TB-Profiler result

Run: SRR5817480
Summary

Run ID: SRR5817480

Sample name:

Date: 04-04-2023 11:13:23

Number of reads: 581924

Percentage reads mapped: 99.22

Strain:

Drug-resistance: MDR-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
lineage1.2.1.2 Indo-Oceanic NA RD239 0.98
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
rpoB 761139 p.His445Tyr missense_variant 1.0 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
inhA 1674481 p.Ser94Ala missense_variant 1.0 isoniazid, ethionamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
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 6382 p.Lys381Asn missense_variant 0.4
gyrB 7158 c.1931_1933delCCG disruptive_inframe_deletion 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7411 p.Val37Gly missense_variant 0.23
gyrA 7444 p.Leu48Arg missense_variant 0.38
gyrA 7527 p.Ser76Ala missense_variant 0.31
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7684 p.Arg128Met missense_variant 0.4
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
fgd1 491769 c.987A>G synonymous_variant 0.15
mshA 575368 c.21T>C synonymous_variant 1.0
mshA 575420 p.Thr25Pro missense_variant 0.21
mshA 576108 p.Ala254Gly missense_variant 0.27
mshA 576123 p.Leu259Arg missense_variant 0.38
mshA 576180 p.Lys278Met missense_variant 0.33
ccsA 619787 c.-104T>G upstream_gene_variant 0.18
ccsA 619958 p.Val23Gly missense_variant 0.29
ccsA 620047 p.Ser53Ala missense_variant 0.33
ccsA 620159 p.Leu90Arg missense_variant 0.2
rpoB 760504 p.Lys233Met missense_variant 0.22
rpoB 761883 p.Gly693Cys missense_variant 0.17
rpoB 762293 c.2487T>A synonymous_variant 0.17
rpoB 762682 p.Glu959Ala missense_variant 0.38
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763207 p.Ser1134Ile missense_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 764327 p.Ile320Leu missense_variant 0.62
rpoC 765717 p.Asp783Ala missense_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775682 c.2799C>A synonymous_variant 0.22
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776128 p.Cys785Ser missense_variant 0.17
mmpL5 776329 p.Phe718Val missense_variant 0.33
mmpL5 776712 p.His590Leu missense_variant 0.14
mmpL5 776776 p.Asn569Tyr missense_variant 0.4
rpsL 781395 c.-165T>C upstream_gene_variant 0.93
rpsL 781798 p.Val80Gly missense_variant 0.22
fbiC 1303726 p.Thr266Pro missense_variant 0.22
fbiC 1305023 p.His698Leu missense_variant 0.23
fbiC 1305058 p.Tyr710Asp missense_variant 0.14
Rv1258c 1406127 p.Leu405Gln missense_variant 0.29
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
rrs 1472079 n.234C>A non_coding_transcript_exon_variant 0.4
rrs 1472759 n.914T>A non_coding_transcript_exon_variant 0.29
rrs 1472804 n.959G>T non_coding_transcript_exon_variant 0.29
fabG1 1673388 c.-52T>G upstream_gene_variant 0.21
fabG1 1673561 p.Lys41Met missense_variant 0.13
inhA 1674162 c.-40C>T upstream_gene_variant 1.0
inhA 1674870 p.Asp223Glu missense_variant 0.38
rpsA 1833949 c.408T>C synonymous_variant 0.2
tlyA 1917826 c.-114A>C upstream_gene_variant 0.38
tlyA 1917835 c.-105A>C upstream_gene_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918168 p.Phe77Val missense_variant 0.15
tlyA 1918621 p.Ser228Cys missense_variant 0.31
ndh 2102337 p.Leu236Val missense_variant 0.13
ndh 2103150 c.-108T>G upstream_gene_variant 0.25
ndh 2103194 c.-152T>G upstream_gene_variant 0.18
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155358 p.Phe252Val missense_variant 0.33
katG 2155735 p.Met126Lys missense_variant 0.25
katG 2155997 p.Trp39Gly missense_variant 0.2
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169190 p.Phe475Ile missense_variant 0.27
PPE35 2169976 p.Gly213Ser missense_variant 0.12
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
kasA 2519048 p.Gly312Ser missense_variant 1.0
