TB-Profiler result

Run: ERR4627377
Summary

Run ID: ERR4627377

Sample name:

Date: 01-04-2023 06:34:22

Number of reads: 1318950

Percentage reads mapped: 78.85

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
ethA 4327102 c.371dupG frameshift_variant 0.12 ethionamide
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 9143 c.1842T>C synonymous_variant 1.0
gyrA 9217 p.Asp639Ala missense_variant 1.0
gyrA 9303 p.Gly668Asn missense_variant 0.12
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 762138 c.2333delT frameshift_variant 0.12
rpoB 762939 p.Met1045Leu missense_variant 0.14
rpoB 762942 p.Ile1046Val missense_variant 0.14
rpoC 762947 c.-423C>G upstream_gene_variant 0.14
rpoC 762962 c.-408C>T upstream_gene_variant 0.13
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
Rv1258c 1407521 c.-181C>T upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472625 n.780T>C non_coding_transcript_exon_variant 0.22
rrl 1474008 n.351G>A non_coding_transcript_exon_variant 0.17
rrl 1474759 n.1102A>T non_coding_transcript_exon_variant 1.0
rrl 1476426 n.2769A>T non_coding_transcript_exon_variant 0.4
rpsA 1834455 p.Val305Ala missense_variant 0.11
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 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 2168181 p.Leu811Pro missense_variant 0.14
PPE35 2168319 p.Thr765Ile missense_variant 1.0
PPE35 2168814 c.1798dupA frameshift_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.3
PPE35 2170053 p.Thr187Ser missense_variant 0.3
PPE35 2170527 p.Ser29Trp missense_variant 0.17
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 2518166 p.Ala18Pro missense_variant 0.12
eis 2715125 p.Thr70Ala missense_variant 1.0
folC 2746832 p.Val256Gly missense_variant 0.14
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
ald 3087927 c.1108C>T synonymous_variant 0.12
Rv3083 3448783 p.Val94Ile missense_variant 1.0
fprA 3473810 c.-197A>G upstream_gene_variant 0.14
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 3612965 c.150_151delGG frameshift_variant 0.12
rpoA 3878630 c.-124delC upstream_gene_variant 1.0
clpC1 4038403 c.2302T>C synonymous_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242680 p.Ala940Ser missense_variant 1.0
embA 4242970 c.-263C>T upstream_gene_variant 1.0
embA 4244220 c.988C>T synonymous_variant 1.0
embA 4244692 p.Tyr487Cys missense_variant 0.11
embB 4245539 c.-975C>T upstream_gene_variant 0.17
embB 4246544 p.Thr11Pro missense_variant 0.13
embB 4246547 p.Pro12Thr missense_variant 0.13
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 4267006 p.Val611Ile missense_variant 0.14
aftB 4267858 p.Ile327Val missense_variant 1.0
ubiA 4268930 p.Gly302Arg missense_variant 0.11
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 4326412 c.1062G>A synonymous_variant 0.12
ethA 4327158 p.Ser106Gly missense_variant 0.14
ethA 4327530 c.-57G>A upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0