TB-Profiler result

Run: SRR13986566
Summary

Run ID: SRR13986566

Sample name:

Date: 03-04-2023 09:43:57

Number of reads: 1052758

Percentage reads mapped: 85.57

Strain: La1.7.1

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
La1 M.bovis None None 1.0
La1.7 M.bovis None None 1.0
La1.7.1 M.bovis None None 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
rrs 1472644 n.799C>T non_coding_transcript_exon_variant 0.33 streptomycin
pncA 2289073 p.His57Asp missense_variant 1.0 pyrazinamide
gid 4407908 p.Glu99* stop_gained 0.22 streptomycin
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 5752 c.513G>A synonymous_variant 1.0
gyrA 6406 c.-896C>T upstream_gene_variant 1.0
gyrB 6446 p.Ala403Ser missense_variant 1.0
gyrA 6835 c.-467C>T upstream_gene_variant 0.2
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7437 p.Asp46Tyr missense_variant 0.25
gyrA 7481 c.180C>T synonymous_variant 0.17
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7642 p.Gly114Val missense_variant 0.12
gyrA 7678 p.Ala126Glu missense_variant 0.15
gyrA 7887 p.Glu196* stop_gained 0.14
gyrA 8285 c.984C>T synonymous_variant 1.0
gyrA 8327 c.1026C>T synonymous_variant 0.17
gyrA 8751 p.Ala484Ser missense_variant 0.18
gyrA 8940 p.Ala547Ser missense_variant 0.13
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9217 p.Asp639Ala missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491281 p.Asp167Asn missense_variant 0.22
fgd1 491284 p.Gly168Arg missense_variant 0.2
fgd1 491296 p.Val172Ile missense_variant 0.2
fgd1 491645 p.Ser288* stop_gained 0.12
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575359 c.12G>A synonymous_variant 0.14
mshA 576286 c.939C>A synonymous_variant 0.12
mshA 576729 p.Ser461Leu missense_variant 0.29
mshA 576771 p.Arg475His missense_variant 0.15
ccsA 619705 c.-186G>A upstream_gene_variant 0.2
ccsA 619868 c.-23G>A upstream_gene_variant 0.15
ccsA 619909 p.Asn7His missense_variant 0.25
ccsA 620028 c.138G>T synonymous_variant 0.25
ccsA 620278 p.Arg130Cys missense_variant 0.33
rpoB 759620 c.-187A>C upstream_gene_variant 0.26
rpoB 759931 p.Leu42Pro missense_variant 0.13
rpoB 760815 p.Glu337* stop_gained 0.13
rpoB 761254 p.Pro483His missense_variant 0.2
rpoB 761433 p.Asp543Asn missense_variant 0.22
rpoB 761791 p.Arg662His missense_variant 0.17
rpoB 762646 p.Pro947Leu missense_variant 0.18
rpoB 763017 p.Gln1071Lys missense_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763394 p.Glu9* stop_gained 0.17
rpoC 763405 c.36C>T synonymous_variant 0.14
rpoC 763464 p.Glu32Gly missense_variant 0.11
rpoC 763883 p.Ala172Ser missense_variant 0.5
rpoC 763958 p.Val197Phe missense_variant 0.5
rpoC 764335 c.966G>A synonymous_variant 0.14
rpoC 764467 c.1098C>A synonymous_variant 0.14
rpoC 766439 p.Ile1024Val missense_variant 0.11
rpoC 766942 c.3573C>A synonymous_variant 0.12
rpoC 766975 c.3606C>A synonymous_variant 0.2
rpoC 767013 p.Leu1215Pro missense_variant 0.25
rpoC 767061 p.Arg1231Leu missense_variant 0.33
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776340 p.His714Arg missense_variant 0.14
mmpL5 776443 p.Phe680Leu missense_variant 0.12
mmpL5 776694 p.Val596Ser missense_variant 0.18
mmpL5 776702 c.1779C>T synonymous_variant 0.17
