TB-Profiler result

Run: ERR6336755
Summary

Run ID: ERR6336755

Sample name:

Date: 02-04-2023 02:02:23

Number of reads: 2448984

Percentage reads mapped: 99.12

Strain: lineage1.2.1.2.1

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 1.0
lineage1.2.1.2.1 Indo-Oceanic NA 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
katG 2155262 c.848_849delTG frameshift_variant 0.14 isoniazid
fbiA 3641290 p.Lys250* stop_gained 0.15 delamanid
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
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
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575360 p.Arg5Trp missense_variant 0.12
mshA 575368 c.21T>C synonymous_variant 1.0
mshA 575468 p.Ala41Thr missense_variant 0.17
mshA 575616 p.Thr90Ile missense_variant 0.14
mshA 576704 p.Gln453Lys missense_variant 0.2
ccsA 619700 c.-191C>A upstream_gene_variant 0.29
ccsA 620299 p.Leu137Val missense_variant 0.33
ccsA 620323 p.Val145Met missense_variant 0.13
rpoB 760928 c.1122G>A synonymous_variant 0.14
rpoB 761152 p.Leu449Gln missense_variant 0.26
rpoB 761466 c.1660C>T synonymous_variant 0.14
rpoB 761710 p.Val635Asp missense_variant 0.2
rpoB 761713 p.Val636Asp missense_variant 0.17
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
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 764528 p.Arg387Gly missense_variant 0.14
rpoC 766025 p.Val886Met missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 0.95
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777269 c.1212T>C synonymous_variant 0.25
mmpL5 777947 c.534G>A synonymous_variant 0.13
mmpR5 778055 c.-935G>A upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303144 p.Ser72Pro missense_variant 0.29
fbiC 1303155 c.225G>A synonymous_variant 0.14
fbiC 1303160 p.Gly77Glu missense_variant 0.13
fbiC 1303924 p.Gln332* stop_gained 0.67
fbiC 1304098 p.Gln390* stop_gained 0.17
Rv1258c 1406284 p.Thr353Ala missense_variant 0.15
Rv1258c 1406312 c.1029T>C synonymous_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
atpE 1460907 c.-138T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 1.0
inhA 1674162 c.-40C>T upstream_gene_variant 1.0
inhA 1674778 p.Pro193Ser missense_variant 0.15
rpsA 1833779 p.Val80Leu missense_variant 1.0
rpsA 1834934 c.1395delC frameshift_variant 0.14
tlyA 1918075 p.Val46Met missense_variant 0.33
tlyA 1918296 c.357G>A synonymous_variant 0.2
tlyA 1918410 c.471C>T synonymous_variant 0.19
ndh 2102144 p.Ala300Val missense_variant 0.2
ndh 2102201 p.Ser281Leu missense_variant 0.25
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155287 c.825C>T synonymous_variant 0.2
katG 2155854 c.258C>T synonymous_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170098 p.Leu172Pro missense_variant 0.33
PPE35 2170403 c.210C>G synonymous_variant 0.22
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288714 c.528C>A synonymous_variant 0.19
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518758 p.Ala215Val missense_variant 0.15
kasA 2518842 p.Gly243Asp missense_variant 0.24
kasA 2518976 p.Gly288Ser missense_variant 0.12
kasA 2519048 p.Gly312Ser missense_variant 1.0
eis 2715193 p.Val47Glu missense_variant 0.25
eis 2715215 p.Val40Met missense_variant 0.12
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2746358 p.Val414Asp missense_variant 0.67
folC 2747716 c.-118T>C upstream_gene_variant 0.17
pepQ 2860022 p.Glu133Lys missense_variant 0.12
ribD 2987266 p.Leu143Pro missense_variant 0.11
Rv2752c 3065003 p.His397Asn missense_variant 0.25
thyX 3067240 p.Ala236Thr missense_variant 0.29
thyX 3067350 p.Arg199Gln missense_variant 0.2
thyX 3067965 c.-20C>A upstream_gene_variant 0.5
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087280 p.Gly154Glu missense_variant 0.2
ald 3087838 p.Ala340Val missense_variant 0.14
ald 3087890 c.1072dupG frameshift_variant 0.14
