TB-Profiler result

Run: ERR4627362
Summary

Run ID: ERR4627362

Sample name:

Date: 01-04-2023 06:33:17

Number of reads: 1293919

Percentage reads mapped: 96.82

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 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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575459 p.Val38Ile missense_variant 0.15
mshA 576459 c.1117_1147delGCGGTGGGCGGGCTGCCCGTCGCGGTGCGCG frameshift_variant 0.5
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
mmpL5 776131 p.Leu784Ile missense_variant 0.12
mmpL5 776206 p.Gly759Cys missense_variant 0.14
mmpL5 777195 p.Glu429Gly missense_variant 0.1
mmpL5 777417 p.Pro355Gln missense_variant 0.12
mmpS5 778698 p.Asn70Tyr missense_variant 0.12
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 1472160 n.315C>T non_coding_transcript_exon_variant 0.11
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.14
rrs 1472223 n.378C>G non_coding_transcript_exon_variant 0.12
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.12
rrs 1472228 n.383G>C non_coding_transcript_exon_variant 0.12
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.13
rrl 1474467 n.810A>C non_coding_transcript_exon_variant 1.0
rrl 1476238 n.2581T>C non_coding_transcript_exon_variant 0.17
rrl 1476248 n.2591G>C non_coding_transcript_exon_variant 0.14
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.13
rrl 1476259 n.2602C>G non_coding_transcript_exon_variant 0.14
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.15
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.15
rrl 1476306 n.2649A>G non_coding_transcript_exon_variant 0.1
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.1
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.1
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.13
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.18
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 0.19
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.28
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.26
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.33
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.34
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.32
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.32
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.32
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.19
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.17
rpsA 1834166 p.Gly209Arg missense_variant 1.0
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 2102790 p.Leu85Met missense_variant 0.12
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 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289540 c.-299A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
eis 2715125 p.Thr70Ala missense_variant 1.0
pepQ 2859560 c.858delC frameshift_variant 0.29
ribD 2986991 c.153C>A synonymous_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
Rv3083 3448783 p.Val94Ile missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474387 p.Asp127Glu missense_variant 0.12
fprA 3474427 p.Val141Ile missense_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3613127 c.-11G>T upstream_gene_variant 0.13
rpoA 3878630 c.-124delC upstream_gene_variant 1.0
clpC1 4038301 p.Val802Phe missense_variant 0.12
clpC1 4038403 c.2302T>C synonymous_variant 1.0
clpC1 4039605 p.Glu367Ala missense_variant 0.12
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
embA 4244220 c.988C>T synonymous_variant 1.0
embB 4246551 p.Asn13Ser missense_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.2
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4247297 p.Pro262Thr missense_variant 0.12
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4267498 p.Glu447Lys missense_variant 0.14
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 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408237 c.-35C>A upstream_gene_variant 1.0