mmpL5 776726 c.1755C>T synonymous_variant 0.38
mmpL5 776746 p.Arg579Ser missense_variant 0.2
mmpL5 777016 p.Gly489Arg missense_variant 0.14
mmpL5 777122 c.1359C>T synonymous_variant 0.12
mmpL5 777128 c.1353A>G synonymous_variant 0.12
mmpL5 777136 p.Met449Leu missense_variant 0.11
mmpL5 777270 p.Gly404Val missense_variant 0.25
mmpL5 778137 p.Arg115Ile missense_variant 0.14
mmpR5 778319 c.-671T>C upstream_gene_variant 0.1
mmpS5 778740 p.Val56Leu missense_variant 0.17
mmpL5 778822 c.-342C>A upstream_gene_variant 0.22
mmpS5 779615 c.-710C>G upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781506 c.-54C>A upstream_gene_variant 0.14
rplC 801081 c.273C>T synonymous_variant 0.22
rplC 801248 p.Arg147His missense_variant 0.18
fbiC 1302849 c.-82G>A upstream_gene_variant 0.2
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
fbiC 1303262 p.Pro111Leu missense_variant 0.17
fbiC 1303403 p.Ala158Glu missense_variant 0.14
fbiC 1303632 c.702T>C synonymous_variant 0.22
fbiC 1303895 p.Arg322Gln missense_variant 0.15
fbiC 1304110 p.Ala394Ser missense_variant 0.14
fbiC 1304413 p.Val495Met missense_variant 0.14
fbiC 1305355 p.Gly809Ser missense_variant 0.12
Rv1258c 1406460 p.Ala294Val missense_variant 0.17
Rv1258c 1406496 p.Ala282Asp missense_variant 0.14
Rv1258c 1406941 p.Arg134Trp missense_variant 0.25
Rv1258c 1407022 p.Ala107Thr missense_variant 0.22
Rv1258c 1407233 p.Gln36His missense_variant 1.0
Rv1258c 1407450 c.-110G>A upstream_gene_variant 0.2
embR 1416435 p.Ala305Ser missense_variant 0.12
embR 1416606 p.Arg248Cys missense_variant 0.2
embR 1416743 p.Pro202His missense_variant 0.12
embR 1416938 p.His137Arg missense_variant 0.17
atpE 1461070 p.Ala9Asp missense_variant 0.5
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472062 n.217G>A non_coding_transcript_exon_variant 0.33
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 1.0
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 1.0
rrs 1472612 n.767G>T non_coding_transcript_exon_variant 0.67
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.33
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.33
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.67
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.67
rrs 1472690 n.845C>T non_coding_transcript_exon_variant 1.0
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 1.0
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 1.0
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.5
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.5
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.4
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.33
rrs 1473215 n.1370A>C non_coding_transcript_exon_variant 0.25
rrl 1473703 n.46C>T non_coding_transcript_exon_variant 0.5
rrl 1474422 n.765C>A non_coding_transcript_exon_variant 0.33
rrl 1475129 n.1472G>T non_coding_transcript_exon_variant 1.0
rrl 1475154 n.1497C>A non_coding_transcript_exon_variant 1.0
rrl 1475175 n.1518G>A non_coding_transcript_exon_variant 1.0
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.2
rrl 1475866 n.2209T>A non_coding_transcript_exon_variant 0.2
rrl 1476477 n.2820G>T non_coding_transcript_exon_variant 1.0
fabG1 1673657 p.Thr73Met missense_variant 0.12
