TB-Profiler result

Run: ERR4818637
Summary

Run ID: ERR4818637

Sample name:

Date: 01-04-2023 15:40:09

Number of reads: 495018

Percentage reads mapped: 90.01

Strain: lineage4.8

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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 1472733 n.888G>A non_coding_transcript_exon_variant 1.0 streptomycin
gid 4407952 p.Pro84Leu missense_variant 0.18 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 5205 c.-35G>A upstream_gene_variant 0.25
gyrB 5234 c.-6C>T upstream_gene_variant 0.2
gyrB 5642 p.Leu135Ile missense_variant 0.25
gyrB 5863 c.624G>A synonymous_variant 0.22
gyrB 6227 p.Lys330* stop_gained 0.25
gyrB 6432 p.Ala398Asp missense_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7434 p.Arg45Cys missense_variant 0.18
gyrA 7847 c.546G>T synonymous_variant 0.2
fgd1 490670 c.-113G>T upstream_gene_variant 0.4
fgd1 490878 p.Met32Ile missense_variant 0.15
fgd1 491030 p.Pro83His missense_variant 0.33
fgd1 491746 p.Glu322* stop_gained 0.17
mshA 575983 c.636G>A synonymous_variant 0.29
mshA 576427 c.1080G>A synonymous_variant 0.14
mshA 576576 p.Ala410Val missense_variant 0.12
ccsA 620176 p.Val96Leu missense_variant 0.2
rpoB 759682 c.-125G>T upstream_gene_variant 0.17
rpoB 760565 c.759A>T synonymous_variant 0.14
rpoB 760657 p.Glu284Gly missense_variant 0.2
rpoB 760681 p.Asn292Ser missense_variant 1.0
rpoB 761012 p.Asp402Glu missense_variant 0.14
rpoB 761540 c.1734C>A synonymous_variant 0.5
rpoB 761929 p.Ala708Val missense_variant 0.22
rpoB 762021 p.Asp739Tyr missense_variant 0.18
rpoB 762681 p.Glu959* stop_gained 0.18
rpoB 762748 p.Gly981Ala missense_variant 0.17
rpoC 763977 p.Arg203His missense_variant 0.2
rpoC 764671 c.1302G>A synonymous_variant 0.22
rpoC 764854 c.1485G>T synonymous_variant 0.17
rpoC 765374 p.Gly669Cys missense_variant 0.18
rpoC 765403 c.2034G>A synonymous_variant 0.2
rpoC 765448 p.Gln693His missense_variant 0.33
rpoC 766053 p.Arg895His missense_variant 0.17
rpoC 766616 c.3247C>A synonymous_variant 0.15
mmpL5 775634 c.2847G>A synonymous_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776247 p.Ala745Asp missense_variant 0.2
mmpL5 776378 p.Phe701Leu missense_variant 0.33
mmpL5 776923 p.Ala520Ser missense_variant 0.67
mmpL5 777182 c.1299C>A synonymous_variant 0.29
mmpL5 777521 c.960C>G synonymous_variant 0.22
mmpL5 777655 p.Asp276Tyr missense_variant 0.22
mmpL5 777948 p.Pro178Leu missense_variant 0.2
mmpS5 779682 c.-777G>T upstream_gene_variant 0.5
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800789 c.-20G>A upstream_gene_variant 0.15
rplC 801022 p.Ala72Thr missense_variant 0.29
fbiC 1304625 c.1695C>T synonymous_variant 0.15
fbiC 1304927 p.Gly666Val missense_variant 0.2
fbiC 1305086 p.Trp719Leu missense_variant 0.17
fbiC 1305193 p.Gly755Cys missense_variant 0.17
Rv1258c 1407350 c.-10C>T upstream_gene_variant 0.13
Rv1258c 1407446 c.-106G>A upstream_gene_variant 0.17
embR 1416348 p.Asp334Tyr missense_variant 0.22
embR 1416645 p.Leu235Met missense_variant 0.22
embR 1417050 p.Gly100Ser missense_variant 0.25
embR 1417212 p.Arg46Cys missense_variant 0.15
embR 1417242 p.Arg36Trp missense_variant 0.15
embR 1417496 c.-149C>T upstream_gene_variant 0.2
atpE 1460916 c.-129G>A upstream_gene_variant 0.33
rrs 1472094 n.249T>G non_coding_transcript_exon_variant 1.0
rrs 1472100 n.255T>C non_coding_transcript_exon_variant 1.0
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 1.0
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 1.0
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 1.0
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 1.0
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 1.0
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 1.0
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 1.0
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 1.0
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 1.0
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 1.0
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 1.0
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 1.0
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 1.0
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 1.0
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 1.0
