TB-Profiler result

Run: SRR4019491
Summary

Run ID: SRR4019491

Sample name:

Date: 04-04-2023 05:48:37

Number of reads: 8518779

Percentage reads mapped: 99.22

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 0.99
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 0.99
gyrB 6446 p.Ala403Ser missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7493 c.192C>T synonymous_variant 0.36
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8285 c.984C>T synonymous_variant 0.99
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9217 p.Asp639Ala missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 0.98
fgd1 491742 c.960T>C synonymous_variant 0.99
rpoB 759831 p.Thr9Pro missense_variant 0.18
rpoC 762836 c.-534C>G upstream_gene_variant 0.7
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764725 p.Phe452Leu missense_variant 0.13
rpoC 764751 p.Val461Gly missense_variant 0.31
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777399 p.Thr361Arg missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
atpE 1461083 c.39T>G synonymous_variant 0.3
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473343 n.1498G>T non_coding_transcript_exon_variant 0.25
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.18
fabG1 1673449 p.Thr4Pro missense_variant 0.56
inhA 1674952 p.Pro251Ala missense_variant 0.12
rpsA 1834631 p.Gln364Lys missense_variant 0.17
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918069 p.Thr44Pro missense_variant 0.26
ndh 2102891 p.Phe51Ser missense_variant 0.12
ndh 2103173 c.-132delG upstream_gene_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 0.99
PPE35 2167926 p.Leu896Ser missense_variant 0.99
PPE35 2168011 p.Ser868Arg missense_variant 1.0
PPE35 2168319 p.Thr765Ile missense_variant 0.98
PPE35 2168814 c.1798dupA frameshift_variant 1.0
PPE35 2169379 p.Phe412Val missense_variant 0.15
PPE35 2169866 c.747G>C synonymous_variant 0.21
PPE35 2170351 p.Thr88Ala missense_variant 0.29
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
ahpC 2726756 c.564C>G synonymous_variant 0.15
pepQ 2859381 c.1038C>G synonymous_variant 0.3
ribD 2987392 p.Arg185Pro missense_variant 0.23
Rv2752c 3064552 p.Arg547Pro missense_variant 0.18
Rv2752c 3064741 p.Gly484Ala missense_variant 0.17
thyX 3067995 c.-50A>C upstream_gene_variant 0.2
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 3087811 p.Ala331Gly missense_variant 0.17
fbiD 3339153 p.Leu12Phe missense_variant 0.13
fbiD 3339273 c.156T>G synonymous_variant 0.15
Rv3083 3448783 p.Val94Ile missense_variant 1.0
Rv3083 3448929 p.Tyr142* stop_gained 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474427 p.Val141Ile missense_variant 1.0
fprA 3474929 p.Gly308Asp missense_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
fprA 3475280 p.Val425Gly missense_variant 0.21
fbiB 3642478 p.Asp315Ala missense_variant 0.98
alr 3840214 p.Arg403Cys missense_variant 1.0
alr 3840268 p.Thr385Pro missense_variant 0.14
rpoA 3878238 p.Asp90Glu missense_variant 0.15
rpoA 3878630 c.-124delC upstream_gene_variant 1.0
ddn 3987013 p.Gly57Ala missense_variant 0.2
clpC1 4038403 c.2302T>C synonymous_variant 1.0
clpC1 4039363 p.Ala448Pro missense_variant 0.2
clpC1 4039932 p.Gly258Val missense_variant 0.25
embC 4239842 c.-21C>A upstream_gene_variant 0.12
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241056 c.1194C>G synonymous_variant 0.33
embC 4241783 p.Trp641Gly missense_variant 0.37
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.36
embA 4242970 c.-263C>T upstream_gene_variant 1.0
embA 4244220 c.988C>T synonymous_variant 0.97
embA 4246423 p.Val1064Gly missense_variant 0.17
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 4248725 p.Ser738Ala missense_variant 0.26
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 4326911 p.Val188Gly missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0