inhA 1674423 p.Leu74Phe missense_variant 0.17
inhA 1674846 c.645C>A synonymous_variant 0.33
inhA 1674988 p.Gly263Ile missense_variant 0.2
rpsA 1833937 p.Glu132Asp missense_variant 0.17
rpsA 1834022 c.481C>T synonymous_variant 0.2
rpsA 1834124 p.Gln195Lys missense_variant 0.12
rpsA 1834758 p.Gly406Val missense_variant 0.15
rpsA 1834831 c.1290G>T synonymous_variant 0.12
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918362 c.423G>A synonymous_variant 0.5
ndh 2101759 p.Gln428His missense_variant 0.12
ndh 2103151 c.-109G>T upstream_gene_variant 0.2
ndh 2103173 c.-132delG upstream_gene_variant 1.0
ndh 2103193 c.-151G>A upstream_gene_variant 0.17
ndh 2103205 c.-163G>T upstream_gene_variant 0.2
ndh 2103225 c.-183A>C upstream_gene_variant 0.29
katG 2153996 p.Ala706Ser missense_variant 0.13
katG 2154018 c.2094C>T synonymous_variant 0.22
katG 2154217 p.Arg632Leu missense_variant 0.17
katG 2154591 c.1521C>A synonymous_variant 0.13
katG 2154711 p.Leu467Phe missense_variant 0.13
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154826 p.Pro429Gln missense_variant 0.2
katG 2154984 c.1128G>A synonymous_variant 1.0
katG 2155089 p.Trp341Cys missense_variant 0.33
katG 2155403 p.Gly237Ser missense_variant 0.2
katG 2155503 c.609C>T synonymous_variant 1.0
katG 2155710 p.Ser134Arg missense_variant 0.2
katG 2155830 p.Asp94Glu missense_variant 0.5
katG 2156025 c.87C>A synonymous_variant 1.0
PPE35 2167745 p.Thr956Arg missense_variant 0.5
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167936 p.Thr893Ala missense_variant 0.11
PPE35 2167937 c.2676A>C synonymous_variant 0.1
PPE35 2167965 p.Ala883Gly missense_variant 0.12
PPE35 2167967 c.2646A>C synonymous_variant 0.12
PPE35 2168011 p.Ser868Arg missense_variant 1.0
PPE35 2168319 p.Thr765Ile missense_variant 1.0
PPE35 2168814 c.1798dupA frameshift_variant 1.0
PPE35 2169180 p.Pro478His missense_variant 0.12
PPE35 2170518 p.Asp32Thr missense_variant 0.25
Rv1979c 2222173 p.Ala331Gly missense_variant 0.2
Rv1979c 2222212 p.Ala318Glu missense_variant 0.14
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223026 p.Ala47Thr missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223336 c.-172G>T upstream_gene_variant 0.14
pncA 2288880 p.Arg121Gln missense_variant 0.13
pncA 2289020 c.222C>T synonymous_variant 1.0
pncA 2289217 p.Val9Met missense_variant 0.15
pncA 2289512 c.-271G>T upstream_gene_variant 0.25
pncA 2289913 c.-672T>C upstream_gene_variant 0.14
pncA 2290219 c.-978C>A upstream_gene_variant 0.17
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518195 c.81G>T synonymous_variant 0.15
kasA 2518411 c.297C>A synonymous_variant 0.14
kasA 2518725 p.Ala204Val missense_variant 0.33
kasA 2518895 p.Pro261Thr missense_variant 0.2
kasA 2519096 p.Val328Phe missense_variant 0.25
kasA 2519180 p.Val356Met missense_variant 0.17
kasA 2519243 p.Asp377Asn missense_variant 0.17
eis 2714240 p.Arg365Ser missense_variant 0.2
ahpC 2725968 c.-225C>T upstream_gene_variant 0.14
ahpC 2726104 c.-89T>G upstream_gene_variant 1.0
ahpC 2726427 p.Asp79Asn missense_variant 0.14
folC 2746166 p.Ala478Val missense_variant 0.18
folC 2746241 c.1355_1357delCCG disruptive_inframe_deletion 0.25
folC 2746453 c.1146G>T synonymous_variant 0.14
