TB-Profiler result

Run: ERR11488822
Summary

Run ID: ERR11488822

Sample name:

Date: 08-01-2024 16:36:34

Number of reads: 2902949

Percentage reads mapped: 96.46

Strain: lineage4.1.2.1;lineage2.2.1

Drug-resistance: Pre-XDR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin R rpoB p.Ser450Leu (0.94)
Isoniazid R fabG1 c.-15C>T (0.90), katG p.Ser315Thr (0.14)
Ethambutol R embB p.Met306Val (0.86)
Pyrazinamide R pncA p.Thr135Pro (0.15)
Streptomycin
Fluoroquinolones R gyrA p.Asp89Asn (0.79)
Moxifloxacin R gyrA p.Asp89Asn (0.79)
Ofloxacin R gyrA p.Asp89Asn (0.79)
Levofloxacin R gyrA p.Asp89Asn (0.79)
Ciprofloxacin R gyrA p.Asp89Asn (0.79)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R fabG1 c.-15C>T (0.90), ethR p.Ala95Thr (0.90)
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage2 East-Asian Beijing RD105 0.88
lineage4 Euro-American LAM;T;S;X;H None 0.11
lineage4.1 Euro-American T;X;H None 0.09
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.89
lineage4.1.2 Euro-American T;H None 0.05
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.89
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.06
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
gyrA 7566 p.Asp89Asn missense_variant 0.79 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.94 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.9 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.14 isoniazid
pncA 2288839 p.Thr135Pro missense_variant 0.15 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.86 ethambutol
ethR 4327831 p.Ala95Thr missense_variant 0.9 ethionamide
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8693 c.1392T>C synonymous_variant 0.2
gyrA 8711 c.1410A>C synonymous_variant 0.19
gyrA 8714 c.1413A>G synonymous_variant 0.19
gyrA 8729 c.1428T>C synonymous_variant 0.16
gyrA 8731 p.Gly477Ala missense_variant 0.16
gyrA 8751 p.Ala484Asn missense_variant 0.14
gyrA 8762 c.1461G>C synonymous_variant 0.15
gyrA 8767 p.Arg489Lys missense_variant 0.14
gyrA 8783 c.1482G>C synonymous_variant 0.13
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9583 p.Arg761Lys missense_variant 0.14
gyrA 9585 c.2284T>C synonymous_variant 0.14
gyrA 9590 c.2289T>C synonymous_variant 0.14
gyrA 9599 p.Leu766Phe missense_variant 0.13
gyrA 9623 c.2322G>C synonymous_variant 0.17
gyrA 9626 c.2325T>C synonymous_variant 0.16
gyrA 9630 p.Val777Ile missense_variant 0.17
gyrA 9635 c.2334T>C synonymous_variant 0.17
gyrA 9644 c.2343T>C synonymous_variant 0.17
gyrA 9650 c.2349G>C synonymous_variant 0.18
gyrA 9665 c.2364A>G synonymous_variant 0.19
gyrA 9674 c.2373T>C synonymous_variant 0.21
fgd1 491742 c.960T>C synonymous_variant 0.96
mshA 575772 p.Val142Ala missense_variant 0.13
mshA 575782 c.435G>C synonymous_variant 0.17
mshA 575785 c.438T>G synonymous_variant 0.2
mshA 575806 c.459G>C synonymous_variant 0.26
mshA 575824 c.477T>C synonymous_variant 0.28
mshA 575842 c.495G>C synonymous_variant 0.26
mshA 575848 c.501C>T synonymous_variant 0.26
mshA 575878 c.531A>C synonymous_variant 0.22
mshA 575881 c.534C>T synonymous_variant 0.22
mshA 575887 c.540G>C synonymous_variant 0.27
mshA 575893 c.546C>G synonymous_variant 0.26
mshA 575907 p.Ala187Val missense_variant 0.73
ccsA 620247 p.Leu119Phe missense_variant 0.18
ccsA 620249 p.Ser120Cys missense_variant 0.18
ccsA 620253 c.363G>C synonymous_variant 0.17
ccsA 620256 c.366C>G synonymous_variant 0.18
ccsA 620257 p.Ile123Val missense_variant 0.17
ccsA 620268 c.378G>C synonymous_variant 0.17
