TB-Profiler result

Run: ERR6336803
Summary

Run ID: ERR6336803

Sample name:

Date: 02-04-2023 02:03:54

Number of reads: 443568

Percentage reads mapped: 99.33

Strain: lineage1.2.1.2.1

Drug-resistance: Other

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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
embB 4249583 p.Asp1024Asn missense_variant 0.5 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 5468 p.Val77Ile missense_variant 0.12
gyrB 5923 c.684G>A synonymous_variant 0.2
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrB 6495 p.Ala419Glu missense_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7658 c.357A>G synonymous_variant 0.15
gyrA 8091 p.Arg264Cys missense_variant 0.15
gyrA 8113 p.Ile271Thr missense_variant 0.18
gyrA 8407 p.Gln369Arg missense_variant 0.25
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 8554 p.Arg418Gln missense_variant 0.17
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 9753 p.Asn818Tyr missense_variant 0.17
fgd1 491313 c.531C>G synonymous_variant 0.43
fgd1 491395 p.Glu205Lys missense_variant 0.17
fgd1 491411 p.Ala210Val missense_variant 0.14
fgd1 491738 p.Arg319Gln missense_variant 0.14
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575368 c.21T>C synonymous_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.25
mshA 576482 p.Val379Leu missense_variant 0.33
mshA 576498 p.Gly384Val missense_variant 0.4
ccsA 620314 c.424C>T synonymous_variant 0.13
ccsA 620320 p.Pro144Ser missense_variant 0.12
ccsA 620503 p.Glu205Lys missense_variant 0.33
ccsA 620811 c.921G>A synonymous_variant 0.13
rpoB 759836 c.31delG frameshift_variant 0.22
rpoB 760544 c.738C>T synonymous_variant 0.33
rpoB 760742 c.936G>A synonymous_variant 0.33
rpoB 760756 p.His317Arg missense_variant 0.2
rpoB 760901 c.1095C>T synonymous_variant 0.25
rpoB 762322 p.Gly839Asp missense_variant 0.2
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763353 c.-17A>T upstream_gene_variant 0.13
rpoC 763459 c.90G>A synonymous_variant 0.25
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 764138 p.Gly257Arg missense_variant 0.22
rpoC 764938 c.1569G>A synonymous_variant 0.2
rpoC 765767 p.Ile800Val missense_variant 0.13
rpoC 765903 p.Thr845Ile missense_variant 0.33
rpoC 767217 p.Tyr1283Cys missense_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776683 c.1798C>T synonymous_variant 0.14
mmpL5 776791 p.Val564Ile missense_variant 0.33
mmpL5 776821 p.Val554Ile missense_variant 0.33
mmpL5 776876 c.1605G>A synonymous_variant 0.33
mmpL5 778212 p.Ala90Glu missense_variant 0.2
mmpL5 778422 p.Ala20Val missense_variant 0.15
mmpL5 778426 p.Ala19Thr missense_variant 0.15
mmpS5 778755 p.Phe51Leu missense_variant 0.15
mmpS5 779645 c.-740C>T upstream_gene_variant 0.22
rpsL 781384 c.-176G>A upstream_gene_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303812 c.882C>T synonymous_variant 1.0
fbiC 1304322 c.1392C>T synonymous_variant 0.12
fbiC 1304575 p.Asn549Asp missense_variant 0.14
fbiC 1304731 p.Met601Val missense_variant 0.14
fbiC 1304736 c.1806G>A synonymous_variant 0.14
fbiC 1304873 p.Ser648Asn missense_variant 0.22
Rv1258c 1406312 c.1029T>C synonymous_variant 1.0
Rv1258c 1406649 p.Ile231Asn missense_variant 0.12
Rv1258c 1407058 p.Gly95Arg missense_variant 0.11
Rv1258c 1407421 c.-81A>T upstream_gene_variant 0.29
embR 1416316 c.1032C>A synonymous_variant 0.15
embR 1416848 p.Val167Glu missense_variant 0.22
embR 1416916 c.432A>G synonymous_variant 0.13
embR 1417019 p.Cys110Tyr missense_variant 1.0
atpE 1460861 c.-184C>T upstream_gene_variant 0.14
