TB-Profiler result

Run: ERR9901856
Summary

Run ID: ERR9901856

Sample name:

Date: 02-04-2023 13:33:43

Number of reads: 295072

Percentage reads mapped: 99.12

Strain: lineage1.1.2

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
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 1.0
lineage1.1.2 Indo-Oceanic EAI3;EAI5 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
rpsA 1834962 p.Arg474Leu missense_variant 0.18 pyrazinamide
tlyA 1917991 p.Arg18* stop_gained 0.29 capreomycin
katG 2155193 p.Gly307Arg missense_variant 0.18 isoniazid
pncA 2289073 p.His57Asn missense_variant 0.18 pyrazinamide
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 5660 p.Arg141Ser missense_variant 0.17
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrB 6124 c.885C>T synonymous_variant 1.0
gyrA 6904 c.-398C>A upstream_gene_variant 0.22
gyrB 7118 p.Asp627Tyr missense_variant 0.17
gyrA 7153 c.-149G>T upstream_gene_variant 0.29
gyrA 7264 c.-38C>A upstream_gene_variant 0.2
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7961 p.Met220Ile missense_variant 0.25
gyrA 8400 p.Asp367Tyr missense_variant 0.18
gyrA 8406 p.Gln369Lys missense_variant 0.36
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 8577 p.Asp426Tyr missense_variant 0.2
gyrA 8607 p.Leu436Met missense_variant 0.22
gyrA 8649 p.Arg450Cys missense_variant 0.29
gyrA 8763 p.Asp488Tyr missense_variant 0.29
gyrA 8922 p.Gly541Cys missense_variant 0.25
gyrA 8936 p.Gln545His missense_variant 0.17
gyrA 8958 p.Asp553Tyr missense_variant 0.22
gyrA 9058 p.Glu586Ala missense_variant 0.13
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9215 c.1914C>A synonymous_variant 0.2
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9350 p.Phe683Leu missense_variant 0.2
gyrA 9359 c.2058C>A synonymous_variant 0.22
gyrA 9536 c.2235C>T synonymous_variant 0.22
gyrA 9560 c.2259C>A synonymous_variant 0.25
gyrA 9768 p.Gly823Cys missense_variant 0.29
gyrA 9785 c.2484G>T synonymous_variant 0.22
fgd1 490676 c.-107G>A upstream_gene_variant 0.2
fgd1 490815 c.33G>T synonymous_variant 0.29
fgd1 490870 p.His30Asn missense_variant 0.25
fgd1 490993 p.Gly71Cys missense_variant 0.17
fgd1 491132 p.Gly117Val missense_variant 0.18
fgd1 491139 p.Glu119Asp missense_variant 0.55
fgd1 491256 p.Lys158Asn missense_variant 0.33
fgd1 491307 c.525C>A synonymous_variant 0.4
fgd1 491325 c.543G>T synonymous_variant 0.29
fgd1 491485 p.Tyr235His missense_variant 0.25
fgd1 491493 c.713_724delACCCGGAGCTGG disruptive_inframe_deletion 0.4
fgd1 491575 p.Pro265Thr missense_variant 0.2
fgd1 491581 p.Glu267* stop_gained 0.2
fgd1 491704 p.Leu308Met missense_variant 0.17
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575188 c.-160G>T upstream_gene_variant 0.18
mshA 575378 p.Gly11Trp missense_variant 0.2
mshA 575745 p.Ala133Asp missense_variant 0.33
mshA 575773 c.426C>A synonymous_variant 0.4
mshA 575831 p.Gly162Cys missense_variant 0.33
mshA 575951 p.Gly202Trp missense_variant 0.25
mshA 576246 p.Gly300Val missense_variant 0.4
mshA 576278 p.Gly311* stop_gained 0.33
mshA 576394 c.1047G>T synonymous_variant 0.2
mshA 576484 c.1137C>A synonymous_variant 0.2
mshA 576520 c.1173C>A synonymous_variant 0.2
mshA 576577 c.1230C>A synonymous_variant 0.29
mshA 576758 p.His471Asn missense_variant 0.29
ccsA 619754 c.-137C>A upstream_gene_variant 0.5
ccsA 619789 c.-102G>T upstream_gene_variant 0.29
ccsA 619802 c.-89G>T upstream_gene_variant 0.29
ccsA 620008 p.Arg40Ser missense_variant 0.33
ccsA 620155 p.Gly89Trp missense_variant 0.33
ccsA 620175 c.285C>A synonymous_variant 0.25
ccsA 620249 p.Ser120Tyr missense_variant 0.18
ccsA 620251 p.Gly121Trp missense_variant 0.18
ccsA 620263 p.Gly125Cys missense_variant 0.2
ccsA 620319 c.429C>A synonymous_variant 0.2
ccsA 620563 p.Leu225Met missense_variant 0.31
ccsA 620603 p.Pro238His missense_variant 0.31
rpoB 760250 p.Met148Ile missense_variant 0.2
rpoB 760490 c.684C>T synonymous_variant 1.0
rpoB 760604 p.Glu266Asp missense_variant 0.17
rpoB 760640 c.834C>A synonymous_variant 0.17
rpoB 760768 p.Pro321His missense_variant 0.18
rpoB 760838 p.Glu344Asp missense_variant 0.25
rpoB 760991 c.1185G>T synonymous_variant 0.25
rpoB 761129 c.1323G>T synonymous_variant 0.29
