TB-Profiler result

Run: ERR6336756
Summary

Run ID: ERR6336756

Sample name:

Date: 02-04-2023 02:02:24

Number of reads: 2195848

Percentage reads mapped: 98.93

Strain:

Drug-resistance: Sensitive

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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
lineage1.2.1.2.1 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
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 7617 p.Arg106Cys missense_variant 0.13
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9109 p.Gln603Arg missense_variant 0.11
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 9671 p.Gln790His missense_variant 0.12
fgd1 491337 c.555C>T synonymous_variant 0.15
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575169 c.-179A>G upstream_gene_variant 0.12
mshA 575172 c.-176C>G upstream_gene_variant 0.12
mshA 575310 c.-38G>A upstream_gene_variant 0.22
mshA 575368 c.21T>C synonymous_variant 1.0
mshA 576283 c.936G>C synonymous_variant 0.22
mshA 576401 p.Ser352Pro missense_variant 0.18
mshA 576665 p.Ser440Gly missense_variant 0.22
mshA 576729 p.Ser461Leu missense_variant 0.25
ccsA 620056 p.Thr56Pro missense_variant 0.4
rpoB 761373 p.Val523Met missense_variant 0.14
rpoB 761688 p.Ala628Thr missense_variant 0.33
rpoB 761704 p.Gly633Asp missense_variant 0.17
rpoB 761846 c.2040G>A synonymous_variant 0.17
rpoB 762294 p.Ser830Pro missense_variant 0.15
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 764669 p.Pro434Ser missense_variant 0.12
mmpL5 775626 p.Trp952Ser missense_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775640 c.2841C>A synonymous_variant 0.15
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776303 c.2177delC frameshift_variant 0.22
mmpL5 777370 p.Lys371Gln missense_variant 0.29
mmpL5 777886 p.Ala199Thr missense_variant 0.12
mmpR5 778055 c.-935G>A upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304044 p.Pro372Ser missense_variant 0.33
fbiC 1304377 c.1447C>T synonymous_variant 0.2
Rv1258c 1406312 c.1029T>C synonymous_variant 1.0
embR 1416441 c.907C>T synonymous_variant 0.2
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 0.99
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 1.0
fabG1 1673558 p.His40Arg missense_variant 0.4
inhA 1673602 c.-600C>T upstream_gene_variant 0.12
inhA 1674162 c.-40C>T upstream_gene_variant 1.0
inhA 1674724 p.Val175Met missense_variant 0.12
rpsA 1833779 p.Val80Leu missense_variant 1.0
tlyA 1917937 c.-3G>A upstream_gene_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918216 p.Thr93Ser missense_variant 0.2
tlyA 1918366 p.Ala143Pro missense_variant 0.15
ndh 2102412 p.Val211Met missense_variant 0.25
ndh 2102429 p.Asp205Ala missense_variant 0.27
ndh 2102430 c.612_613insA frameshift_variant 0.2
ndh 2102440 c.603C>T synonymous_variant 0.17
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155281 c.831C>A synonymous_variant 0.22
katG 2155407 c.705G>C synonymous_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170476 p.Gly46Asp missense_variant 0.2
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 2518588 c.474T>C synonymous_variant 0.11
kasA 2518897 c.783G>A synonymous_variant 0.13
kasA 2519048 p.Gly312Ser missense_variant 1.0
eis 2714781 c.552G>A synonymous_variant 0.5
eis 2714794 p.Glu180Gly missense_variant 0.4
eis 2714980 p.Leu118Pro missense_variant 0.18
eis 2715179 p.Ala52Pro missense_variant 0.12
ahpC 2726017 c.-176C>T upstream_gene_variant 0.14
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2746167 p.Ala478Thr missense_variant 0.12
folC 2746934 p.Arg222Gln missense_variant 0.33
folC 2747340 p.Thr87Ala missense_variant 0.25
folC 2747472 c.125_126delGC frameshift_variant 0.13
folC 2747779 c.-181G>A upstream_gene_variant 0.5
pepQ 2859694 p.Ala242Val missense_variant 0.14
ribD 2987106 p.Ile90Val missense_variant 0.12
Rv2752c 3064672 p.Ala507Gly missense_variant 0.12
Rv2752c 3064709 p.Arg495Trp missense_variant 0.15
Rv2752c 3066320 c.-129A>G upstream_gene_variant 0.2
thyX 3067229 c.717C>T synonymous_variant 0.67
thyX 3067336 p.Ala204Pro missense_variant 0.12
thyX 3067595 c.351C>T synonymous_variant 0.14
thyX 3067913 c.33G>C synonymous_variant 0.29
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086997 p.Thr60Gly missense_variant 0.29
ald 3087805 p.Trp329* stop_gained 0.17
fbiD 3339128 p.Thr4Ile missense_variant 0.12