atpE 1460907 c.-138T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471759 n.-87A>G upstream_gene_variant 0.14
rrs 1471768 n.-78T>C upstream_gene_variant 0.12
rrs 1472717 n.872C>T non_coding_transcript_exon_variant 0.14
rrl 1473516 n.-142G>T upstream_gene_variant 0.25
rrl 1474425 n.768A>G non_coding_transcript_exon_variant 0.25
rrl 1474428 n.771C>T non_coding_transcript_exon_variant 0.29
rrl 1475226 n.1569C>T non_coding_transcript_exon_variant 0.17
rrl 1475250 n.1593C>T non_coding_transcript_exon_variant 0.2
rrl 1475478 n.1821G>A non_coding_transcript_exon_variant 0.18
rrl 1475711 n.2054T>C non_coding_transcript_exon_variant 0.22
rrl 1475744 n.2087A>G non_coding_transcript_exon_variant 0.29
rrl 1476274 n.2617G>A non_coding_transcript_exon_variant 0.18
fabG1 1673251 c.-189T>A upstream_gene_variant 0.18
inhA 1673718 c.-484G>T upstream_gene_variant 0.2
inhA 1674162 c.-40C>T upstream_gene_variant 1.0
rpsA 1834060 c.519C>T synonymous_variant 0.15
rpsA 1834330 c.789C>T synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918215 c.276G>A synonymous_variant 0.25
tlyA 1918367 p.Ala143Val missense_variant 0.25
tlyA 1918670 p.Arg244His missense_variant 0.18
ndh 2102221 c.821delA frameshift_variant 0.2
ndh 2102659 c.384C>T synonymous_variant 0.22
katG 2154056 p.Lys686Glu missense_variant 0.15
katG 2154271 p.Ala614Val missense_variant 0.22
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155107 c.1005C>T synonymous_variant 0.12
katG 2155785 c.327T>G synonymous_variant 0.4
katG 2156215 c.-104G>A upstream_gene_variant 0.15
katG 2156360 c.-249T>C upstream_gene_variant 0.15
katG 2156364 c.-253T>G upstream_gene_variant 0.17
katG 2156501 c.-390C>T upstream_gene_variant 0.2
PPE35 2167693 p.Gly974Ser missense_variant 1.0
PPE35 2167836 p.Gly926Glu missense_variant 0.18
PPE35 2167898 c.2715G>A synonymous_variant 0.13
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168079 p.Thr845Ile missense_variant 0.12
PPE35 2169003 p.Leu537Ser missense_variant 0.29
PPE35 2169466 p.Asn383Asp missense_variant 0.5
PPE35 2170223 c.390T>C synonymous_variant 0.38
PPE35 2170678 c.-66C>T upstream_gene_variant 0.14
Rv1979c 2221820 p.Ile449Phe missense_variant 0.18
Rv1979c 2222169 c.996C>T synonymous_variant 0.2
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222336 p.Leu277Phe missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288905 p.Gly113Ser missense_variant 0.14
pncA 2289102 p.Thr47Ile missense_variant 0.15
pncA 2289541 c.-300G>A upstream_gene_variant 0.12
pncA 2289897 c.-656G>T upstream_gene_variant 0.13
pncA 2289987 c.-746C>T upstream_gene_variant 0.22
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518322 p.Ser70Gly missense_variant 0.17
kasA 2519048 p.Gly312Ser missense_variant 1.0
kasA 2519076 p.Ala321Val missense_variant 0.22
eis 2714207 p.Arg376Cys missense_variant 0.2
eis 2714501 c.832C>T synonymous_variant 0.2
eis 2714528 p.Thr269Ser missense_variant 0.22
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726515 c.326delC frameshift_variant 0.22
ahpC 2726670 p.Glu160Gln missense_variant 0.18
folC 2746147 c.1452T>C synonymous_variant 0.14
pepQ 2859914 p.Glu169Lys missense_variant 0.22
Rv2752c 3065220 c.972C>T synonymous_variant 0.14
Rv2752c 3065398 p.Ser265Leu missense_variant 0.14
Rv2752c 3065646 c.546C>T synonymous_variant 0.29
Rv2752c 3066035 p.Asp53Asn missense_variant 0.2
thyX 3067661 c.285C>T synonymous_variant 0.14
thyA 3074367 c.105C>G synonymous_variant 0.2
thyA 3074567 c.-96C>T upstream_gene_variant 0.13
thyA 3074594 c.-123C>T upstream_gene_variant 1.0
ald 3086769 c.-50delT upstream_gene_variant 0.29
