TB-Profiler result

Run: ERR4819691
Summary

Run ID: ERR4819691

Sample name:

Date: 01-04-2023 16:15:09

Number of reads: 401331

Percentage reads mapped: 98.99

Strain: La1.2.BCG

Drug-resistance: Other

Download CSV Download TXT Download PDF Download JSON
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
La1.2 M.bovis None None 1.0
La1.2.BCG M.bovis BCG 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
gid 4408100 c.102delG frameshift_variant 0.29 streptomycin
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
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7636 p.Gly112Asp missense_variant 0.33
gyrA 8285 c.984C>T synonymous_variant 1.0
gyrA 8624 c.1323G>T synonymous_variant 1.0
gyrA 8741 c.1440C>T synonymous_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575346 c.-2G>T upstream_gene_variant 0.12
mshA 575890 c.543C>A synonymous_variant 0.22
mshA 576368 p.Arg341Trp missense_variant 0.11
mshA 576531 p.Val395Ala missense_variant 0.22
rpoB 760981 p.Arg392Gln missense_variant 0.18
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763575 p.Arg69Pro missense_variant 1.0
rpoC 764627 p.Lys420Glu missense_variant 0.67
rpoC 765099 p.Pro577Gln missense_variant 0.22
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
rpsL 781568 c.9C>T synonymous_variant 1.0
rplC 801363 c.555C>G synonymous_variant 0.29
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
Rv1258c 1406464 p.Thr293Ala missense_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1674150 p.Ile237Met missense_variant 0.29
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101896 p.Gly383Cys missense_variant 0.22
ndh 2102106 p.Gly313Arg missense_variant 1.0
ndh 2102153 p.Leu297Pro missense_variant 0.18
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
katG 2156465 c.-354C>T upstream_gene_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168011 p.Ser868Arg missense_variant 1.0
PPE35 2168814 c.1798dupA frameshift_variant 1.0
PPE35 2168920 p.Val565Phe missense_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518214 p.Lys34Glu missense_variant 0.4
eis 2715547 c.-216delG upstream_gene_variant 0.29
pepQ 2859392 p.Val343Ile missense_variant 0.14
pepQ 2859470 c.948delA frameshift_variant 0.12
pepQ 2860065 c.354C>T synonymous_variant 0.25
Rv2752c 3064609 p.Arg528Gln missense_variant 0.5
Rv2752c 3067176 c.-985A>G upstream_gene_variant 0.2
thyX 3067217 c.729C>T synonymous_variant 0.2
ald 3087084 c.266delA frameshift_variant 1.0
fbiD 3339009 c.-109C>T upstream_gene_variant 0.25
Rv3083 3448745 p.Ile81Ser missense_variant 1.0
Rv3083 3448783 p.Val94Ile missense_variant 1.0
Rv3083 3448797 c.294T>A synonymous_variant 0.18
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
whiB7 3568745 c.-66C>A upstream_gene_variant 0.13
alr 3840554 c.867G>C synonymous_variant 0.18
clpC1 4038403 c.2302T>C synonymous_variant 1.0
clpC1 4038620 p.Gln695His missense_variant 0.29
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4242029 c.2167C>T synonymous_variant 1.0
embC 4242539 p.Ser893Thr missense_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242970 c.-263C>T upstream_gene_variant 1.0
embC 4243131 p.Pro1090Gln missense_variant 0.29
embA 4244220 c.988C>T synonymous_variant 1.0
embA 4244614 p.Ala461Val missense_variant 0.25
embA 4244970 p.Leu580Val missense_variant 0.25
embA 4246345 p.Arg1038His missense_variant 0.15
embB 4246551 p.Asn13Ser missense_variant 1.0
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4247173 c.660G>A synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4249140 c.2629delG frameshift_variant 0.29
embB 4249358 c.2846delT frameshift_variant 0.13
aftB 4267636 p.Arg401Trp missense_variant 0.29
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 4269689 p.Val49Ile missense_variant 1.0
ethA 4326076 c.1398G>T synonymous_variant 0.2
ethR 4327141 c.-408G>A upstream_gene_variant 0.4
ethR 4327751 p.Lys68Met missense_variant 0.33
ethA 4328236 c.-763A>G upstream_gene_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408017 c.183_185delCGG disruptive_inframe_deletion 0.12
Rv1979c 2221058 c.-8682_*660del transcript_ablation 1.0