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 1.0
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 1.0
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.95
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.92
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.61
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.97
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.97
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.97
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.19
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.97
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.98
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 1.0
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 1.0
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 1.0
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 1.0
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 1.0
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 1.0
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 1.0
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 1.0
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 1.0
rrs 1472953 n.1108G>A non_coding_transcript_exon_variant 1.0
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 1.0
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 1.0
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 1.0
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 1.0
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 1.0
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 0.5
rrs 1473364 n.1519G>T non_coding_transcript_exon_variant 0.5
rrl 1474218 n.561T>A non_coding_transcript_exon_variant 1.0
rrl 1474228 n.571T>C non_coding_transcript_exon_variant 1.0
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 1.0
rrl 1474252 n.595T>A non_coding_transcript_exon_variant 1.0
rrl 1474275 n.618T>C non_coding_transcript_exon_variant 1.0
rrl 1475129 n.1472G>A non_coding_transcript_exon_variant 1.0
rrl 1475154 n.1497C>G non_coding_transcript_exon_variant 1.0
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 1.0
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 1.0
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 0.88
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 1.0
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.8
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 1.0
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.8
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 1.0
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 1.0
fabG1 1673536 p.Gln33Lys missense_variant 0.67
inhA 1674993 c.792G>A synonymous_variant 1.0
rpsA 1833354 c.-188G>A upstream_gene_variant 0.25
rpsA 1834595 p.Asp352Tyr missense_variant 0.2
tlyA 1918474 p.Pro179Ser missense_variant 0.17
tlyA 1918602 c.663C>T synonymous_variant 0.22
ndh 2102218 c.825C>T synonymous_variant 0.22
ndh 2103020 p.Thr8Ile missense_variant 0.29
ndh 2103209 c.-167C>T upstream_gene_variant 0.17
katG 2155740 c.372C>A synonymous_variant 0.5
katG 2156236 c.-125C>A upstream_gene_variant 0.33
katG 2156483 c.-372C>A upstream_gene_variant 0.18
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2169393 p.Ala407Asp missense_variant 0.18
PPE35 2169458 c.1155C>A synonymous_variant 0.4
PPE35 2169908 p.Asn235Lys missense_variant 0.5
PPE35 2170463 c.150C>A synonymous_variant 0.2
Rv1979c 2221893 c.1272C>A synonymous_variant 0.25
Rv1979c 2222132 p.Gln345Lys missense_variant 0.2
Rv1979c 2222502 p.Met221Ile missense_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288825 c.417G>T synonymous_variant 0.2
kasA 2518970 p.Arg286Cys missense_variant 0.33
eis 2714944 p.Gly130Asp missense_variant 0.2
eis 2714969 p.Glu122Lys missense_variant 0.33
eis 2715492 c.-160G>T upstream_gene_variant 0.29
eis 2715528 c.-196G>T upstream_gene_variant 0.5
ahpC 2725963 c.-230G>T upstream_gene_variant 0.22
ahpC 2726192 c.-1C>A upstream_gene_variant 0.25
folC 2746159 c.1440C>A synonymous_variant 0.22
folC 2746287 p.Asp438His missense_variant 0.33
pepQ 2860217 p.Ala68Ser missense_variant 0.29
pepQ 2860297 p.Gly41Val missense_variant 0.33
pepQ 2860365 c.54G>A synonymous_variant 0.18
ribD 2986878 p.Leu14Ile missense_variant 0.13
ribD 2987549 c.711G>A synonymous_variant 0.14