ald 3087896 c.1077G>A synonymous_variant 0.14
ald 3087897 p.Gly360Arg missense_variant 0.14
ald 3087919 p.Ala367Asp missense_variant 0.18
fbiD 3339053 c.-65G>A upstream_gene_variant 0.33
fbiD 3339213 c.96G>A synonymous_variant 0.2
fbiD 3339417 c.300A>G synonymous_variant 1.0
fbiD 3339537 c.420C>T synonymous_variant 0.14
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
whiB7 3568428 c.252A>G synonymous_variant 0.22
whiB7 3568431 c.249C>G synonymous_variant 0.19
whiB7 3568488 c.191delG frameshift_variant 1.0
Rv3236c 3612579 p.Glu180Gln missense_variant 0.18
fbiB 3640557 c.-978T>C upstream_gene_variant 1.0
fbiA 3641155 p.Asp205Asn missense_variant 0.12
fbiA 3641162 p.Asp207Val missense_variant 0.12
fbiA 3641188 p.Pro216Thr missense_variant 0.29
fbiB 3641289 c.-246A>G upstream_gene_variant 0.15
fbiA 3641333 p.Gly264Ala missense_variant 0.13
fbiA 3641340 p.Asp266Glu missense_variant 0.14
fbiB 3642195 p.Gly221Ser missense_variant 0.5
rpoA 3878639 c.-132C>G upstream_gene_variant 0.3
ddn 3986670 c.-174G>A upstream_gene_variant 0.15
ddn 3986693 c.-150delG upstream_gene_variant 0.11
clpC1 4039538 c.1167C>T synonymous_variant 0.13
clpC1 4039594 p.Arg371Trp missense_variant 0.17
clpC1 4040232 p.Arg158His missense_variant 0.25
clpC1 4040241 p.Thr155Phe missense_variant 0.4
clpC1 4040249 p.Glu152Gly missense_variant 0.29
clpC1 4040304 c.400delG frameshift_variant 0.4
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4239998 c.138delC frameshift_variant 0.12
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241006 p.Ala382Thr missense_variant 0.5
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241154 c.1293delC frameshift_variant 0.22
embC 4242429 p.Ala856Val missense_variant 0.4
embC 4242536 p.Asp892Asn missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243580 c.348G>A synonymous_variant 1.0
embA 4243629 p.Ala133Pro missense_variant 0.29
embA 4243823 c.591G>A synonymous_variant 0.12
embA 4244184 p.Ser318Leu missense_variant 0.32
embA 4244194 p.Gly321Ala missense_variant 0.15
embA 4244266 p.Arg345Gln missense_variant 0.17
embA 4244420 c.1188G>C synonymous_variant 1.0
embA 4245496 p.Gly755Ala missense_variant 0.15
embA 4245648 p.Ile806Val missense_variant 0.17
embA 4245799 p.Trp856* stop_gained 0.13
embA 4245969 p.Pro913Ser missense_variant 1.0
embA 4246029 p.Pro933Thr missense_variant 0.25
embB 4246544 p.Thr11Pro missense_variant 0.33
embB 4246548 p.Pro12Gln missense_variant 0.36
embB 4246555 c.42G>C synonymous_variant 0.38
embB 4246556 p.Ala15Pro missense_variant 0.38
embB 4246563 p.Leu17Trp missense_variant 0.47
embB 4246567 c.54G>T synonymous_variant 0.38
embB 4246616 c.103C>T synonymous_variant 0.12
embB 4246682 p.Asp57Asn missense_variant 0.17
embB 4247223 p.Trp237* stop_gained 0.14
embB 4247578 c.1065G>A synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4247867 p.Val452Met missense_variant 0.25
embB 4248324 p.Ala604Gly missense_variant 0.38
embB 4248644 c.2133delC frameshift_variant 0.17
embB 4249156 c.2643C>T synonymous_variant 0.17
embB 4249497 p.Pro995Leu missense_variant 0.14
embB 4249705 c.3192G>C synonymous_variant 0.14
aftB 4267422 p.Thr472Ile missense_variant 0.15
aftB 4267607 c.1230G>A synonymous_variant 0.25
aftB 4268793 p.Val15Ala missense_variant 0.12
aftB 4268816 p.Trp7* stop_gained 0.17
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ubiA 4269864 c.-32delG upstream_gene_variant 1.0
ethR 4327601 p.Ala18Val missense_variant 0.5
ethA 4328436 c.-963G>C upstream_gene_variant 1.0
whiB6 4338330 c.192C>T synonymous_variant 0.22
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 4407578 p.Lys209* stop_gained 0.14
gid 4407581 p.Gly208Arg missense_variant 0.14
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0
gid 4408139 c.63delG frameshift_variant 0.4
gid 4408147 p.Ala19Gly missense_variant 0.29