TB-Profiler result

Run: SRR13986561
Summary

Run ID: SRR13986561

Sample name:

Date: 03-04-2023 09:44:03

Number of reads: 1512972

Percentage reads mapped: 65.24

Strain: La1.7

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
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 576090 p.Arg248Leu missense_variant 0.15
mshA 576107 p.Ala254Thr missense_variant 0.2
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764160 p.Leu264Gln missense_variant 0.13
rpoC 766149 p.Thr927Ile missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpR5 778082 c.-908T>C upstream_gene_variant 0.19
mmpR5 778088 c.-902C>G upstream_gene_variant 0.19
mmpR5 778094 c.-896A>G upstream_gene_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
fbiC 1303948 p.Gly340Ser missense_variant 0.25
fbiC 1304280 c.1350C>A synonymous_variant 0.18
Rv1258c 1407224 c.117C>A synonymous_variant 0.15
Rv1258c 1407269 c.72C>A synonymous_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476131 n.2474C>G non_coding_transcript_exon_variant 1.0
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1917984 c.45C>A synonymous_variant 0.2
tlyA 1918141 p.His68Asn missense_variant 0.2
ndh 2103173 c.-132delG upstream_gene_variant 1.0
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 2167965 p.Ala883Gly missense_variant 0.2
PPE35 2167967 c.2646A>C synonymous_variant 0.2
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 2169269 c.1344A>G synonymous_variant 0.14
PPE35 2169272 c.1341C>G synonymous_variant 0.14
PPE35 2169281 c.1332T>G synonymous_variant 0.12
PPE35 2169902 p.Leu237Phe missense_variant 0.14
PPE35 2170147 p.Ser156Ala missense_variant 0.12
PPE35 2170159 p.Ala152Ser missense_variant 0.17
PPE35 2170385 c.228G>T synonymous_variant 0.14
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 2518683 p.Ala190Gly missense_variant 0.18
kasA 2518809 p.Lys232Arg missense_variant 0.19
kasA 2519140 c.1026G>C synonymous_variant 0.13
kasA 2519143 c.1029G>C synonymous_variant 0.13
eis 2714299 p.Ala345Val missense_variant 1.0
eis 2714363 p.Ser324Pro missense_variant 1.0
eis 2714762 p.Leu191Ile missense_variant 0.15
eis 2714778 p.Gln185His missense_variant 0.12
folC 2747579 p.Gly7Asp missense_variant 0.29
pepQ 2859632 p.Ala263Ser missense_variant 0.12
ribD 2987282 c.444C>A synonymous_variant 0.14
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 3474427 p.Val141Ile missense_variant 1.0
fprA 3474984 c.978G>T synonymous_variant 0.13
fprA 3475159 p.Asn385Asp missense_variant 1.0
rpoA 3878630 c.-124delC upstream_gene_variant 1.0
clpC1 4038403 c.2302T>C synonymous_variant 1.0
clpC1 4040681 c.24T>C synonymous_variant 1.0
embC 4240129 p.Gln89His missense_variant 0.18
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241313 p.Ala484Glu missense_variant 0.12
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
embB 4246551 p.Asn13Ser missense_variant 1.0
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4247426 p.Gly305Thr missense_variant 0.2
embB 4247646 p.Glu378Ala missense_variant 1.0
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
ubiA 4269945 c.-112G>T upstream_gene_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0