TB-Profiler result

Run: ERR9891994

Summary

Run ID: ERR9891994

Sample name:

Date: 02-04-2023 13:26:48

Number of reads: 533586

Percentage reads mapped: 99.23

Strain: La1.2

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
La1.2 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 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 7821 c.520C>T synonymous_variant 1.0
gyrA 8285 c.984C>T synonymous_variant 1.0
gyrA 8741 c.1440C>T synonymous_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490670 c.-113G>T upstream_gene_variant 0.11
fgd1 491027 p.Asn82Thr missense_variant 0.25
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575917 c.570C>T synonymous_variant 0.11
ccsA 620532 c.642T>G synonymous_variant 0.25
rpoB 760388 p.His194Gln missense_variant 0.14
rpoB 761351 p.Asp515Glu missense_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776250 p.Glu744Gly missense_variant 0.18
mmpR5 779320 p.Met111Leu missense_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
fbiC 1303116 c.186C>A synonymous_variant 0.22
Rv1258c 1406623 p.Leu240Met missense_variant 0.11
embR 1416989 c.358delA frameshift_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473994 n.337C>G non_coding_transcript_exon_variant 0.13
inhA 1674296 p.Gln32Pro missense_variant 0.12
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101896 p.Gly383Cys missense_variant 0.12
ndh 2102106 p.Gly313Arg missense_variant 1.0
ndh 2102577 p.Glu156* stop_gained 0.13
ndh 2102602 p.Leu147Phe missense_variant 0.12
ndh 2102692 c.351C>G synonymous_variant 0.13
ndh 2102698 c.345G>C synonymous_variant 0.11
ndh 2103173 c.-132delG upstream_gene_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155383 c.729C>A synonymous_variant 1.0
katG 2155503 c.609C>T synonymous_variant 1.0
katG 2156025 c.87C>A synonymous_variant 1.0
katG 2156465 c.-354C>T upstream_gene_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168011 p.Ser868Arg missense_variant 1.0
PPE35 2168814 c.1798dupA frameshift_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.29
PPE35 2170524 p.Ala30Gly missense_variant 0.2
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222415 c.750G>A synonymous_variant 1.0
Rv1979c 2222590 p.Asn192Ser missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288694 p.Val183Ala missense_variant 0.2
kasA 2518132 c.18C>T synonymous_variant 1.0
folC 2747518 c.80delT frameshift_variant 0.12
Rv2752c 3065395 p.Met266Thr missense_variant 0.13
thyX 3067352 p.Met198Ile missense_variant 0.12
thyX 3067786 p.Thr54Ala missense_variant 1.0
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 3087250 p.Val144Asp missense_variant 0.14
fbiD 3339154 p.Ile13Leu missense_variant 1.0
fbiD 3339204 c.87G>A synonymous_variant 1.0
fbiD 3339693 c.576C>A synonymous_variant 0.18
fbiD 3339757 p.Arg214Cys missense_variant 0.25
Rv3083 3448745 p.Ile81Ser missense_variant 1.0
Rv3083 3448783 p.Val94Ile missense_variant 1.0
Rv3083 3449083 p.Pro194Ser missense_variant 0.29
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474427 p.Val141Ile missense_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 0.96
fbiA 3641280 p.Ile246Met missense_variant 0.13
alr 3841057 p.Pro122Thr missense_variant 0.12
alr 3841100 c.318_320delCGC disruptive_inframe_deletion 0.12
rpoA 3878630 c.-124delC upstream_gene_variant 1.0
clpC1 4038162 p.Arg848Leu missense_variant 0.29
clpC1 4038208 p.Ala833Thr missense_variant 0.13
clpC1 4038403 c.2302T>C synonymous_variant 1.0
clpC1 4038692 c.2013C>T synonymous_variant 0.11
panD 4044397 c.-116G>T upstream_gene_variant 0.11
embC 4239917 p.Val19Met missense_variant 0.18
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241034 p.Pro391Leu missense_variant 0.12
embC 4241107 c.1245G>T synonymous_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 4245836 c.-678G>C upstream_gene_variant 0.15
embB 4246551 p.Asn13Ser missense_variant 1.0
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4247173 c.660G>A synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248830 p.Ser773Pro missense_variant 0.2
aftB 4267561 p.Ala426Thr missense_variant 0.11
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 4269747 c.86dupA frameshift_variant 0.17
ubiA 4269763 p.Arg24Pro missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0