TB-Profiler result

Run: SRR18391667

Summary

Run ID: SRR18391667

Sample name:

Date: 03-04-2023 19:39:14

Number of reads: 265256

Percentage reads mapped: 63.99

Strain: La1.7.1

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
La1.7 M.bovis None None 1.0
La1.7.1 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 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 9576 p.Arg759Cys missense_variant 0.14
fgd1 490737 c.-46C>T upstream_gene_variant 0.12
fgd1 490751 c.-32T>G upstream_gene_variant 0.31
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 619762 c.-129C>T upstream_gene_variant 0.14
rpoB 760255 p.Asp150Val missense_variant 0.12
rpoB 760422 p.Leu206Ile missense_variant 0.13
rpoB 760961 c.1155C>T synonymous_variant 0.14
rpoB 761437 p.Ala544Val missense_variant 0.2
rpoB 761988 p.Ala728Ser missense_variant 0.12
rpoB 762911 p.Ile1035Met missense_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763826 p.Ala153Thr missense_variant 0.14
rpoC 766306 p.Tyr979* stop_gained 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 778669 c.-189G>A upstream_gene_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781436 c.-124C>G upstream_gene_variant 0.17
rplC 800987 p.Arg60His missense_variant 0.12
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
fbiC 1305439 p.Ala837Thr missense_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474470 n.813G>A non_coding_transcript_exon_variant 0.17
rrl 1476741 n.3084G>A non_coding_transcript_exon_variant 0.13
rpsA 1834820 p.Met427Val missense_variant 0.17
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 2154378 c.1734A>G synonymous_variant 0.1
katG 2154666 c.1446G>A synonymous_variant 0.12
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 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 2169208 p.Gly469* stop_gained 0.12
PPE35 2169548 c.1065A>G synonymous_variant 0.17
PPE35 2169682 p.Gly311Arg missense_variant 0.33
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518151 p.Ser13Arg missense_variant 0.22
eis 2714458 p.Asp292Val missense_variant 0.12
folC 2746562 p.Pro346His missense_variant 0.29
pepQ 2860119 c.300C>T synonymous_variant 0.12
ribD 2986887 p.Leu17Phe missense_variant 0.2
Rv2752c 3065483 p.Cys237Arg missense_variant 0.2
ald 3086709 c.-111G>T upstream_gene_variant 0.14
ald 3086728 c.-92C>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087047 c.228A>G synonymous_variant 0.18
ald 3087084 c.266delA frameshift_variant 1.0
ald 3087282 p.Gly155Cys missense_variant 0.18
Rv3083 3448560 c.57G>T synonymous_variant 0.2
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
Rv3236c 3612300 c.816delG frameshift_variant 0.18
Rv3236c 3612661 c.456G>A synonymous_variant 0.18
Rv3236c 3612766 c.351C>T synonymous_variant 0.2
fbiA 3641000 p.His153Arg missense_variant 0.25
fbiB 3642478 p.Asp315Ala missense_variant 1.0
fbiB 3642875 c.1341G>A synonymous_variant 1.0
ddn 3987014 c.171C>T synonymous_variant 0.12
ddn 3987038 p.Tyr65* stop_gained 0.11
clpC1 4038403 c.2302T>C synonymous_variant 1.0
clpC1 4038738 p.Asp656Val missense_variant 0.12
clpC1 4039217 c.1488G>T synonymous_variant 0.14
clpC1 4039584 p.Ile374Asn missense_variant 0.12
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4242139 c.2277G>A synonymous_variant 0.13
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 4244503 c.1275delG frameshift_variant 0.2
embA 4244974 p.Ala581Gly missense_variant 0.33
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 4249690 c.3177C>A synonymous_variant 0.17
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 4327366 p.Glu36Asp missense_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.95
gid 4407990 c.213A>T synonymous_variant 0.12