folC 2746949 p.Ala217Val missense_variant 0.25
folC 2747320 c.279C>T synonymous_variant 0.17
folC 2747371 c.228C>A synonymous_variant 0.17
folC 2747651 c.-53C>A upstream_gene_variant 0.25
folC 2747754 c.-156C>G upstream_gene_variant 0.18
pepQ 2859380 p.Gly347Trp missense_variant 0.14
pepQ 2859408 c.1011C>T synonymous_variant 0.14
pepQ 2859667 p.Gln251Arg missense_variant 0.12
pepQ 2859693 c.726C>T synonymous_variant 1.0
pepQ 2860083 c.336C>G synonymous_variant 0.14
pepQ 2860151 p.Ala90Ser missense_variant 0.25
pepQ 2860162 p.Arg86Leu missense_variant 0.25
ribD 2986658 c.-181_-180insGG upstream_gene_variant 0.33
ribD 2986710 c.-129C>G upstream_gene_variant 0.2
ribD 2986801 c.-38G>A upstream_gene_variant 0.14
ribD 2986921 c.88delC frameshift_variant 0.17
ribD 2987510 c.672G>A synonymous_variant 0.2
ribD 2987515 p.Arg226His missense_variant 0.2
Rv2752c 3064695 c.1497A>G synonymous_variant 0.13
Rv2752c 3064783 p.Ser470* stop_gained 0.17
Rv2752c 3064894 p.Ala433Val missense_variant 0.12
Rv2752c 3065529 c.663G>T synonymous_variant 0.17
Rv2752c 3065533 p.Pro220Leu missense_variant 0.2
Rv2752c 3065949 p.His81Gln missense_variant 0.33
Rv2752c 3066027 c.165C>A synonymous_variant 0.2
thyX 3067534 p.Ala138Thr missense_variant 0.25
thyX 3067732 p.Val72Leu missense_variant 0.12
thyA 3073860 c.612C>A synonymous_variant 0.12
thyA 3073913 p.Met187Val missense_variant 0.1
thyA 3074565 c.-94C>A upstream_gene_variant 0.17
thyA 3074645 c.-174T>G upstream_gene_variant 0.22
ald 3086728 c.-92C>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086993 c.174C>A synonymous_variant 0.17
ald 3087084 c.266delA frameshift_variant 1.0
ald 3087215 c.396G>C synonymous_variant 0.17
ald 3087560 c.741C>A synonymous_variant 0.25
Rv3083 3448756 p.Ile85Phe missense_variant 0.25
Rv3083 3448783 p.Val94Ile missense_variant 1.0
Rv3083 3449049 c.546C>G synonymous_variant 0.25
Rv3083 3449054 p.Gly184Asp missense_variant 0.25
Rv3083 3449058 c.555C>T synonymous_variant 0.25
Rv3083 3449357 p.Asn285Ser missense_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474353 p.Gly116Val missense_variant 0.14
fprA 3474427 p.Val141Ile missense_variant 1.0
fprA 3475020 c.1014C>T synonymous_variant 0.17
fprA 3475026 c.1020C>A synonymous_variant 0.17
fprA 3475159 p.Asn385Asp missense_variant 1.0
fprA 3475267 p.Ala421Thr missense_variant 0.15
Rv3236c 3612387 p.Ala244Ser missense_variant 0.17
Rv3236c 3613059 p.Val20Leu missense_variant 0.12
fbiA 3640771 p.Arg77Ser missense_variant 0.17
fbiA 3640783 p.Gln81Lys missense_variant 0.12
fbiA 3640913 p.Pro124His missense_variant 0.12
fbiB 3641481 c.-54G>A upstream_gene_variant 0.17
fbiB 3641754 p.Arg74Cys missense_variant 0.2
fbiB 3642013 p.Gln160Arg missense_variant 0.29
fbiB 3642344 c.810G>T synonymous_variant 0.17
fbiB 3642478 p.Asp315Ala missense_variant 1.0
alr 3840380 p.Met347Ile missense_variant 0.12
alr 3840652 p.Val257Leu missense_variant 0.15
alr 3840705 p.Ala239Glu missense_variant 0.25
rpoA 3877794 c.714G>A synonymous_variant 0.25
rpoA 3877976 p.Val178Leu missense_variant 0.17
rpoA 3878566 c.-59C>T upstream_gene_variant 0.25
rpoA 3878630 c.-124delC upstream_gene_variant 1.0
clpC1 4038403 c.2302T>C synonymous_variant 1.0
