TB-Profiler result

Run: ERR6336804
Summary

Run ID: ERR6336804

Sample name:

Date: 02-04-2023 02:04:00

Number of reads: 618038

Percentage reads mapped: 98.92

Strain: lineage1.2.1.2

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 1.0
lineage1.2.1 Indo-Oceanic EAI2 RD239 1.0
lineage1.2.1.2 Indo-Oceanic NA RD239 0.99
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
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2153909 p.Asp735Asn missense_variant 0.2 isoniazid
gid 4407796 p.Ser136* stop_gained 1.0 streptomycin
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 5669 p.Tyr144His missense_variant 0.12
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrA 6622 c.-680C>T upstream_gene_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
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 9260 c.1959G>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9513 p.Glu738Lys missense_variant 0.18
gyrA 9606 p.Asp769Asn missense_variant 0.12
fgd1 491005 c.223C>T synonymous_variant 0.17
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575327 c.-21G>A upstream_gene_variant 0.22
mshA 575368 c.21T>C synonymous_variant 1.0
mshA 575391 p.Gln15Arg missense_variant 0.25
mshA 576007 c.660A>G synonymous_variant 0.11
ccsA 619762 c.-129C>T upstream_gene_variant 0.29
ccsA 619940 p.Ala17Val missense_variant 0.13
ccsA 620558 p.Gln223Arg missense_variant 0.11
ccsA 620698 p.Val270Ile missense_variant 0.15
rpoB 760045 p.Leu80Gln missense_variant 0.15
rpoB 761451 p.Val549Phe missense_variant 0.14
rpoB 761605 p.Leu600Pro missense_variant 0.14
rpoB 761610 p.Gly602Arg missense_variant 0.17
rpoB 761652 p.Glu616Lys missense_variant 0.13
rpoB 761814 p.Ala670Thr missense_variant 0.18
rpoB 762097 p.Thr764Ser missense_variant 0.13
rpoB 762116 c.2310C>T synonymous_variant 0.22
rpoB 762293 c.2487T>A synonymous_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763342 c.-28C>T upstream_gene_variant 0.12
rpoC 763531 c.162G>C synonymous_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 764548 c.1179G>A synonymous_variant 0.2
rpoC 765391 c.2022C>T synonymous_variant 0.17
rpoC 765523 c.2154C>T synonymous_variant 0.15
rpoC 765557 p.Thr730Ser missense_variant 0.17
rpoC 767022 p.Asp1218Gly missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777255 p.Pro409Leu missense_variant 0.17
mmpL5 778033 p.Gln150* stop_gained 0.13
mmpL5 778210 p.Ala91Thr missense_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781647 p.Arg30Cys missense_variant 0.15
rplC 801359 p.Lys184Arg missense_variant 0.11
fbiC 1302870 c.-61G>A upstream_gene_variant 0.17
fbiC 1304159 p.Val410Ala missense_variant 0.11
fbiC 1304313 c.1383A>G synonymous_variant 0.13
fbiC 1304817 c.1887T>C synonymous_variant 0.14
Rv1258c 1406531 c.810C>T synonymous_variant 0.22
Rv1258c 1407092 c.249T>C synonymous_variant 0.12
embR 1416915 p.Trp145Gly missense_variant 0.25
embR 1417019 p.Cys110Tyr missense_variant 1.0
embR 1417038 p.Ser104Gly missense_variant 0.15
embR 1417049 p.Gly100Asp missense_variant 0.18
embR 1417063 c.285C>A synonymous_variant 0.2
embR 1417087 c.261G>T synonymous_variant 0.2
atpE 1460907 c.-138T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472753 n.908A>C non_coding_transcript_exon_variant 1.0
rrl 1474468 n.811G>A non_coding_transcript_exon_variant 0.12
rrl 1474732 n.1075A>G non_coding_transcript_exon_variant 1.0
rrl 1476196 n.2539C>G non_coding_transcript_exon_variant 0.11
rrl 1476483 n.2826G>A non_coding_transcript_exon_variant 0.12
fabG1 1673755 p.Glu106Lys missense_variant 0.12
inhA 1674300 c.99C>T synonymous_variant 0.12
inhA 1674484 p.Ile95Leu missense_variant 1.0
rpsA 1833380 c.-162G>A upstream_gene_variant 0.18
rpsA 1834896 p.Ser452Thr missense_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102372 p.Met224Thr missense_variant 0.29
ndh 2102379 c.663delG frameshift_variant 0.17
katG 2154494 p.Phe540Leu missense_variant 0.12
katG 2154495 c.1617C>T synonymous_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155772 p.Arg114Cys missense_variant 0.2
katG 2155914 c.198G>A synonymous_variant 0.15
PPE35 2167861 p.Gly918Cys missense_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168464 p.Pro717Ser missense_variant 0.17
PPE35 2169022 p.Gly531Arg missense_variant 0.14
PPE35 2170048 p.Leu189Val missense_variant 0.29
Rv1979c 2222214 c.951C>G synonymous_variant 0.15