ribD 2987556 p.Cys240Ser missense_variant 0.15
Rv2752c 3064581 c.1611C>A synonymous_variant 0.25
Rv2752c 3064753 p.Arg480Lys missense_variant 0.17
Rv2752c 3064820 p.Gly458Ser missense_variant 0.22
Rv2752c 3065306 p.Ala296Thr missense_variant 0.12
Rv2752c 3065322 c.870C>T synonymous_variant 0.14
Rv2752c 3066360 c.-170delG upstream_gene_variant 0.17
thyX 3067436 c.510C>T synonymous_variant 0.15
thyA 3074403 c.69C>A synonymous_variant 0.29
ald 3087069 p.Arg84Ser missense_variant 0.2
ald 3087152 c.333C>A synonymous_variant 1.0
ald 3087203 c.384C>A synonymous_variant 0.29
ald 3087243 p.Ala142Ser missense_variant 0.29
ald 3087287 c.468C>T synonymous_variant 0.25
ald 3087460 p.Arg214Gln missense_variant 0.33
fbiD 3339008 c.-110A>G upstream_gene_variant 0.13
fbiD 3339506 p.Ser130Leu missense_variant 0.25
Rv3083 3448350 c.-154G>A upstream_gene_variant 0.12
Rv3083 3448361 c.-143G>A upstream_gene_variant 0.18
fprA 3473999 c.-8G>T upstream_gene_variant 0.2
fprA 3474511 p.Asp169Tyr missense_variant 0.2
fprA 3474711 p.Asp235Glu missense_variant 0.29
fprA 3474834 c.828C>T synonymous_variant 0.15
fprA 3474885 c.879G>A synonymous_variant 0.22
whiB7 3568431 c.249C>T synonymous_variant 0.13
whiB7 3568822 c.-143C>G upstream_gene_variant 0.17
Rv3236c 3612351 p.Ala256Thr missense_variant 0.15
Rv3236c 3612877 c.240C>T synonymous_variant 0.4
fbiA 3640714 p.Val58Phe missense_variant 0.12
fbiA 3641503 p.Arg321Cys missense_variant 0.2
fbiB 3641608 p.Pro25His missense_variant 0.2
alr 3840409 p.Val338Leu missense_variant 0.17
alr 3840459 p.Ser321Leu missense_variant 0.29
alr 3840719 c.702A>G synonymous_variant 0.15
alr 3841059 p.Gly121Glu missense_variant 0.13
alr 3841084 p.Leu113Met missense_variant 0.12
alr 3841185 c.235delC frameshift_variant 1.0
rpoA 3877539 c.969C>T synonymous_variant 0.15
rpoA 3877959 c.549C>T synonymous_variant 0.33
ddn 3986753 c.-91G>T upstream_gene_variant 0.22
ddn 3986843 c.-1C>A upstream_gene_variant 0.33
ddn 3987173 c.330C>T synonymous_variant 0.17
clpC1 4038383 c.2322G>A synonymous_variant 0.13
clpC1 4038771 p.Gly645Val missense_variant 0.33
clpC1 4039671 p.Val345Glu missense_variant 0.15
clpC1 4039729 p.Asp326Asn missense_variant 1.0
clpC1 4040896 c.-192C>T upstream_gene_variant 0.22
embC 4240320 p.Gln153Arg missense_variant 0.22
embC 4241137 c.1275G>T synonymous_variant 0.33
embC 4241197 c.1335G>T synonymous_variant 0.22
embC 4242216 p.Phe785Ser missense_variant 0.4
embC 4242491 p.Arg877Trp missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242675 p.Ser938Asn missense_variant 0.33
embA 4242724 c.-509G>A upstream_gene_variant 0.25
embC 4242762 p.Arg967Leu missense_variant 0.14
embA 4242997 c.-236G>A upstream_gene_variant 0.4
embA 4243846 p.Ala205Asp missense_variant 0.18
embA 4244195 c.963C>A synonymous_variant 0.14
embA 4245098 c.1866C>T synonymous_variant 0.15
embA 4245314 c.2082G>A synonymous_variant 0.25
embA 4246265 p.His1011Gln missense_variant 0.13
embB 4246821 p.Pro103His missense_variant 0.18
embB 4246979 p.Gly156Ser missense_variant 0.17
embB 4247606 c.1093C>T synonymous_variant 0.18
embB 4247689 c.1176G>A synonymous_variant 0.13
embB 4248298 p.His595Gln missense_variant 0.15
embB 4249077 p.Gln855Leu missense_variant 0.14
embB 4249151 p.Ala880Ser missense_variant 0.15
aftB 4266961 p.Arg626Trp missense_variant 0.14
aftB 4267061 p.Leu592Phe missense_variant 0.14
aftB 4267128 p.Ala570Glu missense_variant 0.4
aftB 4267284 p.Thr518Ile missense_variant 0.14
aftB 4268332 p.Gln169Lys missense_variant 0.14
aftB 4268350 p.Arg163Trp missense_variant 0.14
ubiA 4269309 p.Trp175Cys missense_variant 1.0
ubiA 4269490 p.Ala115Asp missense_variant 0.33
aftB 4269621 c.-785C>A upstream_gene_variant 0.17
ubiA 4269959 c.-126C>A upstream_gene_variant 0.29
ethA 4326762 p.Val238Ile missense_variant 0.18
ethA 4328184 c.-711G>A upstream_gene_variant 0.22
ethA 4328215 c.-742C>A upstream_gene_variant 0.15
ethA 4328282 c.-809C>T upstream_gene_variant 0.25
whiB6 4338383 p.Asp47Tyr missense_variant 0.2
whiB6 4338399 p.Trp41Cys missense_variant 0.22
whiB6 4338435 c.87C>A synonymous_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338646 c.-125A>T upstream_gene_variant 0.22
gid 4407914 p.Arg97Cys missense_variant 0.18
gid 4408260 c.-58A>G upstream_gene_variant 0.2