TB-Profiler result

Run: ERR4627356
Summary

Run ID: ERR4627356

Sample name:

Date: 01-04-2023 06:33:00

Number of reads: 1632346

Percentage reads mapped: 69.32

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
gyrB 6404 p.Asn389Asp missense_variant 0.11
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 0.9
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 9264 p.Asp655Asn missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.22
rpoB 761259 p.Gly485Arg missense_variant 0.13
rpoB 761436 p.Ala544Thr missense_variant 0.22
rpoB 761556 p.Ala584Pro missense_variant 0.2
rpoB 762164 c.2360delG frameshift_variant 0.17
rpoC 762557 c.-813G>A upstream_gene_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763504 c.135C>A synonymous_variant 0.11
rpoC 765105 p.Leu579Arg missense_variant 0.11
rpoC 766593 p.Val1075Glu missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775711 p.Phe924Leu missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781485 c.-75C>T upstream_gene_variant 0.14
rpsL 781886 c.327C>T synonymous_variant 0.12
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
Rv1258c 1406081 c.1260A>G stop_lost&splice_region_variant 1.0
embR 1416218 p.Thr377Lys missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.29
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.33
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.33
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.33
rrl 1476572 n.2917delA non_coding_transcript_exon_variant 0.2
fabG1 1673281 c.-159C>T upstream_gene_variant 0.33
inhA 1674464 p.Leu88Pro missense_variant 0.25
rpsA 1833851 p.Lys104Glu 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 2102495 p.Val183Ala missense_variant 0.11
ndh 2102717 p.Gln109Pro missense_variant 0.22
ndh 2103173 c.-132delG upstream_gene_variant 1.0
ndh 2103173 c.-132G>C upstream_gene_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155503 c.609C>T synonymous_variant 1.0
katG 2155596 c.516G>A synonymous_variant 0.11
katG 2156025 c.87C>A synonymous_variant 1.0
katG 2156546 c.-435T>A upstream_gene_variant 0.12
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
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 2714496 c.837C>G synonymous_variant 0.1
eis 2715125 p.Thr70Ala missense_variant 1.0
ribD 2986968 p.Asn44Tyr missense_variant 0.12
Rv2752c 3064837 p.Leu452Ser missense_variant 0.12
Rv2752c 3066190 p.Val1Ala missense_variant 0.15
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 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
Rv3236c 3612836 p.Gly94Val missense_variant 0.15
alr 3840212 c.1209C>T synonymous_variant 0.2
rpoA 3878630 c.-124delC upstream_gene_variant 1.0
clpC1 4038403 c.2302T>C synonymous_variant 1.0
embC 4240440 c.580delC frameshift_variant 0.15
embC 4240671 p.Thr270Ile missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 0.98
embA 4242970 c.-263C>T upstream_gene_variant 1.0
embA 4244220 c.988C>T synonymous_variant 1.0
embA 4244849 c.1617C>T synonymous_variant 0.12
embA 4246380 p.Trp1050Arg missense_variant 0.17
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
embB 4248324 p.Ala604Gly missense_variant 0.23
embB 4249730 c.3221delC frameshift_variant 0.12
aftB 4267858 p.Ile327Val missense_variant 1.0
aftB 4267913 c.923delC frameshift_variant 0.12
aftB 4268042 c.795A>G synonymous_variant 0.5
aftB 4268554 p.Met95Leu 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
ethR 4328192 p.Asn215Ser missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0