TB-Profiler result

Run: SRR15296920
Summary

Run ID: SRR15296920

Sample name:

Date: 03-04-2023 12:42:09

Number of reads: 401256

Percentage reads mapped: 99.16

Strain: La1.7.1

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 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
fabG1 1673432 c.-8T>C upstream_gene_variant 1.0 isoniazid, ethionamide
pncA 2288682 c.559_560insA frameshift_variant&splice_region_variant 1.0 pyrazinamide
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 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 490751 c.-32T>G upstream_gene_variant 0.29
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 619831 c.-60T>G upstream_gene_variant 0.15
rpoB 759615 c.-192A>C upstream_gene_variant 0.33
rpoB 761129 c.1323G>A synonymous_variant 0.22
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
fbiC 1304948 p.Asp673Gly missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917954 c.15C>T synonymous_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103173 c.-132delG upstream_gene_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.92
katG 2154984 c.1128G>A synonymous_variant 0.93
katG 2155468 p.Asp215Gly missense_variant 0.12
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
PPE35 2170004 c.609C>T synonymous_variant 0.14
PPE35 2170048 p.Leu189Val missense_variant 0.31
PPE35 2170053 p.Thr187Ser missense_variant 0.31
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288921 p.Glu107Asp missense_variant 0.13
kasA 2518132 c.18C>T synonymous_variant 1.0
ahpC 2726529 p.Asp113Asn missense_variant 0.4
pepQ 2859693 c.726C>T synonymous_variant 1.0
pepQ 2860178 p.Arg81Ser missense_variant 1.0
ribD 2987071 p.Ala78Val missense_variant 0.11
Rv2752c 3065475 c.717C>T synonymous_variant 0.22
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
fbiB 3641958 p.Val142Ile missense_variant 0.88
fbiB 3642121 p.Asp196Val missense_variant 0.12
fbiB 3642204 p.Asp224Asn missense_variant 0.2
fbiB 3642478 p.Asp315Ala missense_variant 1.0
clpC1 4038403 c.2302T>C synonymous_variant 1.0
clpC1 4038605 p.Glu700Asp missense_variant 0.13
clpC1 4039484 c.1221T>G synonymous_variant 0.33
embC 4240080 p.Pro73Gln missense_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 4244666 c.1434G>C synonymous_variant 0.22
embA 4244721 p.Gln497* stop_gained 0.22
embA 4245603 p.Gly791Arg missense_variant 0.12
embB 4246551 p.Asn13Ser missense_variant 1.0
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4247276 p.Pro255Ser missense_variant 0.12
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248833 p.Trp774Arg missense_variant 0.18
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
ethR 4328045 p.Leu166Pro missense_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0