rpoB 761212 p.Val469Glu missense_variant 0.2
rpoB 761218 p.Pro471Gln missense_variant 0.2
rpoB 761233 p.Arg476Leu missense_variant 0.2
rpoB 761240 p.Cys478* stop_gained 0.18
rpoB 761787 c.1981C>A synonymous_variant 0.29
rpoB 761821 p.Ser672Tyr missense_variant 0.25
rpoB 762109 p.Pro768Gln missense_variant 0.4
rpoB 762164 c.2358C>A synonymous_variant 0.29
rpoB 762825 p.Gly1007Trp missense_variant 0.33
rpoC 762959 c.-411G>T upstream_gene_variant 0.22
rpoB 762963 p.Gly1053Cys missense_variant 0.22
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763785 p.Val139Ala missense_variant 0.15
rpoC 763834 p.Met155Ile missense_variant 0.25
rpoC 763841 p.Glu158* stop_gained 0.25
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 763986 p.Arg206His missense_variant 0.22
rpoC 764021 c.652C>A synonymous_variant 0.18
rpoC 764062 c.693C>A synonymous_variant 0.19
rpoC 764128 c.759C>A synonymous_variant 0.18
rpoC 764243 c.877delC frameshift_variant 0.11
rpoC 764443 c.1074C>A synonymous_variant 0.2
rpoC 764693 p.Gly442Cys missense_variant 0.2
rpoC 764713 c.1344G>T synonymous_variant 0.22
rpoC 764730 p.Pro454Gln missense_variant 0.22
rpoC 764875 c.1506C>A synonymous_variant 0.22
rpoC 765145 c.1776C>A synonymous_variant 0.4
rpoC 765171 p.Pro601Leu missense_variant 1.0
rpoC 765210 p.Ser614* stop_gained 0.22
rpoC 765483 p.Pro705Gln missense_variant 0.22
rpoC 765508 c.2139C>A synonymous_variant 0.67
rpoC 765604 c.2235C>A synonymous_variant 0.25
rpoC 765656 p.Gly763Cys missense_variant 0.25
rpoC 765683 p.Glu772* stop_gained 0.2
rpoC 765738 p.Arg790Leu missense_variant 0.29
rpoC 765805 c.2436C>A synonymous_variant 0.29
rpoC 765813 p.Arg815Gln missense_variant 0.29
rpoC 766038 p.Asp890Val missense_variant 0.33
rpoC 766105 c.2736C>A synonymous_variant 0.33
rpoC 766511 p.Asp1048Tyr missense_variant 0.22
rpoC 766588 p.Glu1073Asp missense_variant 0.17
rpoC 766864 c.3495G>T synonymous_variant 0.31
rpoC 766951 c.3582G>T synonymous_variant 0.25
rpoC 766952 p.Ala1195Ser missense_variant 0.25
rpoC 766964 p.Glu1199* stop_gained 0.25
rpoC 766968 p.Pro1200His missense_variant 0.25
rpoC 767309 p.Asp1314Tyr missense_variant 0.5
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776323 p.Ile720Val missense_variant 0.22
mmpL5 776344 p.Gly713Trp missense_variant 0.29
mmpL5 776371 p.Gly704Cys missense_variant 0.25
mmpL5 776395 p.Phe696Leu missense_variant 1.0
mmpL5 776468 p.Glu671Asp missense_variant 0.29
mmpL5 776500 p.Gly661Trp missense_variant 0.17
mmpL5 776584 p.Gln633Lys missense_variant 0.22
mmpL5 776785 p.Glu566* stop_gained 0.18
mmpL5 776807 c.1674G>T synonymous_variant 0.29
mmpL5 776810 p.Met557Ile missense_variant 0.29
mmpL5 777263 c.1218G>T synonymous_variant 0.29
mmpL5 777425 c.1056C>A synonymous_variant 0.67
mmpL5 777907 p.Leu192Met missense_variant 0.18
mmpR5 777998 c.-992C>A upstream_gene_variant 0.29
mmpL5 778018 p.Gly155Cys missense_variant 0.22
mmpL5 778276 p.Ala69Ser missense_variant 0.14
mmpS5 778646 p.Pro87Gln missense_variant 0.22
mmpL5 778963 c.-483G>T upstream_gene_variant 0.25
mmpL5 779049 c.-569G>T upstream_gene_variant 0.4
mmpL5 779101 c.-621G>T upstream_gene_variant 0.25
mmpS5 779675 c.-770G>T upstream_gene_variant 0.33
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781861 p.Ser101* stop_gained 0.25
rpsL 781895 p.Gln112His missense_variant 0.25
rplC 800708 c.-101C>A upstream_gene_variant 0.22
rplC 800767 c.-42C>A upstream_gene_variant 0.18
rplC 800799 c.-10G>T upstream_gene_variant 0.2
rplC 801100 p.Gly98Trp missense_variant 0.18
rplC 801145 p.Asp113Tyr missense_variant 0.4
rplC 801252 c.444G>T synonymous_variant 0.2
fbiC 1303091 p.Glu54Val missense_variant 0.2
fbiC 1303548 c.618G>T synonymous_variant 0.2
fbiC 1303686 c.756C>A synonymous_variant 0.18
fbiC 1303713 c.783C>A synonymous_variant 0.2
fbiC 1303979 p.Gly350Val missense_variant 0.17
fbiC 1304475 c.1545G>T synonymous_variant 0.5
fbiC 1304547 c.1617C>A synonymous_variant 0.5
fbiC 1304790 c.1860C>A synonymous_variant 0.18
fbiC 1304825 p.Ala632Glu missense_variant 0.33
fbiC 1304834 p.Pro635Gln missense_variant 0.33
fbiC 1304871 c.1941G>T synonymous_variant 0.2
fbiC 1304902 p.Glu658* stop_gained 0.2
