TB-Profiler result

Run: ERR2747617
Summary

Run ID: ERR2747617

Sample name:

Date: 31-03-2023 23:28:12

Number of reads: 375248

Percentage reads mapped: 10.98

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 1473247 n.1402C>A non_coding_transcript_exon_variant 0.5 kanamycin, capreomycin, aminoglycosides, amikacin
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
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 8498 c.1197C>T synonymous_variant 0.2
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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472621 n.776G>T non_coding_transcript_exon_variant 0.4
rrs 1472733 n.888G>T non_coding_transcript_exon_variant 0.67
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.67
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.4
rrs 1472742 n.897C>A non_coding_transcript_exon_variant 0.5
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.5
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.67
rrs 1472785 n.940G>T non_coding_transcript_exon_variant 0.67
rrs 1472786 n.941C>T non_coding_transcript_exon_variant 0.67
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.67
rrs 1472805 n.960C>A non_coding_transcript_exon_variant 0.67
rrs 1472806 n.961A>T non_coding_transcript_exon_variant 0.67
rrs 1472813 n.968A>G non_coding_transcript_exon_variant 0.6
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.86
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.86
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.86
rrs 1473165 n.1320C>T non_coding_transcript_exon_variant 0.86
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.87
rrs 1473172 n.1327T>C non_coding_transcript_exon_variant 0.8
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.8
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.8
rrs 1473193 n.1348G>T non_coding_transcript_exon_variant 0.8
rrs 1473200 n.1355A>C non_coding_transcript_exon_variant 0.73
rrs 1473202 n.1357C>T non_coding_transcript_exon_variant 0.73
rrs 1473204 n.1359C>A non_coding_transcript_exon_variant 0.73
rrs 1473249 n.1404T>C non_coding_transcript_exon_variant 0.43
rrs 1473254 n.1409A>G non_coding_transcript_exon_variant 0.38
rrl 1475750 n.2093A>C non_coding_transcript_exon_variant 1.0
rrl 1476321 n.2664A>T non_coding_transcript_exon_variant 0.62
rrl 1476322 n.2665C>A non_coding_transcript_exon_variant 0.67
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.85
rrl 1476353 n.2696G>A non_coding_transcript_exon_variant 0.95
rrl 1476354 n.2697A>G non_coding_transcript_exon_variant 0.95
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.95
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.94
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.94
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.95
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.95
rrl 1476388 n.2731T>C non_coding_transcript_exon_variant 0.93
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.92
rrl 1476428 n.2771C>A non_coding_transcript_exon_variant 0.93
rrl 1476451 n.2794C>A non_coding_transcript_exon_variant 0.26
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.91
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.83
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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518673 p.Met187Leu missense_variant 0.29
eis 2715125 p.Thr70Ala missense_variant 1.0
Rv2752c 3065988 p.Glu68Asp 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 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
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
embA 4242970 c.-263C>T upstream_gene_variant 1.0
embC 4242981 p.Met1040Thr missense_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 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
whiB6 4338244 p.Gly93Val missense_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0