ccsA 620283 c.393T>G synonymous_variant 0.14
ccsA 620284 p.Ala132Pro missense_variant 0.14
ccsA 620288 p.Arg133Gln missense_variant 0.14
ccsA 620291 p.Tyr134Phe missense_variant 0.14
ccsA 620295 c.405G>C synonymous_variant 0.16
ccsA 620307 c.417C>G synonymous_variant 0.17
ccsA 620310 c.420C>T synonymous_variant 0.17
ccsA 620317 p.Val143Leu missense_variant 0.17
ccsA 620337 c.447C>G synonymous_variant 0.16
ccsA 620343 c.453G>C synonymous_variant 0.16
ccsA 620349 c.459A>T synonymous_variant 0.13
ccsA 620625 p.Ile245Met missense_variant 0.85
rpoB 760115 c.309C>T synonymous_variant 0.19
rpoB 760337 c.531C>G synonymous_variant 0.15
rpoB 760340 c.534G>T synonymous_variant 0.13
rpoB 760361 c.555T>C synonymous_variant 0.18
rpoB 760373 c.567C>T synonymous_variant 0.21
rpoB 760376 p.Asp190Glu missense_variant 0.23
rpoB 760403 c.597C>T synonymous_variant 0.23
rpoB 760406 c.600G>C synonymous_variant 0.23
rpoB 760418 c.612G>C synonymous_variant 0.22
rpoB 760430 c.624T>C synonymous_variant 0.21
rpoB 760475 c.669A>G synonymous_variant 0.18
rpoB 760484 c.678A>G synonymous_variant 0.15
rpoB 760919 c.1113C>G synonymous_variant 0.14
rpoB 760920 c.1114C>T synonymous_variant 0.14
rpoB 760925 c.1119T>C synonymous_variant 0.14
rpoB 760931 c.1125C>G synonymous_variant 0.16
rpoB 760946 c.1140A>G synonymous_variant 0.17
rpoB 760970 c.1164G>C synonymous_variant 0.17
rpoB 760971 c.1165C>A synonymous_variant 0.17
rpoB 760982 c.1176G>C synonymous_variant 0.18
rpoB 760985 c.1179G>C synonymous_variant 0.2
rpoB 761015 c.1209G>C synonymous_variant 0.19
rpoB 761021 c.1215G>C synonymous_variant 0.18
rpoB 761027 c.1221A>G synonymous_variant 0.16
rpoB 761234 c.1428G>C synonymous_variant 0.14
rpoB 761249 c.1443A>G synonymous_variant 0.14
rpoB 761252 c.1446C>G synonymous_variant 0.13
rpoB 761261 c.1455G>T synonymous_variant 0.16
rpoB 761264 c.1458C>G synonymous_variant 0.18
rpoB 761314 p.Phe503Ser missense_variant 0.62
rpoB 761327 c.1521A>G synonymous_variant 0.18
rpoB 761330 c.1524G>C synonymous_variant 0.18
rpoB 761333 c.1527G>T synonymous_variant 0.17
rpoB 761354 c.1548C>T synonymous_variant 0.14
rpoB 761657 c.1851C>G synonymous_variant 0.14
rpoB 761675 c.1869G>C synonymous_variant 0.17
rpoC 762467 c.-903C>T upstream_gene_variant 0.16
rpoC 762476 c.-894C>G upstream_gene_variant 0.18
rpoC 762488 c.-882G>C upstream_gene_variant 0.19
rpoC 762491 c.-879T>C upstream_gene_variant 0.17
rpoB 762510 p.Ala902Pro missense_variant 0.2
rpoC 762533 c.-837T>C upstream_gene_variant 0.24
rpoC 762536 c.-834T>C upstream_gene_variant 0.23
rpoC 762537 c.-833T>C upstream_gene_variant 0.23
rpoC 762545 c.-825C>G upstream_gene_variant 0.26
rpoC 762551 c.-819C>T upstream_gene_variant 0.26
rpoC 762581 c.-789T>C upstream_gene_variant 0.22
rpoC 762582 c.-788T>C upstream_gene_variant 0.22
rpoC 762590 c.-780C>G upstream_gene_variant 0.2
rpoC 762596 c.-774G>C upstream_gene_variant 0.19
rpoC 762599 c.-771T>C upstream_gene_variant 0.2
rpoC 762605 c.-765T>C upstream_gene_variant 0.19
rpoC 762608 c.-762C>G upstream_gene_variant 0.16
rpoC 762929 c.-441G>C upstream_gene_variant 0.16
rpoC 762995 c.-375G>T upstream_gene_variant 0.16
rpoC 763031 c.-339T>C upstream_gene_variant 0.67
rpoC 763070 c.-300T>C upstream_gene_variant 0.18
rpoC 763085 c.-285C>G upstream_gene_variant 0.19
rpoC 763103 c.-267G>C upstream_gene_variant 0.21
rpoC 763115 c.-255T>C upstream_gene_variant 0.18
rpoC 763127 c.-243G>C upstream_gene_variant 0.15
rpoC 763166 c.-204A>G upstream_gene_variant 0.17