fbiC 1305018 c.2088C>A synonymous_variant 0.18
fbiC 1305108 c.2178G>T synonymous_variant 0.22
fbiC 1305458 p.Pro843Gln missense_variant 0.22
Rv1258c 1406361 p.Pro327His missense_variant 0.33
Rv1258c 1406376 p.Gly322Val missense_variant 0.25
Rv1258c 1406515 p.Leu276Met missense_variant 0.29
Rv1258c 1406709 p.Gly211Val missense_variant 0.25
Rv1258c 1406725 p.Gln206Lys missense_variant 0.4
Rv1258c 1406928 p.Ser138* stop_gained 0.2
Rv1258c 1407072 p.Pro90His missense_variant 0.29
Rv1258c 1407116 p.Ser75Tyr missense_variant 0.22
Rv1258c 1407133 p.Gly70Trp missense_variant 0.18
embR 1416539 p.Ala270Asp missense_variant 0.15
embR 1416742 c.606C>A synonymous_variant 0.22
embR 1416829 c.519C>G synonymous_variant 0.67
embR 1417019 p.Cys110Tyr missense_variant 1.0
embR 1417030 c.318C>A synonymous_variant 0.29
embR 1417079 p.Pro90Gln missense_variant 0.25
embR 1417113 p.Leu79Met missense_variant 0.29
embR 1417131 p.His73Asn missense_variant 0.22
embR 1417164 p.Glu62* stop_gained 0.18
embR 1417173 p.Leu59Ile missense_variant 0.27
embR 1417186 c.162C>A synonymous_variant 0.22
embR 1417400 c.-53C>T upstream_gene_variant 0.2
embR 1417403 c.-56G>T upstream_gene_variant 0.2
embR 1417477 c.-130C>A upstream_gene_variant 0.33
embR 1417484 c.-137C>A upstream_gene_variant 0.25
embR 1417522 c.-175C>A upstream_gene_variant 0.2
atpE 1461051 p.Pro3Thr missense_variant 0.2
atpE 1461145 p.Ala34Glu missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472745 n.900A>G non_coding_transcript_exon_variant 0.11
rrs 1472765 n.920G>T non_coding_transcript_exon_variant 0.18
rrl 1474841 n.1184G>A non_coding_transcript_exon_variant 0.25
rrl 1474842 n.1185G>T non_coding_transcript_exon_variant 0.25
rrl 1474923 n.1266G>T non_coding_transcript_exon_variant 0.18
rrl 1475034 n.1377G>T non_coding_transcript_exon_variant 0.17
rrl 1475097 n.1440G>T non_coding_transcript_exon_variant 0.18
rrl 1475102 n.1445C>A non_coding_transcript_exon_variant 0.18
rrl 1475262 n.1605G>T non_coding_transcript_exon_variant 0.21
rrl 1476265 n.2608G>T non_coding_transcript_exon_variant 0.17
rrl 1476337 n.2680C>A non_coding_transcript_exon_variant 0.4
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.2
rrl 1476777 n.3120C>A non_coding_transcript_exon_variant 0.18
fabG1 1673192 c.-248C>A upstream_gene_variant 0.18
fabG1 1673361 c.-79C>A upstream_gene_variant 0.29
fabG1 1673375 c.-65A>G upstream_gene_variant 0.22
fabG1 1673504 p.Gly22Val missense_variant 0.25
fabG1 1673587 p.Gly50* stop_gained 0.29
inhA 1673640 c.-562C>A upstream_gene_variant 0.22
fabG1 1673646 p.Asp69Glu missense_variant 0.2
fabG1 1673828 p.Asn130Ser missense_variant 0.18
fabG1 1673936 p.Ser166* stop_gained 0.33
inhA 1673991 c.-211C>A upstream_gene_variant 0.29
fabG1 1674040 p.Gly201Trp missense_variant 0.25
inhA 1674469 p.Gly90Trp missense_variant 0.3
inhA 1674693 c.492C>A synonymous_variant 0.18
inhA 1674750 c.549T>C synonymous_variant 0.14
inhA 1674861 p.Glu220Asp missense_variant 0.2
inhA 1674880 p.Pro227Thr missense_variant 0.2
inhA 1674918 c.717C>A synonymous_variant 0.33
inhA 1674959 p.Thr253Asn missense_variant 0.25
rpsA 1833432 c.-110C>A upstream_gene_variant 0.18
rpsA 1833514 c.-28C>A upstream_gene_variant 0.33
rpsA 1834175 c.634C>A synonymous_variant 0.22
rpsA 1834192 c.651C>A synonymous_variant 0.22
rpsA 1834194 p.Ser218* stop_gained 0.29
rpsA 1834256 p.Glu239* stop_gained 0.33
rpsA 1834349 p.Glu270* stop_gained 0.18
rpsA 1834385 p.Asp282Tyr missense_variant 0.17
rpsA 1834435 c.894G>T synonymous_variant 0.22
rpsA 1834462 p.Phe307Leu missense_variant 0.33
rpsA 1834870 c.1329C>T synonymous_variant 0.25
tlyA 1917776 c.-164G>T upstream_gene_variant 0.25
tlyA 1917786 c.-154G>A upstream_gene_variant 0.25
tlyA 1917839 c.-101_-100insC upstream_gene_variant 0.5
tlyA 1917891 c.-49G>T upstream_gene_variant 0.4
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918285 p.Gly116Cys missense_variant 0.22
tlyA 1918326 c.387G>T synonymous_variant 0.2
tlyA 1918387 p.Leu150Met missense_variant 0.18
tlyA 1918402 p.Leu155Met missense_variant 0.18
tlyA 1918621 p.Ser228Gly missense_variant 0.11
tlyA 1918737 p.Glu266Asp missense_variant 0.18
ndh 2101679 p.Ser455* stop_gained 0.25
