TB-Profiler result

Run: SRR18391698
Summary

Run ID: SRR18391698

Sample name:

Date: 03-04-2023 19:40:19

Number of reads: 534522

Percentage reads mapped: 97.68

Strain: La1.7.1

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
La1.7 M.bovis None None 1.0
La1.7.1 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
gyrB 6883 p.Leu548Phe missense_variant 0.25
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 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 490749 c.-34G>T upstream_gene_variant 0.12
fgd1 491379 c.597C>T synonymous_variant 0.12
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576549 p.Ala401Gly missense_variant 0.11
rpoB 759793 c.-14T>C upstream_gene_variant 0.12
rpoB 761539 p.Arg578Leu missense_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763530 p.Pro54Arg missense_variant 0.11
rpoC 764038 p.Trp223Cys missense_variant 0.12
rpoC 767071 c.3702C>A synonymous_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775642 p.Pro947Ala missense_variant 0.11
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777264 p.Leu406Pro 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 1472912 n.1067C>A non_coding_transcript_exon_variant 0.29
rrs 1473354 n.1509G>A non_coding_transcript_exon_variant 0.12
rrl 1473592 n.-65delA upstream_gene_variant 0.18
rrl 1476175 n.2518G>T non_coding_transcript_exon_variant 0.29
rrl 1476367 n.2710G>A non_coding_transcript_exon_variant 0.4
rrl 1476787 n.3130C>A non_coding_transcript_exon_variant 0.22
inhA 1673718 c.-484G>T upstream_gene_variant 0.15
inhA 1674449 p.Gly83Val missense_variant 0.12
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102267 p.Val259Ala missense_variant 0.14
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 2155708 p.Trp135Ser missense_variant 0.1
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
PPE35 2169138 p.Thr492Met missense_variant 0.11
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289925 c.-684T>C upstream_gene_variant 0.13
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518284 p.Ala57Glu missense_variant 0.13
kasA 2518511 p.Gly133Ser missense_variant 0.17
eis 2714571 c.762G>A synonymous_variant 0.12
ahpC 2726608 p.Asp139Val missense_variant 0.12
folC 2746474 c.1125G>T synonymous_variant 0.12
folC 2746523 p.Ala359Glu missense_variant 0.12
Rv2752c 3065556 c.636G>T synonymous_variant 0.11
thyA 3073880 p.Glu198Lys missense_variant 0.12
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
Rv3083 3449396 p.Cys298Phe missense_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474427 p.Val141Ile missense_variant 1.0
fprA 3474981 c.975C>A synonymous_variant 0.12
fprA 3475159 p.Asn385Asp missense_variant 1.0
fbiA 3640636 p.Ser32Pro missense_variant 1.0
fbiB 3641325 c.-210G>A upstream_gene_variant 0.12
fbiB 3642239 c.705G>T synonymous_variant 0.14
fbiB 3642478 p.Asp315Ala 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
embA 4244556 p.Arg442Gly missense_variant 0.1
embA 4244711 c.1479C>T synonymous_variant 0.15
embB 4246551 p.Asn13Ser missense_variant 1.0
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4247163 p.Leu217Pro missense_variant 0.11
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4267373 c.1464C>T synonymous_variant 0.12
aftB 4267858 p.Ile327Val missense_variant 1.0
aftB 4268535 p.Gly101Val missense_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
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0