TB-Profiler result

Run: ERR2514929
Summary

Run ID: ERR2514929

Sample name:

Date: 31-03-2023 20:38:54

Number of reads: 950874

Percentage reads mapped: 91.6

Strain: lineage1.1.2

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
lineage1 Indo-Oceanic EAI RD239 0.99
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 1.0
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 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
inhA 1674048 c.-154G>A upstream_gene_variant 1.0 isoniazid, ethionamide
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 6112 p.Met291Ile missense_variant 1.0
gyrB 6124 c.885C>T synonymous_variant 1.0
gyrA 6700 c.-602T>C upstream_gene_variant 0.13
gyrA 6703 c.-599G>T upstream_gene_variant 0.13
gyrA 6706 c.-596G>A upstream_gene_variant 0.13
gyrA 6709 c.-593A>G upstream_gene_variant 0.13
gyrA 6712 c.-590G>C upstream_gene_variant 0.14
gyrA 6715 c.-587C>T upstream_gene_variant 0.13
gyrA 6724 c.-578G>A upstream_gene_variant 0.12
gyrA 6727 c.-575G>T upstream_gene_variant 0.12
gyrA 6728 c.-574_-572delCTAinsTTG upstream_gene_variant 0.12
gyrA 6745 c.-557T>C upstream_gene_variant 0.12
gyrA 6760 c.-542G>C upstream_gene_variant 0.15
gyrA 6764 c.-538C>T upstream_gene_variant 0.14
gyrA 6772 c.-530C>G upstream_gene_variant 0.14
gyrA 6775 c.-527G>T upstream_gene_variant 0.14
gyrA 6778 c.-524C>T upstream_gene_variant 0.15
gyrA 6793 c.-509T>C upstream_gene_variant 0.14
gyrB 6798 p.Gly520Ala missense_variant 0.17
gyrA 6808 c.-494C>G upstream_gene_variant 0.12
gyrA 6811 c.-491C>T upstream_gene_variant 0.11
gyrA 7006 c.-296T>G upstream_gene_variant 0.17
gyrB 7010 p.Leu591Met missense_variant 0.12
gyrA 7018 c.-284G>C upstream_gene_variant 0.14
gyrA 7024 c.-278G>C upstream_gene_variant 0.16
gyrA 7033 c.-269G>C upstream_gene_variant 0.15
gyrB 7051 p.Glu604Asp missense_variant 0.14
gyrA 7054 c.-248C>T upstream_gene_variant 0.14
gyrA 7060 c.-242T>C upstream_gene_variant 0.14
gyrA 7066 c.-236G>C upstream_gene_variant 0.12
gyrA 7078 c.-224A>T upstream_gene_variant 0.16
gyrA 7084 c.-218A>G upstream_gene_variant 0.18
gyrA 7090 c.-212C>T upstream_gene_variant 0.19
gyrA 7093 c.-209T>C upstream_gene_variant 0.2
gyrA 7100 c.-202T>C upstream_gene_variant 0.19
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7523 c.222C>G synonymous_variant 0.12
gyrA 7526 c.225G>C synonymous_variant 0.12
gyrA 7532 c.231T>G synonymous_variant 0.12
gyrA 7535 c.234C>G synonymous_variant 0.12
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576666 p.Ser440Ile missense_variant 0.13
ccsA 620748 c.858T>G synonymous_variant 0.36
rpoB 760490 c.684C>T synonymous_variant 0.96
rpoB 760646 c.840C>G synonymous_variant 0.13
rpoB 760655 c.849A>G synonymous_variant 0.17
rpoB 760661 c.855A>C synonymous_variant 0.12
rpoB 760668 p.Thr288Ala missense_variant 0.12
rpoB 760679 c.873A>G synonymous_variant 0.13
rpoB 760683 c.877T>C synonymous_variant 0.13
rpoB 762879 p.Met1025Leu missense_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 765171 p.Pro601Leu missense_variant 0.95
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776395 p.Phe696Leu missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416274 c.1074C>A synonymous_variant 0.13
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.12
rrs 1473288 n.1443C>T non_coding_transcript_exon_variant 0.2
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.2
rrs 1473291 n.1446G>T non_coding_transcript_exon_variant 0.2