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222625 c.540C>T synonymous_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289133 p.Glu37Lys missense_variant 0.15
pncA 2290095 c.-854C>T upstream_gene_variant 0.17
kasA 2518103 c.-12G>A upstream_gene_variant 0.14
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518302 p.His63Leu missense_variant 0.13
kasA 2519048 p.Gly312Ser missense_variant 1.0
kasA 2519071 c.957C>T synonymous_variant 0.14
kasA 2519335 c.1221C>T synonymous_variant 0.22
eis 2714340 c.993C>T synonymous_variant 0.15
eis 2715278 c.55C>T synonymous_variant 0.12
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726466 p.Ala92Thr missense_variant 0.13
folC 2747565 p.Gly12Arg missense_variant 0.12
Rv2752c 3065305 p.Ala296Val missense_variant 0.18
thyX 3067246 c.699delC frameshift_variant 0.33
thyX 3067929 p.Pro6Leu missense_variant 0.33
thyA 3074575 c.-105delC upstream_gene_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087446 c.627C>A synonymous_variant 0.14
ald 3087716 c.897G>A synonymous_variant 0.13
ald 3087769 p.Thr317Met missense_variant 0.18
fbiD 3339417 c.300A>G synonymous_variant 1.0
fbiD 3339431 p.Glu105Ala missense_variant 0.12
fbiD 3339741 c.624G>T synonymous_variant 0.4
fbiD 3339744 c.627A>C synonymous_variant 0.4
Rv3083 3448701 c.198C>T synonymous_variant 0.14
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449569 p.Met356Val missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3474850 p.Arg282Cys missense_variant 0.13
fprA 3474970 p.Val322Ile missense_variant 0.12
fprA 3475159 p.Asn385Asp missense_variant 1.0
whiB7 3568488 c.191delG frameshift_variant 1.0
whiB7 3568666 p.Thr5Lys missense_variant 0.13
whiB7 3568711 c.-32G>A upstream_gene_variant 0.12
Rv3236c 3611984 p.Pro378Leu missense_variant 0.13
Rv3236c 3612076 c.1041G>A synonymous_variant 0.12
Rv3236c 3612091 c.1026G>C synonymous_variant 0.11
Rv3236c 3612422 p.Val232Ala missense_variant 0.14
Rv3236c 3612450 p.Leu223Val missense_variant 0.13
Rv3236c 3612573 p.Val182Leu missense_variant 0.12
fbiB 3640557 c.-978T>C upstream_gene_variant 1.0
fbiA 3640592 p.Leu17Arg missense_variant 0.12
fbiB 3640599 c.-936C>G upstream_gene_variant 0.13
fbiA 3641104 p.Val188Phe missense_variant 1.0
fbiB 3642033 p.Ala167Thr missense_variant 0.18
fbiB 3642143 c.609C>T synonymous_variant 0.14
alr 3841225 p.Lys66Glu missense_variant 0.14
alr 3841574 c.-154T>C upstream_gene_variant 0.12
rpoA 3877954 p.Gln185Arg missense_variant 0.12
rpoA 3877968 c.540C>T synonymous_variant 0.17
rpoA 3878202 c.306G>A synonymous_variant 0.15
ddn 3986659 c.-185A>C upstream_gene_variant 0.13
ddn 3986928 p.Tyr29His missense_variant 0.12
clpC1 4038579 p.Phe709Ser missense_variant 0.11
clpC1 4040247 p.Ala153Val missense_variant 0.12
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4239790 c.-73C>T upstream_gene_variant 0.14
embC 4240103 p.Asp81Asn missense_variant 0.13
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4240693 c.831T>C synonymous_variant 0.15
embC 4240803 p.Tyr314Cys missense_variant 0.17
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241452 c.1590G>A synonymous_variant 0.18
embC 4241878 c.2016G>C synonymous_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242770 p.Thr970Ala missense_variant 0.11
embA 4243580 c.348G>A synonymous_variant 1.0
embA 4243848 p.Val206Leu missense_variant 0.25
embA 4243945 p.Thr238Ile missense_variant 0.13
embA 4244184 p.Ser318Leu missense_variant 0.2
embA 4244420 c.1188G>C synonymous_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246615 c.102G>A synonymous_variant 0.4
embB 4246811 p.Gly100Ser missense_variant 0.12
embB 4247578 c.1065G>A synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4247916 p.Arg468His missense_variant 0.14
embB 4248325 c.1812G>A synonymous_variant 0.2
aftB 4267926 c.910delG frameshift_variant 0.2
aftB 4268622 p.Trp72Ser missense_variant 0.17
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269603 c.-767C>T upstream_gene_variant 0.14
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326428 p.Phe349Ser missense_variant 0.17
ethA 4326921 p.Ala185Thr missense_variant 0.2
ethR 4328144 p.Val199Ala missense_variant 0.13
whiB6 4338361 p.Arg54Gln missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407792 c.411G>A synonymous_variant 0.15
gid 4407873 c.330G>T synonymous_variant 1.0
gid 4408361 c.-159A>C upstream_gene_variant 0.14