ndh 2101717 c.1326C>A synonymous_variant 0.25
ndh 2102065 c.978G>T synonymous_variant 0.22
ndh 2102121 p.Asp308Tyr missense_variant 0.22
ndh 2102138 p.Arg302Leu missense_variant 0.2
ndh 2102172 p.Glu291* stop_gained 0.25
ndh 2102292 p.Asp251Tyr missense_variant 0.29
ndh 2102293 c.750C>A synonymous_variant 0.29
ndh 2102766 p.Asp93Tyr missense_variant 0.33
ndh 2102830 c.213G>T synonymous_variant 0.18
ndh 2102944 c.99C>A synonymous_variant 0.18
ndh 2102971 p.Phe24Leu missense_variant 0.22
ndh 2103023 p.Pro7His missense_variant 0.33
ndh 2103033 p.Gln4Lys missense_variant 0.33
ndh 2103131 c.-89C>A upstream_gene_variant 0.17
ndh 2103242 c.-200A>G upstream_gene_variant 0.33
katG 2153909 p.Asp735Tyr missense_variant 0.18
katG 2153945 p.Asp723Tyr missense_variant 0.18
katG 2153999 p.Arg705Trp missense_variant 0.2
katG 2154030 c.2082G>T synonymous_variant 0.18
katG 2154034 p.Arg693Leu missense_variant 0.18
katG 2154150 c.1962C>A synonymous_variant 0.67
katG 2154212 p.Leu634Ile missense_variant 0.29
katG 2154414 c.1698C>A synonymous_variant 0.18
katG 2154564 p.Lys516Asn missense_variant 0.17
katG 2154577 p.Gly512Val missense_variant 0.2
katG 2154598 p.Trp505Leu missense_variant 0.25
katG 2154723 p.Arg463Leu missense_variant 0.33
katG 2154761 p.Gly451Ser missense_variant 0.25
katG 2154938 p.Arg392Trp missense_variant 0.22
katG 2155018 p.Pro365Gln missense_variant 0.25
katG 2155090 p.Trp341Leu missense_variant 0.17
katG 2155177 p.Ala312Glu missense_variant 0.17
katG 2155254 c.858C>A synonymous_variant 0.25
katG 2155471 p.Arg214Leu missense_variant 0.18
katG 2155662 c.450G>A synonymous_variant 0.22
katG 2155816 p.Gly99Val missense_variant 0.5
katG 2155871 p.Glu81* stop_gained 0.5
katG 2156106 c.6C>A synonymous_variant 0.22
katG 2156123 c.-12G>T upstream_gene_variant 0.25
katG 2156341 c.-230G>T upstream_gene_variant 0.25
katG 2156488 c.-377C>A upstream_gene_variant 0.25
katG 2156536 c.-425C>A upstream_gene_variant 0.22
PPE35 2167666 p.Gln983Lys missense_variant 0.25
PPE35 2167679 c.2934G>T synonymous_variant 0.2
PPE35 2167790 p.Ser941* stop_gained 0.25
PPE35 2167801 p.Gly938Cys missense_variant 0.22
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2168021 c.2592C>A synonymous_variant 0.18
PPE35 2168186 c.2427C>T synonymous_variant 0.18
PPE35 2168189 c.2424T>G synonymous_variant 0.18
PPE35 2168222 c.2391G>T synonymous_variant 0.25
PPE35 2168275 p.Thr780Ala missense_variant 0.14
PPE35 2169827 c.786G>T synonymous_variant 0.21
PPE35 2169970 p.Gly215Cys missense_variant 0.33
PPE35 2169976 p.Gly213Cys missense_variant 0.33
PPE35 2170097 c.516G>T synonymous_variant 0.33
PPE35 2170150 p.His155Asn missense_variant 0.22
PPE35 2170373 c.240G>T synonymous_variant 0.4
PPE35 2170424 c.189G>T synonymous_variant 0.67
PPE35 2170450 p.Gly55Trp missense_variant 0.4
PPE35 2170548 p.Gly22Val missense_variant 0.17
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222571 c.594G>A synonymous_variant 1.0
Rv1979c 2223093 c.72C>A synonymous_variant 0.2
Rv1979c 2223249 c.-85G>T upstream_gene_variant 0.25
Rv1979c 2223275 c.-111C>A upstream_gene_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288702 c.540C>A synonymous_variant 0.22
pncA 2288903 c.339C>T synonymous_variant 0.22
pncA 2289012 p.Pro77His missense_variant 0.18
pncA 2289197 p.Glu15Asp missense_variant 0.17
pncA 2289267 c.-26C>A upstream_gene_variant 0.14
pncA 2289448 c.-207G>T upstream_gene_variant 0.18
pncA 2289460 c.-219G>T upstream_gene_variant 0.18
pncA 2289505 c.-264G>T upstream_gene_variant 0.5
pncA 2289626 c.-385G>T upstream_gene_variant 0.22
pncA 2289815 c.-574C>A upstream_gene_variant 0.18
kasA 2517948 c.-167C>A upstream_gene_variant 0.17
kasA 2518039 c.-76C>A upstream_gene_variant 0.33
kasA 2518069 c.-46C>A upstream_gene_variant 0.2
kasA 2518075 c.-40C>T upstream_gene_variant 0.2
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518177 c.63G>T synonymous_variant 0.25
kasA 2518363 c.249C>A synonymous_variant 0.33
kasA 2518659 p.Trp182Leu missense_variant 0.67
kasA 2518716 p.Pro201His missense_variant 0.33
kasA 2518945 p.Met277Ile missense_variant 0.33
kasA 2519113 p.Gln333His missense_variant 0.17
kasA 2519178 p.Ser355Leu missense_variant 0.25
