TB-Profiler result

Run: ERR4815298
Summary

Run ID: ERR4815298

Sample name:

Date: 01-04-2023 13:47:06

Number of reads: 683227

Percentage reads mapped: 75.07

Strain: lineage4.3.4.2.1

Drug-resistance: Other

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 1.0
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 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 0.69 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 6140 p.Val301Leu missense_variant 1.0
gyrB 6218 p.Val327Leu missense_variant 0.2
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491008 c.231delC frameshift_variant 0.15
fgd1 491067 p.Cys95* stop_gained 0.14
ccsA 620406 c.516G>T synonymous_variant 0.12
rpoB 761051 c.1245G>C synonymous_variant 0.22
rpoB 761054 c.1248G>C synonymous_variant 0.22
rpoB 761057 c.1251G>C synonymous_variant 0.22
rpoB 761060 c.1254C>G synonymous_variant 0.22
rpoB 761084 c.1278C>A synonymous_variant 0.18
rpoB 761088 c.1282_1283delAGinsTC synonymous_variant 0.17
rpoB 761096 c.1290G>C synonymous_variant 0.17
rpoB 761097 c.1291_1293delAGCinsTCG synonymous_variant 0.17
rpoB 761102 c.1296A>G synonymous_variant 0.17
rpoB 761562 p.Ala586Ser missense_variant 0.17
rpoB 762218 c.2412T>C synonymous_variant 0.15
rpoB 762233 c.2427G>C synonymous_variant 0.18
rpoC 762483 c.-887C>T upstream_gene_variant 0.18
rpoC 762911 c.-459C>T upstream_gene_variant 0.2
rpoC 762917 c.-453C>T upstream_gene_variant 0.15
rpoC 762920 c.-450C>T upstream_gene_variant 0.14
rpoC 762929 c.-441G>T upstream_gene_variant 0.15
rpoC 762944 c.-426C>T upstream_gene_variant 0.13
rpoC 762956 c.-414G>C upstream_gene_variant 0.12
rpoC 762962 c.-408C>T upstream_gene_variant 0.12
rpoC 762983 c.-387C>T upstream_gene_variant 0.11
rpoC 762989 c.-381G>C upstream_gene_variant 0.12
rpoC 763022 c.-348C>A upstream_gene_variant 0.17
rpoC 763028 c.-342T>C upstream_gene_variant 0.15
rpoC 763031 c.-339T>C upstream_gene_variant 0.15
rpoB 763038 p.Thr1078Ala missense_variant 0.23
rpoC 763043 c.-327G>C upstream_gene_variant 0.25
rpoC 763053 c.-317T>C upstream_gene_variant 0.31
rpoC 763070 c.-300T>C upstream_gene_variant 0.26
rpoB 763077 p.Val1091Thr missense_variant 0.28
rpoC 763103 c.-267G>C upstream_gene_variant 0.33
rpoC 763115 c.-255T>C upstream_gene_variant 0.31
rpoB 763119 p.Asn1105Asp missense_variant 0.31
rpoC 763127 c.-243G>C upstream_gene_variant 0.18
rpoC 763133 c.-237G>C upstream_gene_variant 0.17
rpoC 763675 c.306C>G synonymous_variant 0.17
rpoC 763699 c.330G>T synonymous_variant 0.22
rpoC 763708 c.339G>C synonymous_variant 0.22
rpoC 763714 c.345G>C synonymous_variant 0.24
rpoC 763717 c.348T>C synonymous_variant 0.24
rpoC 763718 p.Leu117Val missense_variant 0.22
rpoC 763723 c.354G>C synonymous_variant 0.21
rpoC 763724 p.Asp119Asn missense_variant 0.21
rpoC 763729 c.360G>C synonymous_variant 0.22
rpoC 763732 c.363C>G synonymous_variant 0.22
rpoC 763735 c.366G>C synonymous_variant 0.19
rpoC 763744 c.375G>C synonymous_variant 0.2
rpoC 763751 p.Ile128Val missense_variant 0.2
rpoC 764458 c.1089G>C synonymous_variant 0.22
rpoC 764461 c.1092A>G synonymous_variant 0.22
rpoC 764485 c.1116G>C synonymous_variant 0.4
rpoC 764491 c.1122G>T synonymous_variant 0.4
rpoC 764503 c.1134G>T synonymous_variant 0.31
rpoC 764509 c.1140G>C synonymous_variant 0.31
rpoC 764512 c.1143G>C synonymous_variant 0.31
rpoC 764536 c.1167G>C synonymous_variant 0.25
rpoC 764543 p.Thr392Ala missense_variant 0.2
rpoC 764551 c.1182G>C synonymous_variant 0.25
rpoC 764611 c.1242G>T synonymous_variant 0.4
rpoC 764632 c.1263T>A synonymous_variant 0.29
rpoC 764647 c.1278C>T synonymous_variant 0.25
rpoC 764740 p.Met457Ile missense_variant 0.14
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766141 c.2772C>A synonymous_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777661 p.Ala274Ser missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303462 p.Ala178Thr missense_variant 0.13
embR 1416836 p.Val171Ala missense_variant 0.13
embR 1417083 p.Asp89Tyr missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471922 n.78delT non_coding_transcript_exon_variant 0.2
rrs 1471925 n.80T>C non_coding_transcript_exon_variant 0.2
rrs 1471931 n.87delA non_coding_transcript_exon_variant 0.22
rrs 1471934 n.89A>G non_coding_transcript_exon_variant 0.22
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.79
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.72
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.72
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.72
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.92
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.67
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.65
