TB-Profiler result

Run: SRR11294527
Summary

Run ID: SRR11294527

Sample name:

Date: 02-04-2023 20:45:40

Number of reads: 177081

Percentage reads mapped: 99.41

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 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
katG 2154359 c.1752delT frameshift_variant 0.18 isoniazid
katG 2154845 c.1266delC frameshift_variant 0.14 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 5333 p.Met32Val missense_variant 0.12
gyrB 5752 c.513G>A synonymous_variant 1.0
gyrB 6055 c.816T>C synonymous_variant 0.11
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 491742 c.960T>C synonymous_variant 1.0
ccsA 619831 c.-60T>G upstream_gene_variant 0.33
ccsA 620748 c.858T>G synonymous_variant 0.57
ccsA 620830 p.Thr314Ala missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775916 c.2565T>C synonymous_variant 0.14
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776728 p.Phe585Leu missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
Rv1258c 1406408 c.933G>A synonymous_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475847 n.2190A>G non_coding_transcript_exon_variant 0.33
inhA 1673616 c.-586A>G upstream_gene_variant 0.22
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103173 c.-132delG upstream_gene_variant 1.0
katG 2154444 c.1668A>G synonymous_variant 0.15
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154984 c.1128G>A synonymous_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
PPE35 2169565 p.Gly350Ser missense_variant 0.2
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222942 p.Asn75His missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289020 c.222C>T synonymous_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
eis 2715212 c.119_120dupTG frameshift_variant 0.2
ahpC 2726104 c.-89T>G upstream_gene_variant 1.0
ahpC 2726149 c.-44T>C upstream_gene_variant 0.13
pepQ 2859693 c.726C>T synonymous_variant 1.0
Rv2752c 3065257 p.Met312Thr missense_variant 0.29
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
ald 3087576 c.758delC frameshift_variant 0.18
ald 3087618 p.Ile267Val missense_variant 0.15
Rv3083 3448783 p.Val94Ile missense_variant 1.0
Rv3083 3449060 p.Gly186Asp missense_variant 0.33
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 3642478 p.Asp315Ala missense_variant 1.0
rpoA 3877908 c.600T>C synonymous_variant 0.14
rpoA 3878214 c.294C>A synonymous_variant 1.0
ddn 3987296 c.453C>A synonymous_variant 0.17
clpC1 4038403 c.2302T>C synonymous_variant 1.0
clpC1 4038593 p.His704Gln missense_variant 0.11
clpC1 4038810 p.Gln632Arg missense_variant 0.18
clpC1 4039484 c.1221T>G synonymous_variant 0.2
clpC1 4040652 p.Glu18Gly missense_variant 0.12
panD 4044363 c.-82T>C upstream_gene_variant 0.22
embC 4239897 p.Val12Ala missense_variant 0.2
embC 4240080 p.Pro73Gln missense_variant 1.0
embC 4240648 c.786C>T synonymous_variant 0.25
embC 4240671 p.Thr270Ile missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242833 p.Phe991Leu missense_variant 0.18
embA 4242862 c.-371A>G upstream_gene_variant 0.18
embA 4242970 c.-263C>T upstream_gene_variant 1.0
embA 4244220 c.988C>T synonymous_variant 1.0
embA 4244774 c.1542G>A synonymous_variant 0.67
embB 4246551 p.Asn13Ser missense_variant 1.0
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4246986 p.Phe158Tyr missense_variant 0.29
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248646 c.2133C>G synonymous_variant 0.33
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
ethA 4326180 p.Met432Val missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338700 c.-179T>C upstream_gene_variant 0.1
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408102 p.Gly34Glu missense_variant 1.0