rpoC 763169 c.-201A>G upstream_gene_variant 0.16
rpoC 763202 c.-168A>G upstream_gene_variant 0.15
rpoC 763408 c.39T>C synonymous_variant 0.2
rpoC 763411 c.42T>G synonymous_variant 0.19
rpoC 763414 c.45T>C synonymous_variant 0.18
rpoC 763441 c.72C>T synonymous_variant 0.19
rpoC 763444 c.75T>C synonymous_variant 0.19
rpoC 763456 c.87A>G synonymous_variant 0.21
rpoC 763486 c.117T>G synonymous_variant 0.22
rpoC 763528 c.159G>A synonymous_variant 0.16
rpoC 763537 c.168C>G synonymous_variant 0.16
rpoC 763546 c.177A>G synonymous_variant 0.15
rpoC 763555 c.186C>T synonymous_variant 0.72
rpoC 763570 c.201G>C synonymous_variant 0.14
rpoC 763660 c.291T>G synonymous_variant 0.13
rpoC 763813 c.444C>G synonymous_variant 0.14
rpoC 763831 c.462A>G synonymous_variant 0.15
rpoC 763835 p.Ala156Met missense_variant 0.14
rpoC 763851 p.Ala161Gly missense_variant 0.14
rpoC 763894 c.525A>G synonymous_variant 0.17
rpoC 763921 c.552G>C synonymous_variant 0.22
rpoC 763933 c.564C>T synonymous_variant 0.26
rpoC 763945 c.576T>C synonymous_variant 0.24
rpoC 763948 c.579G>C synonymous_variant 0.24
rpoC 763960 c.591T>C synonymous_variant 0.23
rpoC 763963 c.594C>G synonymous_variant 0.24
rpoC 764005 c.636G>C synonymous_variant 0.23
rpoC 764011 c.642T>C synonymous_variant 0.23
rpoC 764024 c.655T>C synonymous_variant 0.24
rpoC 764040 p.Ser224Asn missense_variant 0.22
rpoC 764044 c.675T>C synonymous_variant 0.22
rpoC 764059 c.690G>C synonymous_variant 0.19
rpoC 764083 c.714A>G synonymous_variant 0.19
rpoC 764087 p.Leu240Ile missense_variant 0.21
rpoC 764098 c.729A>G synonymous_variant 0.19
rpoC 764101 c.732C>G synonymous_variant 0.19
rpoC 764131 c.762T>C synonymous_variant 0.16
rpoC 764140 c.771C>T synonymous_variant 0.22
rpoC 764188 c.819A>G synonymous_variant 0.17
rpoC 764194 c.825G>A synonymous_variant 0.16
rpoC 764203 c.834G>T synonymous_variant 0.15
rpoC 764206 p.Asp279Glu missense_variant 0.14
rpoC 764217 p.Asn283Ser missense_variant 0.14
rpoC 764650 c.1281G>T synonymous_variant 0.13
rpoC 765383 p.Met672Leu missense_variant 0.15
rpoC 765403 c.2034G>C synonymous_variant 0.17
rpoC 765404 p.Leu679Val missense_variant 0.17
rpoC 765409 c.2040T>G synonymous_variant 0.17
rpoC 765421 c.2052C>G synonymous_variant 0.21
rpoC 765454 c.2085C>G synonymous_variant 0.22
rpoC 765478 c.2109T>C synonymous_variant 0.18
rpoC 765499 c.2130C>G synonymous_variant 0.16
rpoC 765688 c.2319G>A synonymous_variant 0.16
rpoC 765694 c.2325G>C synonymous_variant 0.16
rpoC 765700 c.2331T>C synonymous_variant 0.16
rpoC 765712 c.2343C>G synonymous_variant 0.19
rpoC 765724 c.2355C>G synonymous_variant 0.22
rpoC 765734 c.2365T>C synonymous_variant 0.22
rpoC 765752 p.Asp795Ser missense_variant 0.23
rpoC 765763 c.2394G>C synonymous_variant 0.28
rpoC 765772 c.2403C>G synonymous_variant 0.23
rpoC 765784 c.2415C>G synonymous_variant 0.2
rpoC 765787 c.2418C>T synonymous_variant 0.23
rpoC 765793 c.2424C>G synonymous_variant 0.26
rpoC 765796 c.2427C>T synonymous_variant 0.25
rpoC 765811 c.2442T>C synonymous_variant 0.29
rpoC 765814 c.2445A>G synonymous_variant 0.29
rpoC 765826 c.2457T>C synonymous_variant 0.28
rpoC 765835 c.2466C>T synonymous_variant 0.28
rpoC 765883 c.2514C>G synonymous_variant 0.32
rpoC 765886 c.2517C>G synonymous_variant 0.33
rpoC 765892 c.2523T>C synonymous_variant 0.36
rpoC 765967 c.2598C>T synonymous_variant 0.24
rpoC 765982 c.2613C>G synonymous_variant 0.26
rpoC 765994 c.2625A>T synonymous_variant 0.2