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.19
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.77
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 1.0
rrs 1472258 n.413A>G non_coding_transcript_exon_variant 0.6
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.6
rrs 1472285 n.440A>G non_coding_transcript_exon_variant 1.0
rrs 1472338 n.493A>G non_coding_transcript_exon_variant 1.0
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 1.0
rrs 1472379 n.534T>C non_coding_transcript_exon_variant 1.0
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 1.0
rrs 1472412 n.567A>G non_coding_transcript_exon_variant 1.0
rrs 1472416 n.571C>T non_coding_transcript_exon_variant 1.0
rrs 1472422 n.577T>C non_coding_transcript_exon_variant 1.0
rrs 1472427 n.582T>G non_coding_transcript_exon_variant 1.0
rrs 1472498 n.653C>A non_coding_transcript_exon_variant 1.0
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.75
rrs 1472513 n.668T>C non_coding_transcript_exon_variant 0.21
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.79
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.79
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.88
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.9
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.86
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.86
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.84
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.84
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.81
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.16
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 1.0
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.14
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.85
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.85
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.25
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 1.0
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.67
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.33
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.67
rrs 1472670 n.825G>T non_coding_transcript_exon_variant 0.8
rrs 1472673 n.828T>A non_coding_transcript_exon_variant 1.0
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 1.0
rrs 1472677 n.832C>T non_coding_transcript_exon_variant 1.0
rrs 1472681 n.837_838delTT non_coding_transcript_exon_variant 1.0
rrs 1472687 n.843dupT non_coding_transcript_exon_variant 1.0
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 1.0
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.77
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.21
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.71
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.33
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.69
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.68
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.68
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.66
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.34
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.62
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.65
rrs 1472824 n.979T>A 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 1472952 n.1107T>C non_coding_transcript_exon_variant 0.16
rrs 1472954 n.1109T>C non_coding_transcript_exon_variant 0.84
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.16
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 1.0
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 1.0
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.9
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.21
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.21
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 1.0
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.68
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.71
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 1.0
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 1.0
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 1.0
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 1.0
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.67
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.67
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 1.0
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 1.0
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 1.0
rrs 1473101 n.1256C>T non_coding_transcript_exon_variant 0.75
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.25
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 1.0
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 1.0
