TB-Profiler result

Run: SRR13199733
Summary

Run ID: SRR13199733

Sample name:

Date: 03-04-2023 08:23:10

Number of reads: 280823

Percentage reads mapped: 89.6

Strain: La1.2

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
La1.2 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 7962 p.Gly221Trp missense_variant 0.13
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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620216 p.Asn109Ser missense_variant 0.14
ccsA 620303 p.Trp138* stop_gained 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764742 p.Lys458Arg missense_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
fbiC 1304292 p.Asp454Glu missense_variant 0.22
atpE 1461231 p.Ala63Ser missense_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473690 n.33T>C non_coding_transcript_exon_variant 0.4
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.67
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.8
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.8
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.8
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.8
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.8
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.8
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.8
rrl 1476297 n.2640C>A non_coding_transcript_exon_variant 0.8
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.8
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.8
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.8
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.8
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.8
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.8
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.8
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.8
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.67
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.6
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.6
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.5
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.4
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.5
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.4
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.4
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.4
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.4
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.4
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.33
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.33
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.29
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.29
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.29
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.29
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.29
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.29
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.29
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.29
rrl 1476577 n.2920T>G non_coding_transcript_exon_variant 0.29
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.25
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.25
rrl 1476603 n.2946G>A non_coding_transcript_exon_variant 0.29
rrl 1476614 n.2957A>G non_coding_transcript_exon_variant 0.33
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102106 p.Gly313Arg missense_variant 1.0
ndh 2103173 c.-132delG upstream_gene_variant 1.0
katG 2154535 p.Glu526Gly missense_variant 0.15
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
katG 2156465 c.-354C>T upstream_gene_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168011 p.Ser868Arg missense_variant 1.0
PPE35 2168814 c.1798dupA frameshift_variant 1.0
PPE35 2170629 c.-17C>T upstream_gene_variant 0.14
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290145 c.-904A>T upstream_gene_variant 0.17
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518147 c.33C>T synonymous_variant 0.25
eis 2714800 p.Ile178Thr missense_variant 0.18
folC 2746524 p.Ala359Thr missense_variant 0.18
folC 2747463 p.Ser46Gly missense_variant 0.1
folC 2747783 c.-185G>A upstream_gene_variant 0.14
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 3339154 p.Ile13Leu missense_variant 1.0
Rv3083 3448745 p.Ile81Ser missense_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
Rv3236c 3612256 c.861C>T synonymous_variant 0.29
alr 3840986 c.435G>T synonymous_variant 0.11
ddn 3986987 c.144G>T synonymous_variant 0.12
clpC1 4038403 c.2302T>C synonymous_variant 1.0
clpC1 4040170 p.Thr179Ala missense_variant 0.29
embC 4240307 p.Gly149Ser missense_variant 0.14
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
embA 4245463 p.Asp744Gly missense_variant 0.29
embB 4246551 p.Asn13Ser missense_variant 1.0
embB 4246667 p.Thr52Ala missense_variant 0.17
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4247173 c.660G>A synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4249697 p.Gly1062Cys missense_variant 0.22
aftB 4267668 p.Ala390Val missense_variant 0.15
aftB 4267858 p.Ile327Val missense_variant 1.0
aftB 4268850 c.-14T>C upstream_gene_variant 0.12
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
ethR 4327846 p.Glu100Lys missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0