TB-Profiler result

Run: ERR6139678
Summary

Run ID: ERR6139678

Sample name:

Date: 02-04-2023 01:43:23

Number of reads: 1010905

Percentage reads mapped: 99.3

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 0.99
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 6787 c.-515G>A upstream_gene_variant 0.12
gyrB 6969 p.Asp577Gly missense_variant 0.12
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
gyrA 9647 c.2346C>G synonymous_variant 0.21
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576048 p.Arg234Gln missense_variant 0.14
mshA 576108 p.Ala254Gly missense_variant 0.18
mshA 576456 p.Val370Gly missense_variant 0.4
ccsA 620300 p.Leu137Arg missense_variant 0.16
rpoB 760609 p.Leu268Arg missense_variant 0.1
rpoB 761482 p.Ala559Gly missense_variant 0.18
rpoB 761749 p.Ser648Leu missense_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764367 p.Gly333Ala missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777173 c.1308C>A synonymous_variant 0.18
mmpL5 777884 c.597C>G synonymous_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
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
rrl 1476101 n.2444C>T non_coding_transcript_exon_variant 1.0
inhA 1674325 p.Asp42Asn missense_variant 0.2
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101979 p.Asn355Ser missense_variant 0.12
ndh 2102991 p.Val18Met missense_variant 1.0
ndh 2103173 c.-132delG upstream_gene_variant 1.0
katG 2154174 c.1938C>T synonymous_variant 0.12
katG 2154326 p.Asn596Asp missense_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155503 c.609C>T synonymous_variant 1.0
katG 2155952 p.Val54Ile missense_variant 0.12
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 2169799 p.Leu272Met missense_variant 0.18
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289786 c.-545G>C upstream_gene_variant 0.25
kasA 2518132 c.18C>T synonymous_variant 1.0
eis 2715125 p.Thr70Ala missense_variant 1.0
folC 2746323 p.Gly426Arg missense_variant 0.22
folC 2746603 c.996C>T synonymous_variant 0.2
folC 2747631 c.-33C>T upstream_gene_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.2
thyX 3067404 c.541delA frameshift_variant 0.17
thyA 3074399 p.Gly25Arg missense_variant 0.14
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 3087735 p.Pro306Ala missense_variant 0.11
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
whiB7 3568431 c.249C>G synonymous_variant 0.22
whiB7 3568706 c.-27C>T upstream_gene_variant 0.13
Rv3236c 3612686 p.Gly144Val missense_variant 0.2
Rv3236c 3612894 p.Leu75Val missense_variant 0.17
alr 3840887 c.534G>A synonymous_variant 0.12
rpoA 3877481 p.Glu343Lys missense_variant 0.12
ddn 3986915 c.72T>C synonymous_variant 0.11
clpC1 4038403 c.2302T>C synonymous_variant 1.0
embC 4240409 p.Pro183Ala missense_variant 0.2
embC 4240671 p.Thr270Ile missense_variant 1.0
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 4244142 p.Phe304Leu missense_variant 0.11
embA 4244220 c.988C>T synonymous_variant 1.0
embB 4245992 c.-522C>T upstream_gene_variant 0.12
embB 4246527 p.Ala5Gly missense_variant 0.22
embB 4246551 p.Asn13Ser missense_variant 1.0
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4247016 p.Ser168Trp missense_variant 0.2
embB 4247646 p.Glu378Ala missense_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
ethA 4327761 c.-288C>A upstream_gene_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408435 c.-233G>A upstream_gene_variant 0.14
embR 1416583 c.-2382_764del frameshift_variant&start_lost 1.0