TB-Profiler result

Run: ERR4627376
Summary

Run ID: ERR4627376

Sample name:

Date: 01-04-2023 06:33:41

Number of reads: 1434497

Percentage reads mapped: 75.39

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 6544 c.-758C>T upstream_gene_variant 0.12
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 0.88
gyrA 9052 p.Leu584Ser missense_variant 0.11
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 491523 c.745delT frameshift_variant 0.22
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 762176 c.2370T>C synonymous_variant 0.11
rpoB 762185 c.2379G>C synonymous_variant 0.11
rpoB 762194 c.2388G>C synonymous_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 0.94
rpoC 764668 c.1299C>A synonymous_variant 0.18
rpoC 765460 c.2093delA frameshift_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776246 c.2235C>A synonymous_variant 0.12
mmpL5 777709 c.771delG frameshift_variant 0.11
mmpL5 777883 p.Gly200Arg missense_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781402 c.-158_-157insG upstream_gene_variant 0.15
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 1471876 n.31G>A non_coding_transcript_exon_variant 0.12
rrs 1471877 n.32A>T non_coding_transcript_exon_variant 0.12
rrs 1471878 n.33C>T non_coding_transcript_exon_variant 0.12
rrs 1471892 n.47G>A non_coding_transcript_exon_variant 0.12
rrs 1471896 n.51T>C non_coding_transcript_exon_variant 0.12
rrs 1471898 n.53A>T non_coding_transcript_exon_variant 0.12
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.11
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.11
rrs 1472758 n.913T>C non_coding_transcript_exon_variant 0.12
rrs 1472803 n.958T>C non_coding_transcript_exon_variant 0.11
rrs 1472812 n.967A>C non_coding_transcript_exon_variant 0.11
rrs 1473003 n.1158G>C non_coding_transcript_exon_variant 0.15
rrl 1474717 n.1060A>G non_coding_transcript_exon_variant 0.2
rrl 1474952 n.1295A>G non_coding_transcript_exon_variant 0.4
rrl 1475599 n.1942A>T non_coding_transcript_exon_variant 0.22
rrl 1475632 n.1975C>T non_coding_transcript_exon_variant 0.15
rrl 1476227 n.2570C>A non_coding_transcript_exon_variant 0.15
fabG1 1673380 c.-60C>G upstream_gene_variant 0.14
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 2168319 p.Thr765Ile missense_variant 1.0
PPE35 2168814 c.1798dupA frameshift_variant 1.0
PPE35 2168964 p.Val550Ala missense_variant 0.29
PPE35 2169919 p.Leu232Ile missense_variant 0.12
PPE35 2170035 p.Val193Ala missense_variant 0.13
PPE35 2170048 p.Leu189Val missense_variant 0.5
PPE35 2170053 p.Thr187Ser missense_variant 0.58
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 2715062 p.His91Tyr missense_variant 0.12
eis 2715125 p.Thr70Ala missense_variant 1.0
folC 2746816 c.783C>A synonymous_variant 0.29
ribD 2986675 c.-164T>C upstream_gene_variant 0.12
thyA 3074481 c.-11delG upstream_gene_variant 0.29
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 3339738 c.621C>A synonymous_variant 0.4
Rv3083 3448783 p.Val94Ile missense_variant 1.0
Rv3083 3448808 p.Leu102Pro missense_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474393 c.389delG frameshift_variant 0.18
fprA 3474427 p.Val141Ile missense_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3613100 p.Ala6Val missense_variant 0.2
Rv3236c 3613224 c.-108C>T upstream_gene_variant 0.33
rpoA 3878476 c.31delG frameshift_variant 0.5
ddn 3987222 p.Val127Leu missense_variant 0.12
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
embC 4242795 p.Ala978Val missense_variant 0.13
embA 4242970 c.-263C>T upstream_gene_variant 1.0
embA 4244220 c.988C>T synonymous_variant 1.0
embA 4246294 p.Trp1021Ser missense_variant 0.12
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 4248122 p.Leu537Met missense_variant 0.2
aftB 4266962 c.1875G>A synonymous_variant 0.17
aftB 4267858 p.Ile327Val missense_variant 1.0
aftB 4268029 p.Leu270Met missense_variant 0.13
ubiA 4269294 p.Met180Ile missense_variant 0.15
aftB 4269351 c.-515C>T upstream_gene_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
ubiA 4269473 p.Thr121Pro missense_variant 0.25
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ubiA 4269864 c.-32delG upstream_gene_variant 0.2
ubiA 4269943 c.-110T>C upstream_gene_variant 0.2
ethA 4327530 c.-57G>A upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338666 c.-145G>A upstream_gene_variant 0.12
gid 4407588 c.615A>G synonymous_variant 1.0