rpoC 766012 c.2643C>G synonymous_variant 0.15
rpoC 766021 c.2652G>C synonymous_variant 0.16
rpoC 766027 c.2658G>C synonymous_variant 0.15
rpoC 766030 c.2661C>G synonymous_variant 0.14
rpoC 766312 c.2943T>G synonymous_variant 0.18
rpoC 766315 c.2946C>G synonymous_variant 0.17
rpoC 766333 c.2964G>C synonymous_variant 0.19
rpoC 766345 c.2976T>C synonymous_variant 0.21
rpoC 766348 c.2979A>G synonymous_variant 0.2
rpoC 766366 c.2997C>G synonymous_variant 0.23
rpoC 766369 c.3000C>G synonymous_variant 0.23
rpoC 766381 c.3012C>T synonymous_variant 0.25
rpoC 766384 c.3015A>G synonymous_variant 0.27
rpoC 766387 c.3018C>G synonymous_variant 0.28
rpoC 766393 c.3024C>G synonymous_variant 0.26
rpoC 766402 c.3033C>G synonymous_variant 0.26
rpoC 766408 c.3039C>G synonymous_variant 0.24
rpoC 766426 c.3057C>T synonymous_variant 0.21
rpoC 766447 c.3078T>C synonymous_variant 0.19
rpoC 766459 c.3090G>C synonymous_variant 0.16
rpoC 766483 c.3114G>C synonymous_variant 0.15
rpoC 766486 c.3117A>G synonymous_variant 0.15
rpoC 766488 p.Pro1040Arg missense_variant 0.16
rpoC 766492 c.3123T>C synonymous_variant 0.15
rpoC 766726 c.3357T>C synonymous_variant 0.19
rpoC 766733 c.3364C>T synonymous_variant 0.19
rpoC 766738 c.3369G>C synonymous_variant 0.19
rpoC 766765 c.3396A>C synonymous_variant 0.23
rpoC 766774 c.3405T>C synonymous_variant 0.24
rpoC 766801 c.3432C>G synonymous_variant 0.21
rpoC 766804 c.3435A>G synonymous_variant 0.22
rpoC 766861 c.3492G>C synonymous_variant 0.16
rpoC 766864 c.3495G>C synonymous_variant 0.17
rpoC 766882 c.3513C>T synonymous_variant 0.17
rpoC 766883 p.Ser1172Ala missense_variant 0.17
rpoC 766945 c.3576A>G synonymous_variant 0.17
rpoC 766963 c.3594T>C synonymous_variant 0.19
rpoC 766972 c.3603G>C synonymous_variant 0.27
rpoC 766996 c.3627C>T synonymous_variant 0.29
rpoC 767023 c.3654C>T synonymous_variant 0.25
rpoC 767033 c.3664_3666delTCGinsAGC synonymous_variant 0.28
rpoC 767059 c.3690T>G synonymous_variant 0.3
rpoC 767062 c.3693C>A synonymous_variant 0.29
rpoC 767098 c.3729T>C synonymous_variant 0.29
rpoC 767119 c.3750A>G synonymous_variant 0.2
rpoC 767134 c.3765C>A synonymous_variant 0.19
rpoC 767152 c.3783T>C synonymous_variant 0.19
rpoC 767158 c.3789T>C synonymous_variant 0.19
rpoC 767167 c.3798C>G synonymous_variant 0.19
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775885 p.Ile866Leu missense_variant 0.17
mmpL5 775909 p.Leu858Phe missense_variant 0.17
mmpL5 775915 p.Ala856Ser missense_variant 0.19
mmpL5 775937 c.2544G>C synonymous_variant 0.16
mmpL5 776100 p.Thr794Ile missense_variant 0.87
mmpL5 776182 p.Asp767Asn missense_variant 0.81
mmpS5 778979 c.-74G>T upstream_gene_variant 0.85
mmpS5 779615 c.-710C>G upstream_gene_variant 0.86
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781760 c.201T>C synonymous_variant 0.14
rpsL 781763 c.204C>G synonymous_variant 0.15
rpsL 781811 c.252C>T synonymous_variant 0.13
rplC 800612 c.-197A>G upstream_gene_variant 0.22
rplC 800618 c.-191T>C upstream_gene_variant 0.22
rplC 800648 c.-161A>C upstream_gene_variant 0.2
rplC 800654 c.-155T>C upstream_gene_variant 0.19
fbiC 1303785 c.855G>A synonymous_variant 0.15
fbiC 1303789 p.Ile287Val missense_variant 0.15
fbiC 1303818 c.888C>G synonymous_variant 0.16
fbiC 1304853 c.1923C>G synonymous_variant 0.15
Rv1258c 1406760 c.580_581insC frameshift_variant 0.94
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472489 n.644A>G non_coding_transcript_exon_variant 0.35
rrs 1473105 n.1260G>A non_coding_transcript_exon_variant 0.31
