TB-Profiler result

Run: ERR10430717
Summary

Run ID: ERR10430717

Sample name:

Date: 31-03-2023 10:15:29

Number of reads: 712586

Percentage reads mapped: 99.34

Strain: La2

Drug-resistance: HR-TB

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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
La2 M.caprae None None 0.99
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
katG 2153948 c.2163delG frameshift_variant 0.33 isoniazid
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 6307 c.-995T>G upstream_gene_variant 1.0
gyrB 6446 p.Ala403Ser missense_variant 0.98
gyrA 6721 c.-581C>T upstream_gene_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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575320 c.-28C>T upstream_gene_variant 0.22
rpoB 759620 c.-187A>C upstream_gene_variant 0.23
rpoB 761854 p.Ile683Thr missense_variant 1.0
rpoC 762560 c.-810A>G upstream_gene_variant 1.0
rpoB 762699 p.Ile965Val missense_variant 1.0
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
mmpL5 776575 p.Ala636Ser missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
fbiC 1304673 c.1743C>T synonymous_variant 0.12
Rv1258c 1406580 p.His254Arg missense_variant 0.15
embR 1416943 p.Ser135Arg missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1673766 c.-436C>T upstream_gene_variant 1.0
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103225 c.-183A>C upstream_gene_variant 0.33
katG 2154724 p.Arg463Leu missense_variant 0.95
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 2168364 p.Thr750Met missense_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 2518754 c.643delG frameshift_variant 0.15
kasA 2519248 c.1137_1138dupGA frameshift_variant 0.12
eis 2714307 c.1025dupC frameshift_variant 0.15
eis 2714317 p.Arg339Gln missense_variant 1.0
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 3448522 p.Val7Leu missense_variant 1.0
Rv3083 3448783 p.Val94Ile missense_variant 1.0
Rv3083 3449008 p.Trp169Arg missense_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
Rv3236c 3612997 c.120T>G synonymous_variant 0.19
rpoA 3878380 p.Leu43Arg missense_variant 0.11
embC 4240671 p.Thr270Ile missense_variant 1.0
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 4246864 c.351C>T synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4267858 p.Ile327Val missense_variant 1.0
aftB 4269132 c.-296G>A upstream_gene_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
ethR 4328170 p.Val208Leu missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0