TB-Profiler result

Run: ERR4819240
Summary

Run ID: ERR4819240

Sample name:

Date: 01-04-2023 16:00:00

Number of reads: 394255

Percentage reads mapped: 96.25

Strain: La1.8.2

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
La1.8 M.bovis None None 1.0
La1.8.2 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 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
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575323 c.-25G>A upstream_gene_variant 0.67
ccsA 620748 c.858T>G synonymous_variant 0.33
ccsA 620752 p.Arg288Gly missense_variant 0.25
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763135 p.Gly1110Asp missense_variant 0.2
rpoC 766504 c.3135G>A synonymous_variant 0.18
rpoC 766970 p.Ala1201Ser missense_variant 0.33
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777173 c.1308C>T synonymous_variant 0.13
mmpL5 777176 p.Glu435Asp missense_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
atpE 1461173 c.129C>T synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472626 n.781A>T non_coding_transcript_exon_variant 0.18
rpsA 1834795 c.1254C>T synonymous_variant 1.0
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102967 p.Gly26Arg missense_variant 0.15
ndh 2103058 c.-16T>C upstream_gene_variant 1.0
ndh 2103173 c.-132delG upstream_gene_variant 1.0
ndh 2103225 c.-183A>C upstream_gene_variant 0.22
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
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2517952 c.-163A>T upstream_gene_variant 0.22
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518151 p.Ser13Arg missense_variant 0.29
eis 2715125 p.Thr70Ala missense_variant 1.0
ahpC 2726341 p.Val50Gly missense_variant 0.2
folC 2746575 p.Met342Val missense_variant 0.18
folC 2747631 c.-33C>T upstream_gene_variant 1.0
pepQ 2860141 p.Gly93Glu missense_variant 0.25
thyA 3074648 c.-177T>G upstream_gene_variant 0.33
ald 3086728 c.-92C>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087005 c.186C>T synonymous_variant 1.0
ald 3087084 c.266delA frameshift_variant 1.0
fbiD 3338924 c.-194_-193insG upstream_gene_variant 0.1
fbiD 3339146 p.Ile10Thr missense_variant 1.0
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
whiB7 3568561 p.Lys40Met missense_variant 0.15
fbiA 3640808 c.266_267insAGC disruptive_inframe_insertion 0.11
fbiA 3640812 p.Gln90His missense_variant 0.14
fbiA 3640813 p.Glu91Gln missense_variant 0.14
fbiA 3640816 p.Leu92Phe missense_variant 0.14
fbiA 3640819 p.Val93Leu missense_variant 0.14
fbiA 3640822 c.281_283delGCT disruptive_inframe_deletion 0.13
fbiB 3641721 c.189_190dupTC frameshift_variant 0.15
rpoA 3878161 p.Val116Gly missense_variant 0.4
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
embA 4244220 c.988C>T synonymous_variant 1.0
embB 4246551 p.Asn13Ser missense_variant 1.0
embB 4246806 p.Val98Ala missense_variant 0.11
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248372 p.Arg620Pro missense_variant 1.0
aftB 4267671 c.1165delG frameshift_variant 0.29
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 4326905 p.Leu190Pro missense_variant 0.22
ethA 4327440 p.Ala12Thr missense_variant 0.22
whiB6 4338579 c.-58C>T upstream_gene_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407551 p.Met218Val missense_variant 0.25
gid 4407588 c.615A>G synonymous_variant 1.0
eis 2714045 c.1204_*78delNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNC stop_lost&conservative_inframe_deletion&splice_region_variant 1.0