rrs 1473123 n.1278delAinsTT non_coding_transcript_exon_variant 0.28
rrs 1473290 n.1445delCinsTT non_coding_transcript_exon_variant 0.29
rrl 1473758 n.101G>T non_coding_transcript_exon_variant 0.28
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.31
rrl 1473815 n.158T>C non_coding_transcript_exon_variant 0.29
rrl 1473876 n.219G>A non_coding_transcript_exon_variant 0.15
rrl 1474717 n.1060A>T non_coding_transcript_exon_variant 0.32
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.33
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.34
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.32
rrl 1474991 n.1334T>C non_coding_transcript_exon_variant 0.2
rrl 1474995 n.1338T>G non_coding_transcript_exon_variant 0.21
rrl 1475006 n.1349A>G non_coding_transcript_exon_variant 0.22
rrl 1475027 n.1370G>T non_coding_transcript_exon_variant 0.21
rrl 1475028 n.1371G>T non_coding_transcript_exon_variant 0.21
rrl 1475061 n.1404C>T non_coding_transcript_exon_variant 0.28
rrl 1475088 n.1431A>T non_coding_transcript_exon_variant 0.31
rrl 1475206 n.1549C>T non_coding_transcript_exon_variant 0.25
rrl 1475209 n.1552G>A non_coding_transcript_exon_variant 0.28
rrl 1475252 n.1595C>T non_coding_transcript_exon_variant 0.25
rrl 1475266 n.1609T>C non_coding_transcript_exon_variant 0.23
rrl 1475267 n.1610G>A non_coding_transcript_exon_variant 0.23
rrl 1475270 n.1613G>A non_coding_transcript_exon_variant 0.23
rrl 1475275 n.1618C>T non_coding_transcript_exon_variant 0.23
rrl 1475276 n.1619T>C non_coding_transcript_exon_variant 0.24
rrl 1475289 n.1632G>A non_coding_transcript_exon_variant 0.24
rrl 1475291 n.1634A>C non_coding_transcript_exon_variant 0.24
rrl 1475313 n.1656G>A non_coding_transcript_exon_variant 0.25
rrl 1475315 n.1658A>T non_coding_transcript_exon_variant 0.25
rrl 1475355 n.1698C>T non_coding_transcript_exon_variant 0.19
rrl 1475369 n.1712G>C non_coding_transcript_exon_variant 0.15
rrl 1475532 n.1875A>G non_coding_transcript_exon_variant 0.26
rrl 1475573 n.1916G>A non_coding_transcript_exon_variant 0.24
rrl 1475604 n.1947A>C non_coding_transcript_exon_variant 0.18
rrl 1475606 n.1949T>C non_coding_transcript_exon_variant 0.18
rrl 1475608 n.1951T>C non_coding_transcript_exon_variant 0.17
rrl 1475617 n.1960C>G non_coding_transcript_exon_variant 0.17
rrl 1475625 n.1968G>C non_coding_transcript_exon_variant 0.18
rrl 1475637 n.1980T>G non_coding_transcript_exon_variant 0.18
rrl 1475655 n.1998T>C non_coding_transcript_exon_variant 0.19
rrl 1475659 n.2002G>A non_coding_transcript_exon_variant 0.2
rrl 1475758 n.2104delC non_coding_transcript_exon_variant 0.48
rrl 1475765 n.2111delG non_coding_transcript_exon_variant 0.5
rrl 1475883 n.2226A>G non_coding_transcript_exon_variant 0.24
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.2
rrl 1476033 n.2376T>C non_coding_transcript_exon_variant 0.19
rrl 1476035 n.2378G>A non_coding_transcript_exon_variant 0.19
rrl 1476086 n.2429G>A non_coding_transcript_exon_variant 0.19
rrl 1476089 n.2432T>C non_coding_transcript_exon_variant 0.19
rrl 1476095 n.2438C>G non_coding_transcript_exon_variant 0.18
rrl 1476103 n.2446C>G non_coding_transcript_exon_variant 0.19
rrl 1476105 n.2448G>A non_coding_transcript_exon_variant 0.19
rrl 1476106 n.2449A>T non_coding_transcript_exon_variant 0.19
rrl 1476110 n.2453G>C non_coding_transcript_exon_variant 0.18
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.18
rrl 1476117 n.2460G>C non_coding_transcript_exon_variant 0.18
