TB-Profiler result

Run: ERR2747642

Summary

Run ID: ERR2747642

Sample name:

Date: 31-03-2023 23:28:40

Number of reads: 458953

Percentage reads mapped: 79.98

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 6098 p.Val287Leu missense_variant 0.4
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 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
ccsA 620713 p.Tyr275His missense_variant 1.0
rpoB 761369 c.1563G>A synonymous_variant 0.67
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764057 p.Ala230Thr missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775682 c.2799C>T synonymous_variant 0.25
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776300 p.Met727Ile missense_variant 0.25
mmpL5 778692 c.-212C>T upstream_gene_variant 0.22
mmpL5 778789 c.-309G>T upstream_gene_variant 0.4
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
fbiC 1305354 c.2424C>T synonymous_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472017 n.172C>A non_coding_transcript_exon_variant 1.0
rrl 1475750 n.2093A>C non_coding_transcript_exon_variant 1.0
rpsA 1833460 c.-82G>T upstream_gene_variant 0.4
rpsA 1833535 c.-7C>A upstream_gene_variant 0.29
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101755 p.Thr430Ser missense_variant 0.12
ndh 2102193 p.Arg284Trp missense_variant 1.0
ndh 2103173 c.-132delG upstream_gene_variant 1.0
katG 2155503 c.609C>T synonymous_variant 1.0
katG 2156025 c.87C>A synonymous_variant 1.0
PPE35 2167836 p.Gly926Val missense_variant 0.25
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 2170804 c.-192C>T upstream_gene_variant 0.25
Rv1979c 2222236 p.Ile310Lys missense_variant 0.4
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289828 c.-587C>A upstream_gene_variant 0.2
kasA 2518132 c.18C>T synonymous_variant 1.0
eis 2715125 p.Thr70Ala missense_variant 1.0
ahpC 2726076 c.-117C>A upstream_gene_variant 0.13
ahpC 2726373 p.Cys61Gly missense_variant 0.25
folC 2747203 c.396G>A synonymous_variant 0.14
Rv2752c 3064567 p.Gly542Val missense_variant 0.22
Rv2752c 3064626 c.1566C>T synonymous_variant 0.18
Rv2752c 3065988 p.Glu68Asp missense_variant 1.0
thyA 3074177 p.Arg99* stop_gained 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 3087452 p.Phe211Leu missense_variant 0.17
Rv3083 3448499 c.-5G>A upstream_gene_variant 0.4
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 3612000 p.Thr373Ala missense_variant 0.11
rpoA 3877845 c.663G>C synonymous_variant 0.14
clpC1 4038403 c.2302T>C synonymous_variant 1.0
embC 4240658 p.Arg266Cys missense_variant 0.22
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
embA 4244220 c.988C>T synonymous_variant 1.0
embB 4245743 c.-771C>A upstream_gene_variant 0.14
embB 4246241 c.-273G>A upstream_gene_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
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
ethR 4327369 c.-180C>T upstream_gene_variant 0.4
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408230 c.-28C>T upstream_gene_variant 0.29
gid 4408286 c.-84C>A upstream_gene_variant 0.18