clpC1 4038457 p.Val750Leu missense_variant 0.15
clpC1 4038740 c.1965G>A synonymous_variant 0.17
clpC1 4039123 p.Val528Ile missense_variant 0.14
clpC1 4039199 c.1506C>G synonymous_variant 0.33
clpC1 4039229 c.1476C>A synonymous_variant 0.14
clpC1 4039691 c.1014G>C synonymous_variant 0.12
clpC1 4039926 p.Arg260His missense_variant 0.2
clpC1 4040002 p.His235Asn missense_variant 0.17
clpC1 4040144 c.561G>C synonymous_variant 0.17
clpC1 4040220 p.Ser162Phe missense_variant 0.33
panD 4044230 p.Ala18Ser missense_variant 0.25
panD 4044400 c.-119G>T upstream_gene_variant 0.13
embC 4240080 p.Pro73Gln missense_variant 1.0
embC 4240565 p.Ile235Val missense_variant 0.22
embC 4240575 p.Val238Ala missense_variant 0.22
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4242302 p.Leu814Met missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242730 c.-503C>T upstream_gene_variant 0.33
embA 4242802 c.-431G>T upstream_gene_variant 0.14
embA 4242970 c.-263C>T upstream_gene_variant 1.0
embC 4243111 p.Ser1083Arg missense_variant 0.12
embA 4243153 c.-80C>G upstream_gene_variant 0.5
embA 4243462 p.Ser77Leu missense_variant 0.25
embA 4243488 p.Gly86Ser missense_variant 0.25
embA 4243877 c.645G>T synonymous_variant 0.14
embA 4244220 c.988C>T synonymous_variant 1.0
embA 4244428 p.Ser399* stop_gained 0.14
embA 4244487 p.Ala419Thr missense_variant 0.2
embA 4244499 p.Pro423Thr missense_variant 0.2
embA 4244708 c.1476C>A synonymous_variant 0.14
embA 4244724 p.Asp498Tyr missense_variant 0.12
embA 4244831 p.Phe533Leu missense_variant 0.17
embA 4244848 p.Gly539Val missense_variant 0.2
embA 4244899 p.Thr556Met missense_variant 0.14
embB 4245644 c.-870C>G upstream_gene_variant 0.11
embA 4245883 p.Gly884Val missense_variant 0.17
embA 4246131 p.Leu967Met missense_variant 0.13
embA 4246486 p.Gly1085Asp missense_variant 0.17
embB 4246551 p.Asn13Ser missense_variant 1.0
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4247275 p.Arg254Ser missense_variant 0.12
embB 4247569 c.1056G>T synonymous_variant 0.33
embB 4247610 p.Ser366* stop_gained 0.22
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4247725 c.1212G>A synonymous_variant 0.2
embB 4248591 p.Ala693Val missense_variant 0.5
embB 4249332 p.Pro940His missense_variant 0.22
embB 4249360 c.2847G>T synonymous_variant 0.13
embB 4249461 p.Pro983Gln missense_variant 0.22
embB 4249478 p.Ala989Ser missense_variant 0.15
aftB 4267216 p.Gly541Arg missense_variant 0.17
aftB 4267858 p.Ile327Val missense_variant 1.0
aftB 4268173 p.Val222Leu missense_variant 0.14
aftB 4268792 c.45G>A synonymous_variant 0.17
aftB 4268811 p.Ser9* stop_gained 0.13
ubiA 4269198 p.Ser212Arg missense_variant 0.13
ubiA 4269233 p.Arg201Ser missense_variant 0.14
aftB 4269351 c.-515C>T upstream_gene_variant 1.0
aftB 4269372 c.-536G>T upstream_gene_variant 0.17
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ubiA 4269989 c.-156G>C upstream_gene_variant 1.0
ethR 4327572 p.Gln8His missense_variant 0.13
ethR 4327621 p.Arg25Cys missense_variant 0.17
ethR 4327690 p.Asp48Tyr missense_variant 0.17
ethR 4327946 p.Glu133Ala missense_variant 0.11
whiB6 4338334 p.Ala63Glu missense_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408052 p.Asn51Asp missense_variant 1.0