TB-Profiler result

Run: SRR18391732
Summary

Run ID: SRR18391732

Sample name:

Date: 03-04-2023 19:41:35

Number of reads: 553338

Percentage reads mapped: 97.83

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
fgd1 491535 c.753G>A synonymous_variant 0.12
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576043 c.696G>A synonymous_variant 0.15
ccsA 619842 c.-49G>T upstream_gene_variant 0.12
rpoB 761658 p.Pro618Thr missense_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
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 1303059 c.129G>A synonymous_variant 0.12
Rv1258c 1406954 c.387C>A synonymous_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674084 c.-118C>G upstream_gene_variant 0.11
rpsA 1833381 c.-161T>C upstream_gene_variant 0.1
rpsA 1834859 p.Ala440Thr missense_variant 1.0
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 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 2168814 c.1798dupA frameshift_variant 1.0
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 2518671 p.Val186Glu missense_variant 0.15
eis 2714714 p.Ala207Ser missense_variant 0.12
eis 2715396 c.-64G>T upstream_gene_variant 0.12
eis 2715430 c.-98C>T upstream_gene_variant 0.14
eis 2715432 c.-100C>T upstream_gene_variant 0.14
eis 2715436 c.-104G>A upstream_gene_variant 0.14
eis 2715440 c.-108A>C upstream_gene_variant 0.14
eis 2715445 c.-113C>T upstream_gene_variant 0.14
eis 2715447 c.-115T>A upstream_gene_variant 0.14
eis 2715450 c.-118T>C upstream_gene_variant 0.14
eis 2715451 c.-119C>A upstream_gene_variant 0.14
eis 2715454 c.-122T>G upstream_gene_variant 0.14
eis 2715455 c.-123G>A upstream_gene_variant 0.14
eis 2715458 c.-126T>A upstream_gene_variant 0.14
eis 2715460 c.-128A>G upstream_gene_variant 0.14
eis 2715465 c.-133G>T upstream_gene_variant 0.14
eis 2715469 c.-137T>C upstream_gene_variant 0.15
eis 2715473 c.-141A>G upstream_gene_variant 0.15
pepQ 2859494 p.Gly309Trp missense_variant 0.14
ribD 2986942 p.Pro35Leu missense_variant 0.14
ribD 2987422 p.Gly195Glu missense_variant 0.15
thyX 3067569 p.Ala126Val missense_variant 0.12
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 3339179 p.Ala21Glu missense_variant 0.17
Rv3083 3448783 p.Val94Ile missense_variant 1.0
Rv3083 3449503 p.Gly334Arg missense_variant 0.11
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
fbiA 3640636 p.Ser32Pro missense_variant 1.0
fbiB 3641922 p.Ala130Thr missense_variant 1.0
fbiB 3642478 p.Asp315Ala missense_variant 1.0
clpC1 4038167 c.2538C>T synonymous_variant 0.2
clpC1 4038403 c.2302T>C synonymous_variant 1.0
clpC1 4038596 p.Lys703Asn missense_variant 0.12
embC 4240024 p.Gln54His missense_variant 0.15
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241843 p.Leu661Phe missense_variant 0.14
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 4245083 c.1851A>G synonymous_variant 0.11
embB 4245854 c.-660C>T upstream_gene_variant 0.12
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 4248683 p.Ala724Ser missense_variant 0.15
aftB 4267858 p.Ile327Val missense_variant 1.0
aftB 4268536 p.Gly101Trp missense_variant 0.13
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 4269759 p.Gln25His missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408001 p.Ile68Val missense_variant 0.11