TB-Profiler result

Run: ERR2513433
Summary

Run ID: ERR2513433

Sample name:

Date: 31-03-2023 19:40:36

Number of reads: 1305380

Percentage reads mapped: 92.27

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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.4 streptomycin
pncA 2289073 p.His57Asp missense_variant 1.0 pyrazinamide
embA 4244281 p.Gly350Asp missense_variant 0.14 ethambutol
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 5490 p.Ile84Thr missense_variant 0.12
gyrB 5493 p.Pro85Leu missense_variant 0.13
gyrB 5555 p.Gly106Cys missense_variant 0.12
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 7955 c.654G>A synonymous_variant 0.4
gyrA 8048 c.747C>A synonymous_variant 1.0
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
ccsA 619945 p.Thr19Ala missense_variant 0.11
ccsA 620589 c.699G>C synonymous_variant 0.11
rpoB 761437 p.Ala544Glu missense_variant 0.15
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764015 p.Leu216Met missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776275 p.Ala736Ser missense_variant 0.12
mmpL5 776461 p.Ala674Ser missense_variant 0.12
mmpR5 779392 p.Arg135Trp missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801454 p.Glu216Gln missense_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 0.94
fbiC 1304449 p.Ala507Ser missense_variant 0.18
Rv1258c 1406540 c.801C>T synonymous_variant 0.12
Rv1258c 1407377 c.-37C>A upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471935 n.90T>C non_coding_transcript_exon_variant 1.0
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.33
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.33
rrs 1472596 n.751G>T non_coding_transcript_exon_variant 0.5
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.5
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.4
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.4
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.33
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.33
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.33
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.33
rrs 1473129 n.1284C>T non_coding_transcript_exon_variant 0.33
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.4
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.4
rrl 1474530 n.873G>A non_coding_transcript_exon_variant 0.33
rrl 1474974 n.1317G>T non_coding_transcript_exon_variant 0.5
rrl 1475713 n.2056C>G non_coding_transcript_exon_variant 1.0
rrl 1475716 n.2059A>G non_coding_transcript_exon_variant 1.0
rrl 1475895 n.2238C>G non_coding_transcript_exon_variant 0.29
rrl 1475897 n.2240T>G non_coding_transcript_exon_variant 0.29
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 1.0
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 1.0
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 1.0
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 1.0
rrl 1476268 n.2611A>T non_coding_transcript_exon_variant 1.0
rrl 1476275 n.2618T>A non_coding_transcript_exon_variant 1.0
rrl 1476279 n.2622G>A non_coding_transcript_exon_variant 1.0
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 1.0
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.5
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.2
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.33
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.5
inhA 1673715 c.-487C>G upstream_gene_variant 1.0
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102283 p.Arg254Cys missense_variant 0.2
ndh 2103173 c.-132delG upstream_gene_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155503 c.609C>T synonymous_variant 0.96
katG 2156025 c.87C>A synonymous_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168011 p.Ser868Arg missense_variant 0.98
PPE35 2168319 p.Thr765Ile missense_variant 1.0
PPE35 2168814 c.1798dupA frameshift_variant 1.0
PPE35 2169717 p.Asn299Ile missense_variant 0.11
PPE35 2170012 p.Arg201Trp missense_variant 0.12
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 2715125 p.Thr70Ala missense_variant 1.0
ahpC 2726265 p.Lys25Gln missense_variant 0.18
ahpC 2726341 p.Val50Gly missense_variant 0.24
Rv2752c 3065655 c.537C>T synonymous_variant 0.12
Rv2752c 3066124 p.Gly23Asp missense_variant 0.12
thyX 3067514 p.Ser144Arg missense_variant 0.12
thyA 3074645 c.-174T>G upstream_gene_variant 0.2
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 3087563 c.746delT frameshift_variant 0.13
fbiD 3339418 p.Arg101Cys missense_variant 0.13
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
fbiA 3640527 c.-16G>T upstream_gene_variant 0.12
rpoA 3878533 c.-26G>T upstream_gene_variant 0.33
clpC1 4038403 c.2302T>C synonymous_variant 1.0
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 4244220 c.988C>T synonymous_variant 1.0
embA 4245555 p.Glu775Lys 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 4248734 p.Arg741Trp missense_variant 1.0
aftB 4267167 p.Gln557Pro missense_variant 1.0
aftB 4267858 p.Ile327Val missense_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
ethA 4326024 p.Pro484Ser missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0