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.23
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.27
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.29
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.34
rrl 1476583 n.2926G>C non_coding_transcript_exon_variant 0.25
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.22
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.2
inhA 1673664 c.-538A>C upstream_gene_variant 0.14
inhA 1673712 c.-490A>G upstream_gene_variant 0.15
fabG1 1673713 p.Ser92Ala missense_variant 0.15
inhA 1673730 c.-472C>G upstream_gene_variant 0.14
inhA 1673838 c.-364T>C upstream_gene_variant 0.13
inhA 1673841 c.-361A>G upstream_gene_variant 0.15
inhA 1673847 c.-355A>C upstream_gene_variant 0.15
inhA 1673853 c.-349A>C upstream_gene_variant 0.16
inhA 1673856 c.-346T>G upstream_gene_variant 0.16
fabG1 1673870 p.Ser144Thr missense_variant 0.18
inhA 1673901 c.-301A>G upstream_gene_variant 0.19
inhA 1673904 c.-298C>G upstream_gene_variant 0.21
inhA 1673916 c.-286A>C upstream_gene_variant 0.22
inhA 1673919 c.-283G>C upstream_gene_variant 0.2
inhA 1673922 c.-280T>C upstream_gene_variant 0.19
inhA 1673934 c.-268C>T upstream_gene_variant 0.23
inhA 1673946 c.-256C>G upstream_gene_variant 0.22
fabG1 1673950 p.Leu171Met missense_variant 0.22
inhA 1673961 c.-241A>C upstream_gene_variant 0.24
inhA 1673973 c.-229G>C upstream_gene_variant 0.23
inhA 1673976 c.-226T>C upstream_gene_variant 0.24
inhA 1673985 c.-217C>G upstream_gene_variant 0.23
inhA 1674006 c.-196T>C upstream_gene_variant 0.21
fabG1 1674017 p.Ala193Gly missense_variant 0.2
inhA 1674024 c.-178T>C upstream_gene_variant 0.18
inhA 1674033 c.-169T>C upstream_gene_variant 0.18
fabG1 1674037 p.Gln200Glu missense_variant 0.18
inhA 1674051 c.-151A>G upstream_gene_variant 0.14
inhA 1674714 c.513C>G synonymous_variant 0.14
inhA 1674718 c.517A>C synonymous_variant 0.15
inhA 1674729 c.528G>C synonymous_variant 0.18
inhA 1674735 c.534G>A synonymous_variant 0.18
inhA 1674738 c.537C>G synonymous_variant 0.17
inhA 1674743 p.Lys181Thr missense_variant 0.15
inhA 1674750 c.549T>C synonymous_variant 0.16
inhA 1674756 c.555T>C synonymous_variant 0.17
inhA 1674765 c.564C>T synonymous_variant 0.17
inhA 1674774 c.573A>G synonymous_variant 0.17
inhA 1674777 c.576C>A synonymous_variant 0.16
inhA 1674780 c.579T>G synonymous_variant 0.16
inhA 1674801 c.600T>C synonymous_variant 0.15
inhA 1674825 c.624C>T synonymous_variant 0.13
rpsA 1833589 c.48A>T synonymous_variant 0.15
rpsA 1833595 c.54T>G synonymous_variant 0.17
rpsA 1833646 c.105T>C synonymous_variant 0.27
rpsA 1833667 c.126C>G synonymous_variant 0.28
rpsA 1833724 c.183C>G synonymous_variant 0.24
rpsA 1833727 c.186G>C synonymous_variant 0.25
rpsA 1833742 c.201A>G synonymous_variant 0.22
rpsA 1833745 c.204G>C synonymous_variant 0.23
rpsA 1833748 c.207C>G synonymous_variant 0.23
rpsA 1833778 c.237C>T synonymous_variant 0.16
rpsA 1833781 c.240T>C synonymous_variant 0.16
rpsA 1834177 c.636A>C synonymous_variant 0.92
rpsA 1834366 c.825A>G synonymous_variant 0.13
rpsA 1834369 c.828C>G synonymous_variant 0.13
rpsA 1834375 c.834G>A synonymous_variant 0.13
rpsA 1834411 c.870T>C synonymous_variant 0.16
rpsA 1834417 c.876G>C synonymous_variant 0.17
rpsA 1834423 c.882G>C synonymous_variant 0.15
rpsA 1834451 c.910T>C synonymous_variant 0.15
rpsA 1834456 c.915T>G synonymous_variant 0.14
rpsA 1834459 c.918G>A synonymous_variant 0.14
rpsA 1834468 c.927A>G synonymous_variant 0.14