rrl 1475700 n.2043A>G non_coding_transcript_exon_variant 0.5
fabG1 1674076 p.Thr213Pro missense_variant 0.27
rpsA 1834297 c.756C>T synonymous_variant 0.23
rpsA 1834303 c.762T>G synonymous_variant 0.2
rpsA 1834306 c.765T>C synonymous_variant 0.19
rpsA 1834339 c.798C>T synonymous_variant 0.2
rpsA 1834348 c.807T>C synonymous_variant 0.19
rpsA 1834366 c.825A>G synonymous_variant 0.17
rpsA 1834375 c.834G>A synonymous_variant 0.11
rpsA 1834378 c.837T>C synonymous_variant 0.11
rpsA 1834396 c.855G>T synonymous_variant 0.13
rpsA 1834411 c.870T>C synonymous_variant 0.12
rpsA 1834480 c.939C>G synonymous_variant 0.12
rpsA 1834489 c.948T>C synonymous_variant 0.11
rpsA 1834498 c.957C>T synonymous_variant 0.12
rpsA 1834520 p.Ala327Ser missense_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103154 c.-112G>A upstream_gene_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.33
PPE35 2170053 p.Thr187Ser missense_variant 0.36
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 2726051 c.-142G>A upstream_gene_variant 1.0
pepQ 2859397 p.Thr341Ile missense_variant 1.0
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
fbiB 3642780 p.Val416Phe missense_variant 0.12
rpoA 3877629 c.879C>G synonymous_variant 0.13
rpoA 3877656 c.852T>G synonymous_variant 0.15
rpoA 3877662 c.846C>T synonymous_variant 0.14
rpoA 3877665 c.843C>G synonymous_variant 0.14
rpoA 3877668 c.840A>G synonymous_variant 0.14
rpoA 3877677 c.831G>C synonymous_variant 0.13
rpoA 3877680 c.828G>T synonymous_variant 0.16
rpoA 3877686 c.822A>G synonymous_variant 0.16
rpoA 3877692 c.816G>C synonymous_variant 0.17
rpoA 3877704 c.804G>T synonymous_variant 0.17
rpoA 3877728 c.780C>G synonymous_variant 0.11
rpoA 3877734 c.774G>C synonymous_variant 0.11
rpoA 3877737 c.771G>C synonymous_variant 0.12
rpoA 3877743 c.765T>C synonymous_variant 0.12
rpoA 3877752 p.Asp252Glu missense_variant 0.14
rpoA 3877758 c.750G>C synonymous_variant 0.13
rpoA 3877764 c.744C>G synonymous_variant 0.1
rpoA 3877782 c.726T>C synonymous_variant 0.11
rpoA 3877818 c.690A>G synonymous_variant 0.17
rpoA 3877839 c.669G>T synonymous_variant 0.12
rpoA 3877856 c.652T>C synonymous_variant 0.1
rpoA 3878127 c.381G>C synonymous_variant 0.11
clpC1 4038989 c.1716T>C synonymous_variant 0.13
clpC1 4038997 c.1708T>C synonymous_variant 0.13
clpC1 4039064 c.1641C>T synonymous_variant 0.21
clpC1 4039070 c.1635G>C synonymous_variant 0.16
clpC1 4039077 p.Lys543Arg missense_variant 0.15
clpC1 4039079 c.1626C>G synonymous_variant 0.11
clpC1 4039085 c.1620A>G synonymous_variant 0.11
clpC1 4039091 c.1614G>T synonymous_variant 0.11
clpC1 4039097 c.1608G>T synonymous_variant 0.11
clpC1 4039100 c.1605C>G synonymous_variant 0.11
clpC1 4039106 c.1599G>C synonymous_variant 0.11
clpC1 4039112 c.1593C>G synonymous_variant 0.11
clpC1 4040291 c.414G>C synonymous_variant 0.14
clpC1 4040300 c.405C>T synonymous_variant 0.13
clpC1 4040517 p.Val63Ala missense_variant 0.96
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.15
embB 4246555 c.42G>C synonymous_variant 0.2
embB 4246556 p.Ala15Pro missense_variant 0.2
embB 4246563 p.Leu17Trp missense_variant 0.22
embB 4246567 c.54G>T synonymous_variant 0.26
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4247659 c.1146C>T synonymous_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326432 p.Leu348Phe missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.97
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0