TB-Profiler result

Run: SRR8600244
Summary

Run ID: SRR8600244

Sample name:

Date: 04-04-2023 21:39:35

Number of reads: 1419751

Percentage reads mapped: 92.84

Strain: La1.8.1

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
La1.8 M.bovis None None 1.0
La1.8.1 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 5332 c.93C>T synonymous_variant 0.25
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 8201 c.902delA frameshift_variant 0.12
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 9217 p.Asp639Ala missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575307 c.-41G>A upstream_gene_variant 0.12
rpoB 759620 c.-187A>G upstream_gene_variant 0.25
rpoB 762012 p.Val736Ile missense_variant 0.17
rpoC 762582 c.-788T>C upstream_gene_variant 0.2
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766494 p.Gly1042Asp missense_variant 0.17
rpoC 766660 c.3291G>T synonymous_variant 0.2
rpoC 766691 p.Gly1108Cys missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
Rv1258c 1406178 p.Val388Ala missense_variant 0.18
Rv1258c 1406645 p.Asp232Glu missense_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475750 n.2093A>C non_coding_transcript_exon_variant 1.0
rrl 1476535 n.2878G>A non_coding_transcript_exon_variant 0.5
fabG1 1673361 c.-79C>G upstream_gene_variant 0.11
fabG1 1673380 c.-60C>G upstream_gene_variant 0.5
inhA 1673502 c.-700C>A upstream_gene_variant 0.29
rpsA 1834859 p.Ala440Thr missense_variant 0.91
tlyA 1917805 c.-134delT upstream_gene_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102193 p.Arg284Trp missense_variant 1.0
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 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 2169103 p.Pro504Thr missense_variant 0.4
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223325 c.-161G>C upstream_gene_variant 0.18
kasA 2518132 c.18C>T synonymous_variant 1.0
eis 2715125 p.Thr70Ala missense_variant 1.0
eis 2715248 p.Gly29Ser missense_variant 0.12
ahpC 2725945 c.-248G>A upstream_gene_variant 0.15
folC 2746408 c.1190delT frameshift_variant 0.22
Rv2752c 3065988 p.Glu68Asp missense_variant 1.0
thyA 3073875 p.Phe199Leu 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 3449050 p.Ile183Phe missense_variant 0.25
Rv3083 3449580 c.1077C>A synonymous_variant 0.12
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 3568746 c.-67G>A upstream_gene_variant 0.18
rpoA 3878630 c.-124delC upstream_gene_variant 1.0
clpC1 4038403 c.2302T>C synonymous_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242970 c.-263C>T upstream_gene_variant 1.0
embC 4242981 p.Met1040Thr missense_variant 1.0
embA 4244220 c.988C>T synonymous_variant 1.0
embA 4246295 p.Trp1021Cys missense_variant 0.27
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
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 4326280 c.1194G>T synonymous_variant 0.25
ethR 4327868 c.321delC frameshift_variant 0.15
whiB6 4338534 c.-13A>G upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0