rpsA 1834525 c.984G>A synonymous_variant 0.15
rpsA 1834528 c.987T>C synonymous_variant 0.17
rpsA 1834546 c.1005T>C synonymous_variant 0.21
rpsA 1834555 c.1014T>C synonymous_variant 0.22
rpsA 1834609 c.1068T>C synonymous_variant 0.21
rpsA 1834633 c.1092A>G synonymous_variant 0.21
rpsA 1834639 c.1098T>C synonymous_variant 0.23
rpsA 1834669 c.1128G>C synonymous_variant 0.22
rpsA 1834690 c.1149T>C synonymous_variant 0.17
rpsA 1834732 c.1191T>C synonymous_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154113 p.Thr667Pro missense_variant 0.92
katG 2154724 p.Arg463Leu missense_variant 0.83
PPE35 2167926 p.Leu896Ser missense_variant 0.87
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2517941 c.-174C>G upstream_gene_variant 0.26
kasA 2517974 c.-141T>C upstream_gene_variant 0.22
kasA 2517989 c.-126T>G upstream_gene_variant 0.22
kasA 2518076 c.-39C>T upstream_gene_variant 0.15
kasA 2518684 c.570C>T synonymous_variant 0.15
kasA 2518696 c.582C>G synonymous_variant 0.16
kasA 2518705 c.591T>C synonymous_variant 0.19
kasA 2518714 c.600A>C synonymous_variant 0.18
kasA 2518732 c.618C>G synonymous_variant 0.2
kasA 2518741 c.627G>T synonymous_variant 0.24
kasA 2518747 c.633C>G synonymous_variant 0.26
kasA 2518783 c.669T>G synonymous_variant 0.25
kasA 2518789 c.675G>C synonymous_variant 0.21
kasA 2518792 c.678C>G synonymous_variant 0.18
kasA 2518795 c.681C>G synonymous_variant 0.17
kasA 2518798 c.684G>T synonymous_variant 0.16
kasA 2518825 c.711T>C synonymous_variant 0.2
kasA 2518828 c.714G>C synonymous_variant 0.19
kasA 2518864 c.750G>C synonymous_variant 0.16
kasA 2518879 c.765A>G synonymous_variant 0.16
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474168 c.162G>C synonymous_variant 0.13
fprA 3474216 c.210G>T synonymous_variant 0.13
Rv3236c 3612813 p.Thr102Ala missense_variant 0.85
rpoA 3877587 c.921A>G synonymous_variant 0.15
rpoA 3877593 c.915C>T synonymous_variant 0.16
rpoA 3877613 p.Ile299Val missense_variant 0.21
rpoA 3877638 c.870T>G synonymous_variant 0.18
rpoA 3877656 c.852T>C synonymous_variant 0.17
rpoA 3877668 c.840A>G synonymous_variant 0.19
rpoA 3877677 p.Ala277Ser missense_variant 0.21
rpoA 3877686 c.822A>G synonymous_variant 0.24
rpoA 3877692 c.816G>C synonymous_variant 0.23
rpoA 3877704 c.804G>C synonymous_variant 0.18
rpoA 3877737 c.771G>C synonymous_variant 0.15
rpoA 3877818 c.690A>G synonymous_variant 0.16
rpoA 3877841 c.667C>A synonymous_variant 0.15
rpoA 3877875 c.633T>G synonymous_variant 0.16
rpoA 3877893 c.615C>T synonymous_variant 0.16
rpoA 3877896 c.612G>C synonymous_variant 0.16
rpoA 3877962 c.546G>T synonymous_variant 0.2
rpoA 3877986 c.522G>C synonymous_variant 0.22
rpoA 3877989 c.519A>G synonymous_variant 0.2
rpoA 3878001 c.507A>G synonymous_variant 0.18
rpoA 3878019 c.489A>G synonymous_variant 0.2
rpoA 3878022 c.486T>C synonymous_variant 0.2
rpoA 3878028 c.480G>C synonymous_variant 0.2
rpoA 3878031 c.477T>C synonymous_variant 0.2
rpoA 3878040 c.468T>C synonymous_variant 0.22
rpoA 3878046 c.462T>G synonymous_variant 0.21
rpoA 3878049 c.459G>C synonymous_variant 0.22
rpoA 3878055 c.453A>G synonymous_variant 0.26
rpoA 3878067 c.441C>G synonymous_variant 0.25
rpoA 3878070 c.438T>C synonymous_variant 0.26
rpoA 3878082 c.426T>C synonymous_variant 0.29
rpoA 3878103 c.405A>G synonymous_variant 0.25
rpoA 3878106 c.402G>C synonymous_variant 0.24
rpoA 3878118 c.390T>C synonymous_variant 0.25
rpoA 3878130 c.378C>G synonymous_variant 0.22
