TB-Profiler result

Run: SRR18391706
Summary

Run ID: SRR18391706

Sample name:

Date: 03-04-2023 19:40:42

Number of reads: 459189

Percentage reads mapped: 97.21

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 7296 c.-6G>T upstream_gene_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8124 p.Pro275Thr missense_variant 0.15
gyrA 8158 p.Ser286* stop_gained 0.15
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 490926 c.144C>A synonymous_variant 0.12
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620288 p.Arg133Leu missense_variant 0.12
rpoB 759615 c.-192A>C upstream_gene_variant 0.29
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 767056 c.3687C>A synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 778214 p.Ser89Arg missense_variant 0.12
mmpS5 778626 c.279_280insGTGAGCG frameshift_variant 0.13
mmpS5 778630 p.Leu92Phe missense_variant 0.13
mmpS5 778632 c.267_273delGCTCACC frameshift_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
fbiC 1304682 c.1752C>T synonymous_variant 0.12
Rv1258c 1406131 p.Asp404His missense_variant 0.12
Rv1258c 1406782 p.Ala187Thr missense_variant 0.15
Rv1258c 1406892 p.Leu150Pro missense_variant 0.17
embR 1416571 c.777G>A synonymous_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471772 n.-74G>A upstream_gene_variant 0.14
rrs 1472351 n.506G>T non_coding_transcript_exon_variant 0.5
rrs 1472704 n.859C>A non_coding_transcript_exon_variant 0.29
rrl 1473699 n.42A>T non_coding_transcript_exon_variant 0.5
rrl 1475284 n.1627C>A non_coding_transcript_exon_variant 0.33
fabG1 1674131 p.Tyr231Phe missense_variant 0.13
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102272 c.771C>A synonymous_variant 0.12
ndh 2103173 c.-132delG upstream_gene_variant 1.0
ndh 2103200 c.-158C>A upstream_gene_variant 0.13
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155503 c.609C>T synonymous_variant 1.0
katG 2156025 c.87C>A synonymous_variant 1.0
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 2168467 p.Leu716Ile missense_variant 0.14
PPE35 2168814 c.1798dupA frameshift_variant 1.0
PPE35 2170244 c.369G>A synonymous_variant 0.12
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518160 p.Val16Leu missense_variant 0.12
eis 2715118 p.Pro72His missense_variant 0.13
Rv2752c 3065477 p.Ala239Ser missense_variant 0.15
Rv2752c 3066136 p.Thr19Asn missense_variant 0.13
thyX 3067196 c.750C>T synonymous_variant 0.17
thyX 3067530 p.Ala139Val missense_variant 0.14
thyX 3067854 p.Gly31Ala missense_variant 0.11
thyX 3067896 p.Phe17Ser missense_variant 0.1
thyA 3074645 c.-174T>G upstream_gene_variant 0.27
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 3339391 c.274C>T synonymous_variant 0.15
fbiD 3339436 p.Ala107Ser missense_variant 0.17
Rv3083 3448333 c.-171G>A upstream_gene_variant 0.13
Rv3083 3448556 p.Gly18Val missense_variant 0.13
Rv3083 3448783 p.Val94Ile missense_variant 1.0
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 3612424 c.693G>T synonymous_variant 0.12
Rv3236c 3613202 c.-86G>T upstream_gene_variant 0.12
fbiA 3640636 p.Ser32Pro missense_variant 1.0
fbiB 3642478 p.Asp315Ala missense_variant 1.0
alr 3840818 p.Asp201Glu missense_variant 0.12
clpC1 4038403 c.2302T>C synonymous_variant 1.0
clpC1 4038773 c.1931_1932insGT frameshift_variant 0.12
clpC1 4038776 p.Glu643Gly missense_variant 0.12
clpC1 4038782 p.Val641Leu missense_variant 0.15
clpC1 4038785 p.Gln640His missense_variant 0.15
clpC1 4038789 p.Leu639Pro missense_variant 0.15
embC 4240299 p.Gln146Arg missense_variant 0.1
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4242192 c.2333delG frameshift_variant 0.17
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 4244405 c.1173C>A synonymous_variant 0.12
embA 4246505 p.Arg1091Ser missense_variant 1.0
embB 4246551 p.Asn13Ser missense_variant 1.0
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4247386 c.873T>C synonymous_variant 0.1
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4249371 p.Leu953Pro missense_variant 0.12
aftB 4267858 p.Ile327Val missense_variant 1.0
aftB 4268401 p.Ala146Ser missense_variant 0.13
aftB 4268479 p.Ala120Ser missense_variant 0.14
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
ubiA 4269920 c.-87G>A upstream_gene_variant 0.12
ethA 4326278 p.Ser399Leu missense_variant 0.11
ethR 4327846 p.Glu100* stop_gained 0.12
ethA 4328076 c.-603G>A upstream_gene_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408063 p.Arg47Gln missense_variant 0.17
gid 4408148 p.Ala19Thr missense_variant 0.13