eis 2714505 c.828C>A synonymous_variant 0.18
eis 2714525 p.His270Asn missense_variant 0.2
eis 2714795 p.Glu180* stop_gained 0.21
eis 2714928 c.405C>A synonymous_variant 0.15
eis 2715182 p.Gly51Cys missense_variant 0.18
eis 2715238 p.Ser32* stop_gained 0.2
eis 2715525 c.-193G>T upstream_gene_variant 0.25
ahpC 2725978 c.-215G>T upstream_gene_variant 0.27
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726225 c.33C>A synonymous_variant 0.25
ahpC 2726611 p.Pro140His missense_variant 0.22
ahpC 2726732 p.Lys180Asn missense_variant 0.22
folC 2746163 p.Arg479Leu missense_variant 0.29
folC 2746227 p.Gly458Trp missense_variant 0.33
folC 2746270 c.1329C>A synonymous_variant 0.25
folC 2746313 p.Arg429Leu missense_variant 0.33
folC 2746387 c.1212C>A synonymous_variant 0.5
folC 2746438 c.1161G>T synonymous_variant 0.4
folC 2746453 c.1146G>T synonymous_variant 0.29
folC 2746469 p.Gly377Val missense_variant 0.29
folC 2746523 p.Ala359Glu missense_variant 0.15
folC 2746587 c.1012C>A synonymous_variant 0.2
folC 2746876 c.723C>A synonymous_variant 0.67
folC 2746923 p.Gly226Cys missense_variant 0.43
folC 2746933 c.666G>T synonymous_variant 0.25
folC 2746947 p.Gly218Cys missense_variant 0.22
folC 2746956 p.Glu215* stop_gained 0.22
folC 2747012 p.Pro196Gln missense_variant 0.2
folC 2747030 p.Pro190Gln missense_variant 0.25
folC 2747041 c.558G>T synonymous_variant 0.2
folC 2747057 p.Trp181Leu missense_variant 0.29
folC 2747113 p.Ala162Glu missense_variant 0.2
folC 2747272 c.327G>T synonymous_variant 0.25
folC 2747324 p.Arg92Leu missense_variant 0.2
folC 2747419 c.180C>A synonymous_variant 0.27
folC 2747566 c.33G>T synonymous_variant 0.4
folC 2747643 c.-45G>T upstream_gene_variant 0.4
pepQ 2859746 p.Leu225Met missense_variant 0.29
pepQ 2859776 p.Gly215Cys missense_variant 0.29
pepQ 2859777 c.642C>A synonymous_variant 0.29
pepQ 2859872 p.His183Asn missense_variant 0.33
pepQ 2859885 c.534C>A synonymous_variant 0.22
pepQ 2860177 p.Arg81Leu missense_variant 0.18
pepQ 2860189 p.Arg77Leu missense_variant 0.25
pepQ 2860212 c.207C>A synonymous_variant 0.4
pepQ 2860287 c.132G>A synonymous_variant 0.29
pepQ 2860423 c.-5G>T upstream_gene_variant 0.2
ribD 2986702 c.-137G>T upstream_gene_variant 0.25
ribD 2986745 c.-94C>A upstream_gene_variant 0.22
ribD 2986765 c.-74G>T upstream_gene_variant 0.33
ribD 2987249 p.Glu137Asp missense_variant 0.17
Rv2752c 3064527 c.1665C>A synonymous_variant 0.21
Rv2752c 3064565 p.Glu543* stop_gained 0.2
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3064833 c.1359C>A synonymous_variant 0.2
Rv2752c 3065301 c.891C>A synonymous_variant 0.2
Rv2752c 3065388 c.804C>A synonymous_variant 0.15
Rv2752c 3065558 p.Gly212Trp missense_variant 0.25
Rv2752c 3065567 p.Pro209Thr missense_variant 0.29
Rv2752c 3065746 p.Ser149Tyr missense_variant 0.29
Rv2752c 3065800 p.Gly131Asp missense_variant 1.0
Rv2752c 3065957 c.235T>C synonymous_variant 0.25
Rv2752c 3066267 c.-76C>A upstream_gene_variant 0.25
Rv2752c 3066277 c.-86C>A upstream_gene_variant 0.25
Rv2752c 3067011 c.-820C>A upstream_gene_variant 0.22
Rv2752c 3067049 c.-858G>T upstream_gene_variant 0.22
thyX 3067222 p.Ala242Ser missense_variant 0.15
thyX 3067261 p.Asp229Asn missense_variant 0.22
thyX 3067357 p.Ala197Ser missense_variant 0.18
thyX 3067567 p.Asp127Tyr missense_variant 0.25
thyX 3067602 p.Arg115Leu missense_variant 0.5
thyX 3067613 p.Glu111Asp missense_variant 0.33
thyX 3067678 p.Thr90Pro missense_variant 0.18
thyX 3067720 c.223_225delCAT conservative_inframe_deletion 0.33
thyX 3067955 c.-10G>T upstream_gene_variant 0.67
thyX 3067978 c.-33C>A upstream_gene_variant 0.4
thyX 3067990 c.-45C>A upstream_gene_variant 0.4
thyA 3073869 p.Trp201Cys missense_variant 0.33
thyA 3073875 p.Phe199Leu missense_variant 0.33
thyA 3073887 c.585G>T synonymous_variant 0.33
thyA 3074025 p.Phe149Leu missense_variant 0.25
thyA 3074088 c.384C>A synonymous_variant 0.29
thyA 3074161 p.Pro104Gln missense_variant 0.2
thyA 3074555 c.-84C>A upstream_gene_variant 0.23
thyA 3074603 c.-132G>T upstream_gene_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087213 p.Pro132Thr missense_variant 0.29
ald 3087240 p.Ala141Thr missense_variant 0.33