eis 2714191 p.Gln381Leu missense_variant 0.27
eis 2714236 p.Ala366Val missense_variant 0.33
eis 2714247 c.1086A>T synonymous_variant 0.5
eis 2714832 p.Arg167Ser missense_variant 0.38
ahpC 2726001 c.-192T>C upstream_gene_variant 0.12
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726140 c.-53A>G upstream_gene_variant 0.13
ahpC 2726731 p.Lys180Met missense_variant 0.21
folC 2746457 p.Val381Gly missense_variant 0.3
folC 2747036 p.Asn188Thr missense_variant 0.33
folC 2747559 p.Ala14Thr missense_variant 0.17
folC 2747691 c.-93A>C upstream_gene_variant 0.2
pepQ 2859558 c.861C>T synonymous_variant 0.18
pepQ 2859625 p.Leu265Arg missense_variant 0.38
pepQ 2860466 c.-48C>T upstream_gene_variant 0.13
ribD 2987266 p.Leu143Arg missense_variant 0.36
Rv2752c 3064528 p.Val555Gly missense_variant 0.33
Rv2752c 3064543 p.Met550Arg missense_variant 0.22
Rv2752c 3065638 p.Leu185Gln missense_variant 0.25
Rv2752c 3065836 p.Tyr119Cys missense_variant 0.14
Rv2752c 3066085 p.His36Arg missense_variant 0.22
thyX 3067551 p.Leu132Gln missense_variant 0.2
thyA 3074364 p.Tyr36* stop_gained 0.33
thyA 3074492 c.-21T>G upstream_gene_variant 0.31
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339417 c.300A>G synonymous_variant 1.0
fbiD 3339548 p.Leu144His missense_variant 0.3
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449035 p.Lys178* stop_gained 0.29
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474057 c.51C>T synonymous_variant 0.22
fprA 3474074 p.Leu23Arg missense_variant 0.22
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
fprA 3475273 p.Trp423Arg missense_variant 0.38
whiB7 3568488 c.191delG frameshift_variant 1.0
whiB7 3568622 p.Cys20Gly missense_variant 0.18
fbiB 3640557 c.-978T>C upstream_gene_variant 1.0
fbiA 3640924 p.Ile128Leu missense_variant 0.2
fbiB 3642087 p.Asn185Tyr missense_variant 0.2
fbiB 3642336 p.Thr268Pro missense_variant 0.15
fbiB 3642483 p.Trp317Arg missense_variant 0.17
fbiB 3642562 p.Asp343Ala missense_variant 0.25
alr 3840476 c.945A>T synonymous_variant 0.25
rpoA 3878091 c.417C>T synonymous_variant 0.18
clpC1 4038599 c.2106G>A synonymous_variant 1.0
clpC1 4040209 p.Ser166Ala missense_variant 0.2
clpC1 4040249 p.Glu152Ala missense_variant 0.31
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4239883 c.21A>G synonymous_variant 0.25
embC 4240025 p.Thr55Pro missense_variant 0.22
embC 4240281 p.Val140Gly missense_variant 0.33
embC 4240583 p.Thr241Pro missense_variant 0.4
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
embC 4242995 p.Val1045Leu missense_variant 0.14
embA 4243580 c.348G>A synonymous_variant 1.0
embA 4244420 c.1188G>C synonymous_variant 1.0
embA 4245541 p.Val770Gly missense_variant 0.33
embA 4245969 p.Pro913Ser missense_variant 1.0
embA 4246329 p.Thr1033Ser missense_variant 0.25
embB 4246529 p.Ser6Arg missense_variant 0.33
embB 4247578 c.1065G>A synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4249470 p.Leu986Arg missense_variant 0.4
embB 4249574 p.Lys1021* stop_gained 0.18
aftB 4267386 p.His484Leu missense_variant 0.29
aftB 4268807 c.30G>T synonymous_variant 0.67
ubiA 4268959 p.Ile292Thr missense_variant 0.29
ubiA 4269218 p.Ile206Leu missense_variant 0.29
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ubiA 4269754 p.Val27Ala missense_variant 0.17
ubiA 4269864 c.-32delG upstream_gene_variant 1.0
ethA 4326083 p.Asp464Ala missense_variant 0.33
ethA 4326161 p.Tyr438Phe missense_variant 0.33
ethA 4327146 p.Ser110Ala missense_variant 0.13
ethA 4327225 p.Glu83Asp missense_variant 0.17
ethR 4328151 p.Asp201Glu missense_variant 0.2
whiB6 4338361 p.Arg54Gln missense_variant 1.0
whiB6 4338520 c.2T>C start_lost 0.94
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 4407873 c.330G>T synonymous_variant 1.0