TB-Profiler result

Run: ERR4627359
Summary

Run ID: ERR4627359

Sample name:

Date: 01-04-2023 06:33:05

Number of reads: 1211544

Percentage reads mapped: 98.81

Strain: La1.8.1

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
La1.8 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
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 8741 c.1440C>T synonymous_variant 1.0
gyrA 8965 p.Val555Ala missense_variant 0.13
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 491025 p.Tyr81* stop_gained 0.12
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 760110 p.Ser102Thr missense_variant 0.18
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763226 c.-144A>G upstream_gene_variant 0.11
rpoC 765699 p.Ile777Thr missense_variant 0.1
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776147 c.2334C>A synonymous_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781842 p.Tyr95His missense_variant 0.12
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
Rv1258c 1406209 p.Ala378Pro missense_variant 0.11
embR 1417144 c.204A>G synonymous_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473003 n.1158G>A non_coding_transcript_exon_variant 0.29
rrl 1474467 n.810A>C non_coding_transcript_exon_variant 1.0
rrl 1475184 n.1527T>G non_coding_transcript_exon_variant 0.29
rrl 1475973 n.2316T>C non_coding_transcript_exon_variant 0.25
rrl 1476423 n.2766T>A non_coding_transcript_exon_variant 0.22
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.15
inhA 1674968 c.772_774delATC conservative_inframe_deletion 0.15
rpsA 1834166 p.Gly209Arg missense_variant 1.0
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102193 p.Arg284Trp missense_variant 1.0
ndh 2102749 c.294C>T synonymous_variant 0.17
ndh 2103072 c.-30T>C upstream_gene_variant 0.11
ndh 2103173 c.-132delG upstream_gene_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155246 p.Glu289Gly missense_variant 0.14
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 2167963 p.Gly884Arg missense_variant 0.12
PPE35 2167964 c.2649G>C synonymous_variant 0.15
PPE35 2168011 p.Ser868Arg missense_variant 1.0
PPE35 2168319 p.Thr765Ile missense_variant 1.0
PPE35 2168518 p.Ile699Val missense_variant 0.12
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
eis 2714512 p.Pro274Leu missense_variant 0.12
eis 2714785 p.Arg183His missense_variant 1.0
eis 2715125 p.Thr70Ala 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 3448451 c.-53A>G upstream_gene_variant 0.17
Rv3083 3448783 p.Val94Ile missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474142 c.141delG frameshift_variant 0.14
fprA 3474427 p.Val141Ile missense_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
clpC1 4038403 c.2302T>C synonymous_variant 1.0
clpC1 4038446 p.Asp753Glu missense_variant 0.17
clpC1 4038902 c.1803C>T synonymous_variant 0.13
clpC1 4039841 p.Glu288Asp missense_variant 0.25
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 4246551 p.Asn13Ser missense_variant 1.0
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4267822 p.Leu339Met missense_variant 0.15
aftB 4267858 p.Ile327Val missense_variant 1.0
aftB 4268254 c.582delG frameshift_variant 0.12
aftB 4268276 c.561G>A synonymous_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
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408237 c.-35C>A upstream_gene_variant 1.0