TB-Profiler result

Run: SRR10993954
Summary

Run ID: SRR10993954

Sample name:

Date: 02-04-2023 19:49:06

Number of reads: 213102

Percentage reads mapped: 99.42

Strain: La1.6

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
La1.6 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 5639 p.Arg134Trp missense_variant 0.2
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 7042 c.-260C>T upstream_gene_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 491014 p.Thr78Pro missense_variant 0.33
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620768 p.Ala293Gly missense_variant 1.0
rpoB 762483 c.2678_2682delTGCCG frameshift_variant 0.18
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763054 p.Leu1083Ser missense_variant 0.25
rpoC 764346 p.Pro326Gln missense_variant 0.13
rpoC 765046 p.Met559Ile missense_variant 0.12
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 1303016 p.Val29Gly missense_variant 1.0
fbiC 1305049 p.Thr707Ser missense_variant 0.18
Rv1258c 1407392 c.-52G>A upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475473 n.1816A>G non_coding_transcript_exon_variant 0.18
rrl 1476022 n.2365A>G non_coding_transcript_exon_variant 1.0
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 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 2156367 c.-256G>A upstream_gene_variant 1.0
PPE35 2167859 c.2754T>G synonymous_variant 0.22
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
Rv1979c 2222163 c.1002G>A synonymous_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223062 p.Thr35Ala missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
folC 2746173 p.Gly476Trp missense_variant 0.15
folC 2746245 p.Ala452Thr missense_variant 1.0
folC 2746968 p.Gly211Arg missense_variant 0.17
pepQ 2860600 c.-182A>G upstream_gene_variant 0.2
ribD 2986671 c.-168T>C upstream_gene_variant 0.13
ribD 2987615 c.777A>G stop_lost&splice_region_variant 1.0
thyA 3074648 c.-177T>G upstream_gene_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
Rv3083 3448783 p.Val94Ile missense_variant 1.0
Rv3083 3448876 p.Thr125Ala 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 3641551 p.His6Arg missense_variant 0.4
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 4245149 c.1917C>G synonymous_variant 0.4
embA 4246459 c.3230delG frameshift_variant 0.18
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
embB 4247791 c.1278C>T synonymous_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
ethR 4327880 p.Phe111Ser missense_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0