TB-Profiler result

Run: ERR3468577

Summary

Run ID: ERR3468577

Sample name:

Date: 01-04-2023 02:18:13

Number of reads: 144789

Percentage reads mapped: 14.93

Strain: La1

Drug-resistance: HR-TB


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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 0.17
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
katG 2155693 p.Ser140Asn missense_variant 0.45 isoniazid
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
rpoB 760871 c.1065C>T synonymous_variant 0.25
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
rrs 1472210 n.365A>T non_coding_transcript_exon_variant 0.5
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.5
rrs 1472223 n.378C>G non_coding_transcript_exon_variant 0.67
rrs 1472228 n.383G>C non_coding_transcript_exon_variant 0.67
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.5
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.4
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.4
rrs 1472251 n.406G>C non_coding_transcript_exon_variant 0.4
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.67
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 1.0
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 1.0
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 1.0
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 1.0
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 1.0
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 1.0
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 1.0
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 1.0
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.8
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.8
rrl 1476411 n.2754G>T non_coding_transcript_exon_variant 0.8
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.8
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.8
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.8
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.8
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.75
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.75
rrl 1476463 n.2806C>A non_coding_transcript_exon_variant 0.75
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.75
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.75
rrl 1476483 n.2826G>A non_coding_transcript_exon_variant 0.75
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1917987 c.48G>A synonymous_variant 0.29
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 2155655 p.Lys153Gln missense_variant 0.4
katG 2155661 p.Val151Ile missense_variant 0.33
katG 2155662 c.450G>C synonymous_variant 0.33
katG 2155670 c.442C>T synonymous_variant 0.5
katG 2155674 c.438G>C synonymous_variant 0.5
katG 2155680 c.432G>C synonymous_variant 0.5
katG 2155691 c.421T>C synonymous_variant 0.45
katG 2155696 p.Ala139Gly missense_variant 0.45
katG 2155716 c.396T>G synonymous_variant 0.54
katG 2155728 c.384G>C synonymous_variant 0.54
katG 2155735 p.Met126Gln missense_variant 0.54
katG 2155737 c.375C>A synonymous_variant 0.54
katG 2155743 c.369G>C synonymous_variant 0.54
katG 2155765 p.His116Ala missense_variant 0.5
katG 2155768 p.Ile115Thr missense_variant 0.5
katG 2155785 p.Ala109Ser missense_variant 0.5
katG 2155794 c.318G>C synonymous_variant 0.57
katG 2155800 c.312G>C synonymous_variant 0.57
katG 2155806 c.306T>C synonymous_variant 0.57
katG 2155815 c.297G>C synonymous_variant 0.57
katG 2155824 c.288C>G synonymous_variant 0.33
katG 2155828 p.Tyr95Phe missense_variant 0.33
katG 2155833 c.279C>G synonymous_variant 0.33
katG 2155836 c.276C>G synonymous_variant 0.4
katG 2155845 c.267G>C synonymous_variant 0.5
katG 2156025 c.87C>A synonymous_variant 1.0
PPE35 2167926 p.Leu896Ser 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
eis 2715125 p.Thr70Ala 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 3086830 p.Gly4Asp missense_variant 0.33
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
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 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408237 c.-35C>A upstream_gene_variant 1.0