fbiD 3339417 c.300A>G synonymous_variant 1.0
fbiD 3339556 p.Gly147Ser missense_variant 0.33
fbiD 3339728 p.Gly204Glu missense_variant 0.29
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449052 c.549C>T synonymous_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3474701 c.696delC frameshift_variant 0.14
fprA 3475039 p.Gly345Ser missense_variant 0.17
fprA 3475159 p.Asn385Asp missense_variant 1.0
fprA 3475263 c.1257G>A synonymous_variant 0.13
whiB7 3568488 c.191delG frameshift_variant 1.0
Rv3236c 3611999 p.Thr373Cys missense_variant 0.17
Rv3236c 3612187 p.Met310Ile missense_variant 0.25
fbiB 3640557 c.-978T>C upstream_gene_variant 1.0
fbiB 3640588 c.-947C>T upstream_gene_variant 0.22
fbiB 3640614 c.-921C>T upstream_gene_variant 0.17
fbiA 3640655 p.Asp38Ala missense_variant 0.14
fbiA 3640829 p.Gly96Asp missense_variant 0.12
fbiA 3640864 p.Asp108Asn missense_variant 0.17
fbiB 3640915 c.-620C>T upstream_gene_variant 0.15
fbiA 3640951 p.Gln137* stop_gained 0.13
fbiA 3641333 p.Gly264Ala missense_variant 0.12
fbiA 3641340 p.Asp266Glu missense_variant 0.12
fbiB 3642134 c.600G>T synonymous_variant 0.2
fbiB 3642396 p.Ala288Thr missense_variant 0.5
fbiB 3642412 p.Arg293Gln missense_variant 0.14
fbiB 3642674 c.1140C>T synonymous_variant 0.25
rpoA 3877850 p.Gly220Ser missense_variant 0.17
rpoA 3878567 c.-60C>G upstream_gene_variant 0.44
rpoA 3878578 c.-71C>A upstream_gene_variant 0.29
rpoA 3878627 c.-120T>G upstream_gene_variant 0.29
rpoA 3878639 c.-132C>G upstream_gene_variant 0.6
clpC1 4038222 p.Ala828Asp missense_variant 0.22
clpC1 4040066 c.639G>A synonymous_variant 0.13
clpC1 4040233 p.Arg158Cys missense_variant 0.29
clpC1 4040286 p.Gln140Arg missense_variant 0.22
clpC1 4040327 p.Lys126Asn missense_variant 0.15
clpC1 4040517 p.Val63Ala missense_variant 1.0
panD 4044477 c.-196T>C upstream_gene_variant 0.33
embC 4239821 c.-42C>T upstream_gene_variant 0.12
embC 4240308 c.448_449delCC frameshift_variant 0.29
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241493 p.Leu544Pro missense_variant 0.14
embC 4241503 c.1643_1644delTG frameshift_variant 0.11
embA 4242430 c.-803C>G upstream_gene_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243478 c.246G>A synonymous_variant 0.4
embA 4243580 c.348G>A synonymous_variant 1.0
embA 4243763 c.531G>T synonymous_variant 0.17
embA 4243764 p.Lys178Gln missense_variant 0.17
embA 4243772 c.540A>T synonymous_variant 0.17
embA 4243860 p.Gly210Ser missense_variant 0.18
embA 4244184 p.Ser318Leu missense_variant 0.14
embA 4244194 p.Gly321Ala missense_variant 0.11
embA 4244207 c.975C>T synonymous_variant 0.17
embA 4244320 p.Thr363Ile missense_variant 0.13
embA 4244420 c.1188G>C synonymous_variant 1.0
embA 4245441 p.Asp737Asn missense_variant 0.14
embA 4245835 p.Leu868Pro missense_variant 0.18
embB 4245842 c.-672G>T upstream_gene_variant 0.15
embA 4245846 p.Ser872Pro missense_variant 0.13
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.4
embB 4246548 p.Pro12Gln missense_variant 0.46
embB 4246555 c.42G>C synonymous_variant 0.45
embB 4246556 p.Ala15Pro missense_variant 0.45
embB 4246563 p.Leu17Trp missense_variant 0.47
embB 4246567 c.54G>T synonymous_variant 0.45
embB 4246591 c.78G>A synonymous_variant 0.13
embB 4246694 c.181C>A synonymous_variant 0.4
embB 4246942 c.429G>A synonymous_variant 0.14
embB 4246953 p.Arg147His missense_variant 0.12
embB 4246959 p.Glu149Gly missense_variant 0.11
embB 4247172 p.Leu220Gln missense_variant 0.5
embB 4247578 c.1065G>A synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4247867 p.Val452Met missense_variant 0.33
embB 4247950 c.1437G>A synonymous_variant 0.14
embB 4248338 p.Leu609Met missense_variant 0.12
embB 4248343 c.1831delA frameshift_variant 0.12
aftB 4268543 c.294C>T synonymous_variant 0.4
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ubiA 4269727 c.106_107insTG frameshift_variant 0.25
ubiA 4269733 p.Ala34Asp missense_variant 0.25
ubiA 4269864 c.-32delG upstream_gene_variant 1.0
ethA 4327647 c.-174G>C upstream_gene_variant 0.11
ethA 4328413 c.-940C>T upstream_gene_variant 0.22
ethA 4328436 c.-963G>C upstream_gene_variant 1.0
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 0.93
gid 4407873 c.330G>T synonymous_variant 1.0
gid 4408114 p.Gly30Val missense_variant 0.2
gid 4408122 c.81G>A synonymous_variant 0.18