rpoA 3878157 c.351C>G synonymous_variant 0.24
rpoA 3878160 c.348C>G synonymous_variant 0.26
rpoA 3878187 c.321C>G synonymous_variant 0.27
rpoA 3878193 c.315T>G synonymous_variant 0.24
rpoA 3878205 c.303T>C synonymous_variant 0.22
rpoA 3878217 c.291A>G synonymous_variant 0.23
rpoA 3878232 c.276G>C synonymous_variant 0.2
rpoA 3878235 c.273G>A synonymous_variant 0.18
rpoA 3878247 c.261G>C synonymous_variant 0.16
rpoA 3878264 p.Ser82Gly missense_variant 0.14
rpoA 3878283 p.Glu75Asp missense_variant 0.13
rpoA 3878292 c.216T>C synonymous_variant 0.15
rpoA 3878304 c.204G>C synonymous_variant 0.14
rpoA 3878313 c.195G>C synonymous_variant 0.15
rpoA 3878322 c.186A>G synonymous_variant 0.17
rpoA 3878331 c.177A>G synonymous_variant 0.17
rpoA 3878334 c.174T>C synonymous_variant 0.17
rpoA 3878337 c.171T>C synonymous_variant 0.17
rpoA 3878346 c.162T>C synonymous_variant 0.22
rpoA 3878364 c.144A>C synonymous_variant 0.22
rpoA 3878367 c.141C>G synonymous_variant 0.22
rpoA 3878370 c.138T>C synonymous_variant 0.22
rpoA 3878385 c.123C>G synonymous_variant 0.23
rpoA 3878391 c.117T>G synonymous_variant 0.23
rpoA 3878415 c.93C>T synonymous_variant 0.22
rpoA 3878424 c.84G>C synonymous_variant 0.17
rpoA 3878436 c.72A>G synonymous_variant 0.16
rpoA 3878442 c.66G>C synonymous_variant 0.16
rpoA 3878454 c.54A>G synonymous_variant 0.16
rpoA 3878458 p.Asn17Thr missense_variant 0.15
rpoA 3878698 c.-191A>G upstream_gene_variant 0.17
rpoA 3878701 c.-194C>G upstream_gene_variant 0.18
clpC1 4038653 c.2052C>T synonymous_variant 0.14
clpC1 4038695 c.2010C>G synonymous_variant 0.13
clpC1 4038713 c.1992T>C synonymous_variant 0.14
clpC1 4038755 c.1950G>C synonymous_variant 0.15
clpC1 4038764 c.1941C>G synonymous_variant 0.14
clpC1 4038767 c.1938G>T synonymous_variant 0.14
clpC1 4038790 c.1915C>T synonymous_variant 0.14
clpC1 4038812 c.1893T>C synonymous_variant 0.22
clpC1 4038821 c.1884G>A synonymous_variant 0.24
clpC1 4038878 c.1827A>G synonymous_variant 0.21
clpC1 4038908 c.1797C>G synonymous_variant 0.25
clpC1 4038914 c.1791G>C synonymous_variant 0.26
clpC1 4038923 c.1782A>G synonymous_variant 0.26
clpC1 4038953 c.1752A>G synonymous_variant 0.18
clpC1 4038956 c.1749T>C synonymous_variant 0.19
clpC1 4038965 c.1740T>C synonymous_variant 0.2
clpC1 4038971 c.1734T>C synonymous_variant 0.19
clpC1 4038974 c.1731T>C synonymous_variant 0.19
clpC1 4038997 c.1708T>C synonymous_variant 0.19
clpC1 4039022 c.1683A>G synonymous_variant 0.16
clpC1 4040695 c.10C>A synonymous_variant 0.14
clpC1 4040711 c.-7G>A upstream_gene_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.17
embA 4243460 c.228C>T synonymous_variant 0.91
embB 4247491 c.978G>C synonymous_variant 0.19
embB 4247497 c.984T>C synonymous_variant 0.21
embB 4247506 c.993C>G synonymous_variant 0.2
embB 4247512 c.999T>C synonymous_variant 0.17
embB 4247536 c.1023C>A synonymous_variant 0.15
embB 4247539 c.1026T>C synonymous_variant 0.15
embB 4247550 p.Ala346Gly missense_variant 0.15
embB 4247554 c.1041T>C synonymous_variant 0.14
embB 4247566 c.1053C>G synonymous_variant 0.15
embB 4247567 c.1054C>T synonymous_variant 0.14
embB 4247572 c.1059A>C synonymous_variant 0.17
embB 4247579 p.Ala356Ile missense_variant 0.17
embB 4247590 c.1077A>G synonymous_variant 0.15
aftB 4267647 p.Asp397Gly missense_variant 0.86
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338635 c.-114A>C upstream_gene_variant 0.23
gid 4407588 c.615A>G synonymous_variant 0.9
gid 4407927 p.Glu92Asp missense_variant 0.89