TB-Profiler result

Run: ERR4769566
Summary

Run ID: ERR4769566

Sample name:

Date: 01-04-2023 06:44:33

Number of reads: 592577

Percentage reads mapped: 99.36

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 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 6940 c.-362G>A upstream_gene_variant 0.14
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 7655 c.354G>T synonymous_variant 0.15
gyrA 8285 c.984C>T synonymous_variant 1.0
gyrA 8637 p.Leu446Met missense_variant 0.14
gyrA 8694 p.Leu465Met missense_variant 0.25
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
gyrA 9484 p.Ser728Leu missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575293 c.-55T>A upstream_gene_variant 0.13
mshA 576108 p.Ala254Gly missense_variant 0.16
ccsA 620768 p.Ala293Gly missense_variant 1.0
rpoB 762320 c.2514C>T synonymous_variant 0.2
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764176 c.807C>T synonymous_variant 1.0
rpoC 764191 c.822C>A synonymous_variant 0.15
rpoC 766694 p.Gln1109Lys missense_variant 0.15
rpoC 766861 c.3492G>T synonymous_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776354 c.2127C>A synonymous_variant 0.13
mmpL5 777326 c.1155C>A synonymous_variant 0.18
mmpS5 778674 p.Pro78Thr missense_variant 0.14
mmpR5 779058 p.Met23Ile missense_variant 0.2
mmpR5 779115 p.Trp42* stop_gained 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781894 p.Gln112Arg missense_variant 0.11
rplC 800953 p.Ala49Thr missense_variant 0.14
rplC 801232 p.Gln142* stop_gained 0.15
fbiC 1302860 c.-71G>A upstream_gene_variant 0.13
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
fbiC 1303160 p.Gly77Glu missense_variant 0.17
fbiC 1304078 p.Glu383Gly missense_variant 1.0
embR 1417493 c.-146T>A upstream_gene_variant 0.12
atpE 1461192 p.Phe50Ile missense_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472923 n.1078G>T non_coding_transcript_exon_variant 0.15
rrl 1474414 n.757C>A non_coding_transcript_exon_variant 0.29
rrl 1475083 n.1426C>T non_coding_transcript_exon_variant 0.22
rrl 1475702 n.2045G>T non_coding_transcript_exon_variant 0.18
rrl 1475996 n.2339T>C non_coding_transcript_exon_variant 0.18
rrl 1476022 n.2365A>G non_coding_transcript_exon_variant 1.0
fabG1 1673310 c.-130T>C upstream_gene_variant 0.13
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918632 c.693G>T synonymous_variant 0.2
ndh 2101985 p.Gly353Val missense_variant 0.14
ndh 2103173 c.-132delG upstream_gene_variant 1.0
katG 2154369 c.1743G>A synonymous_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
PPE35 2167731 p.Phe961Tyr missense_variant 0.14
PPE35 2167925 p.Leu896Ser missense_variant 0.12
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 2169047 p.Ile522Met missense_variant 0.17
PPE35 2169222 p.Ser464Tyr missense_variant 0.15
PPE35 2169269 c.1344A>G synonymous_variant 0.12
PPE35 2169272 c.1341C>G synonymous_variant 0.12
PPE35 2169444 p.Gly390Asp missense_variant 0.12
PPE35 2169660 p.Asn318Ile missense_variant 0.25
PPE35 2169946 p.Gly223Arg missense_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 0.31
PPE35 2170053 p.Thr187Ser missense_variant 0.29
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
pncA 2289871 c.-630T>A upstream_gene_variant 0.22
pncA 2289890 c.-649C>T upstream_gene_variant 0.22
pncA 2290018 c.-777C>G upstream_gene_variant 0.12
kasA 2518132 c.18C>T synonymous_variant 1.0
ahpC 2726733 p.Gly181Cys missense_variant 0.15
folC 2746245 p.Ala452Thr missense_variant 1.0
folC 2746604 p.Ala332Asp missense_variant 0.17
folC 2746867 c.732G>A synonymous_variant 0.2
folC 2747013 p.Pro196Thr missense_variant 0.2
pepQ 2860144 p.Val92Gly missense_variant 0.33
ribD 2987012 c.174C>A synonymous_variant 0.14
ribD 2987057 c.219G>A synonymous_variant 0.13
ribD 2987279 c.441G>T synonymous_variant 0.2
ribD 2987615 c.777A>G stop_lost&splice_region_variant 1.0
Rv2752c 3065385 c.807C>T synonymous_variant 0.22
Rv2752c 3067083 c.-892C>A upstream_gene_variant 0.17
thyA 3073992 p.Ser160Arg missense_variant 0.17
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 3449289 c.786C>A synonymous_variant 0.15
Rv3083 3449550 c.1047C>T synonymous_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474382 p.Val126Ile missense_variant 0.12
fprA 3474427 p.Val141Ile missense_variant 1.0
fprA 3474738 c.732C>A synonymous_variant 0.15
fprA 3475159 p.Asn385Asp missense_variant 1.0
whiB7 3568872 c.-193C>A upstream_gene_variant 0.17
Rv3236c 3612675 p.Thr148Ser missense_variant 0.33
fbiB 3642797 p.Leu421Phe missense_variant 0.17
alr 3841034 p.Gln129His missense_variant 0.14
clpC1 4038284 p.Trp807Cys missense_variant 0.22
clpC1 4038403 c.2302T>C synonymous_variant 1.0
panD 4044029 p.Val85Leu missense_variant 0.18
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241902 p.His680Gln missense_variant 0.15
embA 4242313 c.-920C>A upstream_gene_variant 0.18
embC 4242608 p.Glu916* stop_gained 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242737 c.2878delC frameshift_variant 0.2
embA 4242970 c.-263C>T upstream_gene_variant 1.0
embA 4243954 p.Arg241Pro missense_variant 0.18
embA 4244220 c.988C>T synonymous_variant 1.0
embA 4245603 p.Gly791Trp missense_variant 0.17
embA 4245781 p.Ala850Asp missense_variant 0.22
embA 4245786 p.Ala852Ser missense_variant 0.22
embB 4246551 p.Asn13Ser missense_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.5
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 4268879 c.-43G>A upstream_gene_variant 0.18
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 4326867 p.Thr203Ala missense_variant 0.12
ethR 4327993 p.Thr149Ala missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408207 c.-5G>T upstream_gene_variant 0.12