonymous_variant 0.12
aftB 4267858 p.Ile327Val missense_variant 1.0
aftB 4268501 c.336C>T synonymous_variant 0.22
aftB 4269351 c.-515C>T upstream_gene_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
ubiA 4269458 p.Leu126Met missense_variant 0.13
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4327437 p.Gly13Arg missense_variant 0.14
ethA 4328258 c.-785G>C upstream_gene_variant 0.12
whiB6 4338417 c.105G>A synonymous_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407802 p.Ala134Val missense_variant 0.13