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087313 p.Gly165Val missense_variant 0.15
ald 3087615 p.Asp266Asn missense_variant 0.17
fbiD 3339155 p.Ile13Thr missense_variant 0.2
fbiD 3339222 c.105C>T synonymous_variant 0.17
fbiD 3339264 c.147C>T synonymous_variant 0.18
fbiD 3339327 c.210T>A synonymous_variant 0.14
fbiD 3339417 c.300A>G synonymous_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.5
Rv3083 3448454 c.-50C>T upstream_gene_variant 0.15
Rv3083 3448707 c.204G>A synonymous_variant 0.17
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3448758 c.255C>T synonymous_variant 0.17
Rv3083 3449134 p.Gln211* stop_gained 0.22
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3474646 p.Glu214Lys missense_variant 0.14
fprA 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3612338 p.Arg260His missense_variant 0.12
Rv3236c 3612816 p.Ala101Thr missense_variant 0.22
fbiB 3640557 c.-978T>C upstream_gene_variant 1.0
fbiB 3642180 p.Val216Met missense_variant 0.18
fbiB 3642513 p.Pro327Ala missense_variant 0.15
fbiB 3642525 p.Ile331Val missense_variant 0.2
alr 3840227 c.1194C>T synonymous_variant 0.15
alr 3840323 c.1098C>T synonymous_variant 0.2
alr 3840630 p.Pro264Leu missense_variant 0.29
ddn 3987044 c.201G>C synonymous_variant 0.22
ddn 3987050 c.207C>T synonymous_variant 0.25
clpC1 4040014 p.Gln231* stop_gained 0.22
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4239847 c.-16C>T upstream_gene_variant 0.25
embC 4240038 p.Leu59Ser missense_variant 0.14
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4240932 p.Trp357* stop_gained 0.17
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4242209 p.Glu783Lys missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243034 p.Gly1058Ser missense_variant 0.22
embA 4243304 c.73delC frameshift_variant 0.2
embA 4243580 c.348G>A synonymous_variant 1.0
embA 4244019 p.Leu263Val missense_variant 0.4
embA 4244420 c.1188G>C synonymous_variant 1.0
embA 4244995 p.Thr588Ile missense_variant 0.25
embA 4245753 p.Gly841Ser missense_variant 0.17
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.5
embB 4246548 p.Pro12Gln missense_variant 0.6
embB 4246555 c.42G>C synonymous_variant 0.43
embB 4246556 p.Ala15Pro missense_variant 0.43
embB 4247123 p.Ala204Thr missense_variant 0.5
embB 4247578 c.1065G>A synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4247679 p.Met389Thr missense_variant 0.11
embB 4248324 p.Ala604Gly missense_variant 0.38
embB 4248913 p.Glu800Asp missense_variant 0.17
embB 4248979 c.2466G>A synonymous_variant 0.12
embB 4249026 p.Asp838Gly missense_variant 0.13
aftB 4267392 p.Pro482Leu missense_variant 0.13
aftB 4267589 p.Gln416His missense_variant 0.2
aftB 4268064 p.Ser258Trp missense_variant 0.14
aftB 4268826 c.10dupG frameshift_variant 0.13
ubiA 4269387 p.Glu149Asp missense_variant 1.0
ubiA 4269436 c.397delG frameshift_variant 0.22
ubiA 4269445 p.Val130Gly missense_variant 0.22
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ubiA 4269773 p.Ile21Val missense_variant 0.11
ubiA 4269864 c.-32delG upstream_gene_variant 1.0
ethA 4326379 c.1095G>A synonymous_variant 0.14
ethA 4326605 p.Asp290Gly missense_variant 0.18
ethA 4327359 p.Glu39Lys missense_variant 0.29
ethA 4328187 c.-714G>A upstream_gene_variant 0.25
ethA 4328193 c.-720G>A upstream_gene_variant 0.33
whiB6 4338214 p.Gly103Asp missense_variant 0.25
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 4407626 p.Ala193Thr missense_variant 0.14
gid 4407873 c.330G>T synonymous_variant 1.0
gid 4408004 p.Asp67Tyr missense_variant 0.17
gid 4408044 c.159C>T synonymous_variant 0.14
gid 4408170 p.Ile11Met missense_variant 1.0