TB-Profiler result

Run: ERR6140663
Summary

Run ID: ERR6140663

Sample name:

Date: 02-04-2023 01:43:44

Number of reads: 428265

Percentage reads mapped: 32.13

Strain: La1.8.2

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
La1.8 M.bovis None None 1.0
La1.8.2 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 5157 c.-83C>A upstream_gene_variant 0.12
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 6864 p.Thr542Arg missense_variant 0.33
gyrA 6964 c.-338C>T upstream_gene_variant 0.25
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7534 p.Ala78Gly missense_variant 0.2
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7921 p.Asn207Ile missense_variant 0.33
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 619736 c.-155G>A upstream_gene_variant 0.5
ccsA 620865 c.975A>G stop_lost&splice_region_variant 0.25
rpoB 762474 p.Gly890Ser missense_variant 0.15
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763151 p.Phe1115Leu missense_variant 0.2
rpoC 764135 p.Met256Leu missense_variant 0.33
rpoC 764855 p.Val496Met missense_variant 0.22
rpoC 765811 c.2442T>C synonymous_variant 0.25
rpoC 766049 p.Glu894Lys missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776097 p.Thr795Ile missense_variant 0.33
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777137 c.1344G>A synonymous_variant 0.22
mmpL5 778176 p.Gly102Asp missense_variant 0.14
mmpS5 778595 p.Leu104His missense_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
fbiC 1302932 p.Val1Glu missense_variant 0.29
Rv1258c 1406889 p.Asn151Thr missense_variant 0.2
embR 1416390 c.958C>T synonymous_variant 1.0
atpE 1461173 c.129C>T synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472357 n.512G>A non_coding_transcript_exon_variant 0.18
rrl 1473635 n.-23A>T upstream_gene_variant 0.4
rrl 1476101 n.2444C>T non_coding_transcript_exon_variant 1.0
inhA 1674335 p.Arg45Gln missense_variant 0.33
rpsA 1834845 p.Phe435Cys missense_variant 0.18
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102096 p.Asn316Ile missense_variant 0.25
ndh 2102991 p.Val18Met missense_variant 1.0
ndh 2103173 c.-132delG upstream_gene_variant 1.0
katG 2154441 p.Lys557Asn missense_variant 0.2
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 2156499 c.-388C>T upstream_gene_variant 0.13
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168011 p.Ser868Arg missense_variant 1.0
PPE35 2168265 p.Gly783Val missense_variant 0.18
PPE35 2168319 p.Thr765Ile missense_variant 1.0
PPE35 2168814 c.1798dupA frameshift_variant 1.0
Rv1979c 2221960 p.Val402Glu missense_variant 0.25
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223281 c.-117T>C upstream_gene_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2519032 c.918C>T synonymous_variant 0.4
kasA 2519324 p.Phe404Val missense_variant 0.2
eis 2714495 p.Thr280Ser missense_variant 0.4
eis 2715125 p.Thr70Ala missense_variant 1.0
ahpC 2726446 p.Val85Gly missense_variant 0.22
folC 2747631 c.-33C>T upstream_gene_variant 1.0
pepQ 2859933 c.486C>G synonymous_variant 0.43
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 3087900 p.Val361Met missense_variant 0.14
Rv3083 3448783 p.Val94Ile missense_variant 1.0
Rv3083 3449348 p.Asp282Val missense_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474427 p.Val141Ile missense_variant 1.0
fprA 3474454 p.Ala150Pro missense_variant 0.2
fprA 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3612750 p.Gly123Arg missense_variant 0.22
fbiA 3640444 c.-98delA upstream_gene_variant 0.25
fbiB 3641639 c.105G>A synonymous_variant 0.29
alr 3841384 p.Asp13His missense_variant 0.33
rpoA 3878308 p.Pro67Leu missense_variant 0.25
ddn 3987234 p.Pro131Ser missense_variant 0.15
ddn 3987298 c.455G>C stop_lost&splice_region_variant 0.14
clpC1 4038403 c.2302T>C synonymous_variant 1.0
clpC1 4039259 c.1446G>A synonymous_variant 0.18
clpC1 4040535 p.Glu57Val missense_variant 0.22
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4240839 p.Trp326* stop_gained 0.13
embC 4242029 p.Leu723Val 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
embB 4245692 c.-822G>A upstream_gene_variant 0.17
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248901 c.2388C>T synonymous_variant 0.22
embB 4249400 p.Val963Met missense_variant 0.29
aftB 4267581 p.Gly419Glu missense_variant 0.4
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
ubiA 4270004 c.-171G>C upstream_gene_variant 0.33
ethA 4326134 p.Pro447Leu missense_variant 0.22
whiB6 4338205 p.Val106Gly missense_variant 0.33
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
embR 1416583 c.-2382_764del frameshift_variant&start_lost 1.0