TB-Profiler result

Run: ERR4627314

Summary

Run ID: ERR4627314

Sample name:

Date: 01-04-2023 06:31:16

Number of reads: 1079271

Percentage reads mapped: 74.35

Strain: La1.8.1

Drug-resistance: HR-TB


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
La1.8 M.bovis None None 1.0
La1.8.1 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
katG 2155764 c.344_347delTCCA frameshift_variant 0.12 isoniazid
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 7934 c.633C>T synonymous_variant 0.12
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 576108 p.Ala254Gly missense_variant 0.5
mshA 576245 p.Gly300Arg missense_variant 0.15
mshA 576329 p.Leu328Met missense_variant 0.12
rpoB 762182 p.Asp792Glu missense_variant 0.11
rpoB 762906 p.Lys1034Glu missense_variant 0.1
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764605 c.1236G>C synonymous_variant 0.12
rpoC 764611 c.1242G>T synonymous_variant 0.13
rpoC 764701 c.1332C>G synonymous_variant 0.11
rpoC 764705 p.Leu446Lys missense_variant 0.11
rpoC 764786 p.Lys473* stop_gained 0.2
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
Rv1258c 1406279 c.1062G>C synonymous_variant 0.12
embR 1417261 c.87A>G synonymous_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472249 n.409delG non_coding_transcript_exon_variant 0.2
rrs 1473022 n.1177G>T non_coding_transcript_exon_variant 0.25
rrl 1474068 n.411T>C non_coding_transcript_exon_variant 0.12
rrl 1476334 n.2681delC non_coding_transcript_exon_variant 0.12
inhA 1674966 c.765T>C synonymous_variant 0.13
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
PPE35 2170048 p.Leu189Val missense_variant 0.31
PPE35 2170053 p.Thr187Ser missense_variant 0.27
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222537 p.Val210Ile missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
eis 2715125 p.Thr70Ala missense_variant 1.0
ribD 2986655 c.-184A>C upstream_gene_variant 0.1
ribD 2987251 c.415delG frameshift_variant 0.13
Rv2752c 3064538 p.Val552Met missense_variant 0.11
Rv2752c 3064544 p.Met550Val missense_variant 0.11
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 3339734 p.Ala206Gly missense_variant 0.27
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
whiB7 3568494 c.186C>A synonymous_variant 0.22
whiB7 3568832 c.-153G>C upstream_gene_variant 0.11
rpoA 3878349 c.159C>T synonymous_variant 1.0
rpoA 3878630 c.-124delC upstream_gene_variant 1.0
clpC1 4038403 c.2302T>C synonymous_variant 1.0
embC 4240532 p.Ser224Cys missense_variant 0.12
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4242642 p.Arg927His missense_variant 1.0
embA 4242970 c.-263C>T upstream_gene_variant 1.0
embA 4243444 p.Ser73Pro missense_variant 0.11
embA 4243623 p.Ile131Val missense_variant 0.13
embA 4244220 c.988C>T synonymous_variant 1.0
embA 4245257 c.2025A>G synonymous_variant 0.12
embB 4246551 p.Asn13Ser missense_variant 1.0
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4247545 p.Ser344Arg missense_variant 0.12
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4249471 c.2958G>T synonymous_variant 0.25
embB 4249708 c.3197delA frameshift_variant 0.22
aftB 4267209 c.1627delT frameshift_variant 0.12
aftB 4267858 p.Ile327Val missense_variant 1.0
aftB 4267871 c.966G>A synonymous_variant 0.15
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
ethA 4326024 p.Pro484Ser missense_variant 1.0
ethA 4327214 p.Ser87Ile missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407697 p.Asp169Gly missense_variant 1.0