TB-Profiler result

Run: ERR3077946
Summary

Run ID: ERR3077946

Sample name:

Date: 01-04-2023 00:12:11

Number of reads: 394741

Percentage reads mapped: 99.49

Strain: lineage3

Drug-resistance: HR-TB

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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
lineage3 East-African-Indian CAS RD750 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
katG 2155221 c.890delG frameshift_variant 0.14 isoniazid
pncA 2288807 p.Asp145Glu missense_variant 0.13 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8056 p.Arg252Leu missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491677 p.Gln299Lys missense_variant 0.22
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575514 p.Pro56Gln missense_variant 0.18
ccsA 619700 c.-191C>A upstream_gene_variant 0.29
rpoB 759615 c.-192A>C upstream_gene_variant 0.22
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 759997 p.Trp64Leu missense_variant 0.18
rpoB 761492 c.1686G>T synonymous_variant 0.2
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoB 762993 p.Gly1063Trp missense_variant 0.2
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763351 c.-19T>C upstream_gene_variant 0.17
rpoC 764341 c.972G>T synonymous_variant 0.12
rpoC 765247 c.1878C>A synonymous_variant 0.2
rpoC 765601 p.Glu744Asp missense_variant 0.13
rpoC 766219 c.2850C>T synonymous_variant 0.13
rpoC 767113 c.3744G>T synonymous_variant 0.15
rpoC 767266 c.3897G>T synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 778748 p.Pro53His missense_variant 0.33
mmpR5 779119 p.Leu44Met missense_variant 0.16
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800705 c.-104G>T upstream_gene_variant 0.25
fbiC 1303016 p.Val29Gly missense_variant 0.29
Rv1258c 1407362 c.-22G>T upstream_gene_variant 0.13
Rv1258c 1407425 c.-85A>G upstream_gene_variant 0.14
embR 1416307 c.1041C>T synonymous_variant 0.14
embR 1416376 p.Asn324Lys missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476379 n.2722G>T non_coding_transcript_exon_variant 0.25
fabG1 1673996 p.Ile186Thr missense_variant 0.14
rpsA 1833987 p.Pro149His missense_variant 0.22
ndh 2102032 c.1011C>A synonymous_variant 0.12
ndh 2102892 p.Phe51Ile missense_variant 0.13
katG 2154224 p.Gly630Cys missense_variant 0.15
katG 2154419 p.Val565Leu missense_variant 0.12
katG 2154597 p.Trp505Cys missense_variant 0.11
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156095 p.Pro6Gln missense_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168017 p.Ile866Val missense_variant 0.22
PPE35 2168359 p.Ser752Gly missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289033 p.Pro70Arg missense_variant 0.13
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
kasA 2518251 p.Leu46Pro missense_variant 0.18
eis 2714872 p.Pro154Gln missense_variant 0.17
ahpC 2725972 c.-221A>G upstream_gene_variant 0.15
ahpC 2726019 c.-174C>A upstream_gene_variant 0.12
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
folC 2747228 c.369_370delCT frameshift_variant 0.17
ribD 2986651 c.-188G>C upstream_gene_variant 0.12
Rv2752c 3064523 p.Glu557* stop_gained 0.18
Rv2752c 3065022 c.1170G>T synonymous_variant 0.25
thyX 3067859 c.87C>A synonymous_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086932 p.Gly38Val missense_variant 0.14
ald 3086999 c.180C>A synonymous_variant 0.18
ald 3087829 p.Pro337Leu missense_variant 0.17
Rv3083 3448488 c.-16C>A upstream_gene_variant 0.14
Rv3083 3448679 p.Met59Thr missense_variant 0.22
Rv3083 3449856 p.Met451Ile missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474505 p.Leu167Phe missense_variant 0.11
Rv3236c 3612424 c.693G>T synonymous_variant 0.12
Rv3236c 3612898 c.219G>T synonymous_variant 0.25
fbiB 3641629 p.Ala32Asp missense_variant 0.14
fbiB 3642424 p.Phe297Tyr missense_variant 0.18
fbiB 3642435 p.Gln301Lys missense_variant 0.18
alr 3841480 c.-60C>A upstream_gene_variant 0.12
rpoA 3878248 p.Ser87Leu missense_variant 0.12
clpC1 4039667 p.Gln346His missense_variant 0.12
clpC1 4040486 c.219G>T synonymous_variant 0.14
clpC1 4040492 p.Gln71His missense_variant 0.17
clpC1 4040572 p.Ala45Thr missense_variant 0.13
clpC1 4040601 p.Leu35Ser missense_variant 0.11
panD 4044124 p.Ala53Asp missense_variant 0.17
embC 4240648 c.786C>T synonymous_variant 0.33
embC 4240655 p.Ala265Pro missense_variant 0.33
embC 4241065 c.1203C>A synonymous_variant 0.13
embC 4241791 c.1929G>T synonymous_variant 0.17
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243730 p.Lys166Asn missense_variant 0.18
embA 4244735 c.1503C>A synonymous_variant 0.12
embA 4245467 c.2235C>A synonymous_variant 0.14
embB 4245575 c.-939C>G upstream_gene_variant 0.18
embA 4245606 p.Leu792Met missense_variant 0.25
embA 4246254 p.Leu1008Met missense_variant 0.2
embB 4246714 c.201G>T synonymous_variant 0.12
embB 4248009 p.Leu499Pro missense_variant 0.12
embB 4248233 p.Leu574Met missense_variant 0.29
aftB 4268277 p.Pro187Leu missense_variant 0.12
ethA 4326159 p.Val439Leu missense_variant 0.12
ethA 4328212 c.-740delC upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408061 p.His48Asn missense_variant 1.0
gid 4408419 c.-217A>G upstream_gene_variant 0.17