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 1.0
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.18
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.79
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.82
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.68
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.84
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.87
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.66
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.69
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.17
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.14
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.15
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.15
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.71
rrs 1473248 n.1403G>A non_coding_transcript_exon_variant 0.12
rrs 1473249 n.1404T>C non_coding_transcript_exon_variant 0.12
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.88
rrs 1473255 n.1410A>G non_coding_transcript_exon_variant 0.12
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.81
rrs 1473260 n.1415G>T non_coding_transcript_exon_variant 0.12
rrs 1473276 n.1431A>C non_coding_transcript_exon_variant 0.85
rrs 1473277 n.1432G>A non_coding_transcript_exon_variant 0.79
rrs 1473301 n.1456T>G non_coding_transcript_exon_variant 0.71
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.83
rrl 1474181 n.524C>A non_coding_transcript_exon_variant 1.0
rrl 1474184 n.527C>T non_coding_transcript_exon_variant 1.0
rrl 1474197 n.540C>T non_coding_transcript_exon_variant 0.9
rrl 1474199 n.542G>C non_coding_transcript_exon_variant 0.9
rrl 1474200 n.545delT non_coding_transcript_exon_variant 1.0
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 1.0
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.67
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.67
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.67
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.67
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.9
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.93
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.93
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.75
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.92
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.87
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.91
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.83
rpsA 1834261 c.720A>G synonymous_variant 0.18
rpsA 1834294 c.753G>C synonymous_variant 0.22
rpsA 1834298 p.Gln253Glu missense_variant 0.18
rpsA 1834306 c.765T>C synonymous_variant 0.18
rpsA 1834307 p.Asp256Gln missense_variant 0.18
rpsA 1834312 c.771G>A synonymous_variant 0.18
rpsA 1834327 c.786G>T synonymous_variant 0.18
rpsA 1834345 c.804C>T synonymous_variant 0.2
rpsA 1834378 c.837T>C synonymous_variant 0.15
rpsA 1834411 c.870T>C synonymous_variant 0.19
rpsA 1834417 c.876G>C synonymous_variant 0.15
tlyA 1917750 c.-190A>T upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918745 c.806A>G stop_lost&splice_region_variant 0.11
katG 2154555 c.1557C>T synonymous_variant 0.5
PPE35 2168022 p.Leu864Pro missense_variant 0.13
Rv1979c 2222023 p.Ala381Asp missense_variant 0.17
Rv1979c 2223025 p.Ala47Val missense_variant 0.15
Rv1979c 2223047 p.Ile40Phe missense_variant 0.14
Rv1979c 2223236 c.-72C>T upstream_gene_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2746185 p.Val472Phe missense_variant 0.13
pepQ 2860163 p.Arg86Trp missense_variant 0.11
thyX 3067737 p.Phe70Ser missense_variant 0.17
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087316 p.Val166Ala missense_variant 0.11
Rv3083 3448563 c.60C>T synonymous_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568640 p.Arg14Gly missense_variant 0.15
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
Rv3236c 3612548 p.Ala190Asp missense_variant 0.17
fbiA 3641017 p.Pro159Thr missense_variant 0.2
alr 3840719 c.702A>G synonymous_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039592 c.1113G>T synonymous_variant 0.15
clpC1 4039610 c.1095G>C synonymous_variant 0.15
clpC1 4039616 c.1089G>C synonymous_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245238 p.Asp669Gly missense_variant 0.11
embA 4245367 p.Arg712His missense_variant 0.13
embA 4245387 p.Ala719Thr missense_variant 0.14
aftB 4267605 p.Arg411His missense_variant 0.5
aftB 4269276 c.-440C>T upstream_gene_variant 0.25
aftB 4269816 c.-980G>T upstream_gene_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407599 p.Val202Met missense_variant 0.14
gid 4407936 c.267T>A synonymous_variant 0.17
gid 4408156 p.Leu16Arg missense_variant 1.0