ald 3087276 p.Gln153Lys missense_variant 0.29
ald 3087614 c.795G>C synonymous_variant 0.12
ald 3087676 p.Pro286Gln missense_variant 0.18
ald 3087686 c.867C>A synonymous_variant 0.18
fbiD 3338920 c.-198G>T upstream_gene_variant 0.22
fbiD 3339038 c.-80C>A upstream_gene_variant 0.25
fbiD 3339148 p.Gly11Cys missense_variant 0.4
fbiD 3339212 p.Ala32Glu missense_variant 0.2
fbiD 3339234 c.117G>A synonymous_variant 0.25
fbiD 3339250 p.Asp45Tyr missense_variant 0.4
Rv3083 3448405 c.-99G>T upstream_gene_variant 0.2
Rv3083 3448586 p.Pro28His missense_variant 0.22
Rv3083 3448603 p.Leu34Ile missense_variant 0.17
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3448851 p.Trp116Cys missense_variant 0.33
Rv3083 3448860 c.357G>T synonymous_variant 0.22
Rv3083 3448888 c.385C>A synonymous_variant 0.2
Rv3083 3448944 c.441G>T synonymous_variant 0.18
Rv3083 3448956 c.453G>T synonymous_variant 0.29
Rv3083 3449030 p.Ser176Tyr missense_variant 0.5
Rv3083 3449258 p.Arg252Leu missense_variant 0.33
Rv3083 3449346 c.843G>T synonymous_variant 0.2
Rv3083 3449437 p.Gly312Cys missense_variant 0.25
Rv3083 3449463 p.Gln320His missense_variant 0.18
Rv3083 3449568 c.1065G>T synonymous_variant 0.33
Rv3083 3449577 c.1074C>A synonymous_variant 0.33
Rv3083 3449583 c.1080G>T synonymous_variant 0.33
Rv3083 3449626 p.Gly375Cys missense_variant 0.25
fprA 3473998 c.-9G>A upstream_gene_variant 1.0
fprA 3473998 c.-10_-9insA upstream_gene_variant 1.0
fprA 3474075 c.69G>T synonymous_variant 0.29
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3474655 p.Asp217Tyr missense_variant 0.25
fprA 3474664 p.Gly220Trp missense_variant 0.25
fprA 3474756 p.Lys250Asn missense_variant 0.17
fprA 3474802 p.Arg266Ser missense_variant 0.18
fprA 3474957 c.951G>T synonymous_variant 0.25
fprA 3474961 p.Val319Met missense_variant 1.0
fprA 3475015 p.Gln337Lys missense_variant 0.25
fprA 3475159 p.Asn385Asp missense_variant 1.0
fprA 3475257 c.1251G>T synonymous_variant 0.4
fprA 3475298 p.Arg431Leu missense_variant 0.4
whiB7 3568624 p.Pro19Gln missense_variant 0.25
whiB7 3568648 p.Pro11His missense_variant 0.22
whiB7 3568749 c.-70A>T upstream_gene_variant 0.4
Rv3236c 3611979 p.Ala380Ser missense_variant 0.4
Rv3236c 3612060 p.Ala353Ser missense_variant 0.4
Rv3236c 3612100 c.1017C>A synonymous_variant 0.33
Rv3236c 3612122 p.Ala332Asp missense_variant 0.33
Rv3236c 3612228 c.889C>T synonymous_variant 0.33
Rv3236c 3612266 p.Pro284Gln missense_variant 0.67
Rv3236c 3612334 p.Met261Ile missense_variant 0.33
Rv3236c 3612507 p.His204Asn missense_variant 0.18
Rv3236c 3612823 c.294C>A synonymous_variant 0.33
Rv3236c 3612999 p.Gly40Cys missense_variant 0.25
Rv3236c 3613054 c.63G>T synonymous_variant 0.25
Rv3236c 3613106 p.Ser4* stop_gained 0.29
Rv3236c 3613149 c.-33G>T upstream_gene_variant 0.4
Rv3236c 3613193 c.-77C>A upstream_gene_variant 0.29
Rv3236c 3613295 c.-179G>T upstream_gene_variant 0.33
fbiA 3640502 c.-41C>A upstream_gene_variant 0.25
fbiA 3640516 c.-27G>T upstream_gene_variant 0.25
fbiA 3640612 p.Gly24Cys missense_variant 0.33
fbiA 3640702 p.His54Asn missense_variant 0.4
fbiA 3640729 p.Asp63His missense_variant 0.25
fbiA 3640855 p.Gly105Trp missense_variant 0.22
fbiB 3640869 c.-666G>T upstream_gene_variant 0.22
fbiA 3640999 p.His153Asn missense_variant 0.18
fbiB 3641010 c.-525C>A upstream_gene_variant 0.22
fbiA 3641077 p.Gln179Lys missense_variant 0.25
fbiA 3641456 p.Ser305* stop_gained 0.22
fbiB 3641576 c.42C>A synonymous_variant 0.29
fbiB 3641813 p.Leu93Phe missense_variant 0.2
fbiB 3641883 p.Glu117* stop_gained 0.2
fbiB 3641915 c.381C>A synonymous_variant 0.18
fbiB 3642075 p.Asp181Tyr missense_variant 0.5
fbiB 3642207 p.Asp225Tyr missense_variant 0.29
fbiB 3642353 c.819C>A synonymous_variant 0.18
fbiB 3642575 c.1041C>A synonymous_variant 0.29
fbiB 3642758 c.1224C>A synonymous_variant 0.29
alr 3840213 p.Arg403Leu missense_variant 0.2
alr 3840489 p.Pro311Gln missense_variant 0.29
alr 3840574 p.Leu283Met missense_variant 0.17
alr 3840846 p.Gly192Val missense_variant 0.17
alr 3841131 p.Ala97Glu missense_variant 0.29
alr 3841145 c.276C>A synonymous_variant 0.29
alr 3841407 p.Trp5Leu missense_variant 0.2
alr 3841550 c.-130G>T upstream_gene_variant 0.13
alr 3841559 c.-139C>A upstream_gene_variant 0.18
alr 3841614 c.-194C>A upstream_gene_variant 0.25
rpoA 3877751 p.Asp253Tyr missense_variant 0.2
rpoA 3878105 p.Glu135Lys missense_variant 0.18
rpoA 3878130 c.378C>A synonymous_variant 0.2
ddn 3986700 c.-144C>A upstream_gene_variant 0.29
ddn 3987003 p.Arg54Ser missense_variant 0.18
ddn 3987042 p.Leu67Met missense_variant 0.2
ddn 3987289 p.Cys149Tyr missense_variant 0.2
ddn 3987296 c.453C>A synonymous_variant 0.2
clpC1 4038390 p.Pro772Gln missense_variant 0.25
clpC1 4038536 c.2169C>A synonymous_variant 0.33
clpC1 4038571 p.Arg712Ser missense_variant 0.29
clpC1 4038655 p.Gly684Cys missense_variant 0.22
clpC1 4038818 p.Lys629Asn missense_variant 0.17
clpC1 4039034 c.1671C>A synonymous_variant 0.2
clpC1 4039058 p.Phe549Leu missense_variant 0.33
clpC1 4039072 p.Pro545Thr missense_variant 0.25
clpC1 4039154 c.1551G>T synonymous_variant 0.22
clpC1 4039949 c.756G>T synonymous_variant 0.18
clpC1 4040139 p.Pro189Gln missense_variant 0.18
clpC1 4040208 p.Ser166Tyr missense_variant 0.22
clpC1 4040214 p.Ser164Tyr missense_variant 0.25
clpC1 4040229 p.Gly159Val missense_variant 0.2
clpC1 4040240 c.465C>A synonymous_variant 0.2
clpC1 4040306 p.Arg133Ser missense_variant 0.18
clpC1 4040330 c.375C>A synonymous_variant 0.2
clpC1 4040517 p.Val63Ala missense_variant 1.0
panD 4044118 p.Leu55Pro missense_variant 0.33
panD 4044288 c.-7G>T upstream_gene_variant 0.4
panD 4044412 c.-131C>A upstream_gene_variant 0.2
embC 4239881 p.Pro7Thr missense_variant 0.25
embC 4239928 c.66G>T synonymous_variant 0.29
embC 4240039 p.Leu59Phe missense_variant 0.29
embC 4240261 c.399G>T synonymous_variant 0.33
embC 4240279 p.Leu139Phe missense_variant 0.33
embC 4240459 c.597G>T synonymous_variant 1.0
embC 4240478 p.Gly206Trp missense_variant 0.5
embC 4240507 c.645G>T synonymous_variant 0.4
embC 4240572 p.Gly237Val missense_variant 0.22
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4240682 p.Asp274Tyr missense_variant 0.2
embC 4240737 p.Ser292Tyr missense_variant 0.2
embC 4240878 p.Thr339Met missense_variant 0.33
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241081 p.Leu407Met missense_variant 0.33
embC 4241215 c.1353C>A synonymous_variant 0.25
embC 4241221 c.1359C>A synonymous_variant 0.25
embC 4241335 p.Gln491His missense_variant 0.17
embC 4241391 p.Leu510Pro missense_variant 0.22
embC 4241420 p.Glu520* stop_gained 0.33
embC 4241645 p.Gly595Trp missense_variant 0.23
embC 4241662 c.1800G>T synonymous_variant 0.23
embC 4241764 p.Phe634Leu missense_variant 0.22
embA 4242274 c.-959G>T upstream_gene_variant 0.33
embC 4242354 p.Gly831Val missense_variant 0.4
embC 4242459 p.Ser866* stop_gained 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242733 p.Trp957Cys missense_variant 0.5
embA 4243046 c.-187C>A upstream_gene_variant 0.18
embA 4243457 c.225C>A synonymous_variant 0.29
embA 4243505 c.273C>A synonymous_variant 0.29
embA 4243672 p.Gly147Val missense_variant 0.29
embA 4243679 c.447C>A synonymous_variant 0.29
embA 4243789 p.Ser186* stop_gained 0.33
embA 4243848 p.Val206Met missense_variant 1.0
embA 4244076 c.844C>A synonymous_variant 0.2
embA 4244167 p.Ala312Val missense_variant 1.0
embA 4244424 p.Arg398Trp missense_variant 0.17
embA 4244448 c.1220delC frameshift_variant 0.15
embA 4244615 c.1383G>T synonymous_variant 0.5
embA 4244921 c.1689C>A synonymous_variant 0.2
embA 4244955 p.Gly575* stop_gained 0.25
embA 4244984 p.Leu584Phe missense_variant 0.25
embA 4244993 c.1761C>A synonymous_variant 0.38
embA 4245079 p.Trp616Leu missense_variant 0.2
embA 4245089 c.1857G>T synonymous_variant 0.18
embA 4245125 c.1893G>T synonymous_variant 0.29
embA 4245149 c.1917C>A synonymous_variant 0.33
embB 4245617 c.-897C>T upstream_gene_variant 0.25
embA 4245969 p.Pro913Ser missense_variant 1.0
embA 4246081 p.Pro950His missense_variant 0.18
embA 4246094 p.Phe954Leu missense_variant 0.22
embA 4246182 p.Ala984Thr missense_variant 0.4
embB 4246244 c.-270G>A upstream_gene_variant 0.22
embB 4246248 c.-266C>A upstream_gene_variant 0.22
embB 4246259 c.-255G>T upstream_gene_variant 0.22
embA 4246413 p.His1061Asn missense_variant 0.29
embB 4246466 c.-48G>T upstream_gene_variant 0.2
embB 4246553 p.Arg14Trp missense_variant 0.22
embB 4246566 p.Gly18Val missense_variant 0.25
embB 4246642 c.129G>T synonymous_variant 0.22
embB 4246669 c.156C>A synonymous_variant 0.18
embB 4246721 p.Pro70Thr missense_variant 0.29
embB 4246744 c.231C>A synonymous_variant 0.33
embB 4246756 c.243C>A synonymous_variant 0.33
embB 4246787 p.Pro92Thr missense_variant 0.25
embB 4246814 p.Thr101Ser missense_variant 0.33
embB 4247073 p.Gly187Val missense_variant 0.33
embB 4247116 c.603G>T synonymous_variant 0.33
embB 4247135 p.Thr208Ser missense_variant 0.33
embB 4247138 c.625C>A synonymous_variant 0.33
embB 4247150 c.637C>A synonymous_variant 0.33
embB 4247183 p.Gly224Trp missense_variant 0.29
embB 4247376 p.Leu288Pro missense_variant 0.15
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4247667 p.Trp385Leu missense_variant 0.29
embB 4248709 c.2196C>A synonymous_variant 0.29
embB 4248887 p.Gly792Arg missense_variant 0.18
embB 4249438 p.Gln975His missense_variant 0.22
embB 4249561 c.3048G>T synonymous_variant 0.18
embB 4249604 p.Gly1031Cys missense_variant 0.2
embB 4249624 c.3111C>A synonymous_variant 0.29
embB 4249748 p.Glu1079* stop_gained 0.4
embB 4249753 p.Leu1080Phe missense_variant 0.4
embB 4249754 p.Gly1081Cys missense_variant 0.4
embB 4249797 p.Arg1095Leu missense_variant 0.4
aftB 4267397 c.1440G>T synonymous_variant 0.25
aftB 4267591 p.Gln416Lys missense_variant 0.22
aftB 4267636 c.1201C>A synonymous_variant 0.18
aftB 4267784 c.1053G>T synonymous_variant 0.18
aftB 4267811 c.1026G>T synonymous_variant 0.29
aftB 4267911 p.Pro309Gln missense_variant 0.33
aftB 4267948 p.Asp297Tyr missense_variant 0.4
aftB 4268344 p.Arg165Ser missense_variant 0.38
aftB 4268518 p.Ala107Ser missense_variant 0.25
aftB 4268535 p.Gly101Val missense_variant 0.2
aftB 4268552 p.Met95Ile missense_variant 0.2
aftB 4268561 c.276G>T synonymous_variant 0.2
aftB 4268565 p.Ser91* stop_gained 0.2
aftB 4268756 c.81C>A synonymous_variant 0.29
aftB 4268868 c.-32G>T upstream_gene_variant 0.2
aftB 4268872 c.-36G>T upstream_gene_variant 0.2
aftB 4268908 c.-72C>A upstream_gene_variant 0.2
ubiA 4268948 p.Gly296Trp missense_variant 0.22
ubiA 4269196 p.Tyr213Phe missense_variant 0.15
aftB 4269270 c.-434G>T upstream_gene_variant 0.18
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269396 c.-560G>T upstream_gene_variant 0.25
aftB 4269489 c.-653C>A upstream_gene_variant 0.2
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ubiA 4269727 p.Pro36Leu missense_variant 0.29
ubiA 4269788 p.Gly16Trp missense_variant 0.22
aftB 4269816 c.-980G>A upstream_gene_variant 0.4
ubiA 4269921 c.-88C>A upstream_gene_variant 0.2
ubiA 4269990 c.-157G>T upstream_gene_variant 0.22
ethA 4326046 p.Glu476Asp missense_variant 0.17
ethA 4326432 p.Leu348Phe missense_variant 1.0
ethA 4326535 c.939G>T synonymous_variant 0.25
ethR 4326820 c.-729C>A upstream_gene_variant 0.18
ethA 4327202 p.Met91Thr missense_variant 0.11
ethA 4327361 p.Arg38Leu missense_variant 0.3
ethA 4327528 c.-55C>A upstream_gene_variant 0.4
ethR 4327745 p.Pro66Gln missense_variant 0.18
ethA 4327788 c.-315G>T upstream_gene_variant 0.36
ethR 4327895 p.Ser116* stop_gained 0.22
ethR 4327931 p.Arg128Met missense_variant 0.22
ethA 4327956 c.-483T>C upstream_gene_variant 0.18
ethA 4328052 c.-579G>T upstream_gene_variant 0.17
ethA 4328273 c.-800C>A upstream_gene_variant 0.2
ethA 4328398 c.-925C>A upstream_gene_variant 0.18
whiB6 4338193 p.Arg110Leu missense_variant 0.2
whiB6 4338262 p.Ala87Val missense_variant 0.33
whiB6 4338264 c.258G>T synonymous_variant 0.33
whiB6 4338312 c.210G>T synonymous_variant 0.18
whiB6 4338500 p.Glu8* stop_gained 0.18
whiB6 4338535 c.-14C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407542 p.Gly221* stop_gained 0.17
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407643 p.Arg187Met missense_variant 0.2
gid 4407645 c.558C>A synonymous_variant 0.18
gid 4407660 c.543G>T synonymous_variant 0.18
gid 4407688 p.Arg172Leu missense_variant 0.27
gid 4407858 c.345G>T synonymous_variant 0.25
gid 4407873 c.330G>T synonymous_variant 1.0
gid 4407878 p.Gly109Cys missense_variant 0.33
gid 4408324 c.-122C>A upstream_gene_variant 0.18
gid 4408445 c.-243G>T upstream_gene_variant 0.25