TB-Profiler result

Run: ERR3324329

Summary

Run ID: ERR3324329

Sample name:

Date: 01-04-2023 01:49:28

Number of reads: 325520

Percentage reads mapped: 82.1

Strain: lineage4.1.1.3

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 1.0
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 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
katG 2155299 c.811_812delAC frameshift_variant 0.17 isoniazid
katG 2155581 c.527_530delTGGG frameshift_variant 0.17 isoniazid
gid 4408100 c.102dupG frameshift_variant 0.29 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 5459 p.Gly74Arg missense_variant 0.25
gyrB 5500 c.261C>G synonymous_variant 0.33
gyrA 7075 c.-227T>C upstream_gene_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8077 c.777delA frameshift_variant 0.29
gyrA 8091 p.Arg264Cys missense_variant 0.29
gyrA 8740 p.Arg480Pro missense_variant 0.17
gyrA 9117 c.1818delA frameshift_variant 0.13
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9495 p.Ala732Ser missense_variant 0.13
mshA 575411 p.Glu22Lys missense_variant 1.0
ccsA 620164 c.274C>T synonymous_variant 0.33
rpoB 760822 p.Leu339Pro missense_variant 0.22
rpoB 761487 p.Glu561* stop_gained 0.15
rpoB 762252 p.Arg816Cys missense_variant 0.15
rpoB 762373 p.Pro856Leu missense_variant 0.1
rpoB 762949 p.Gln1048Arg missense_variant 0.14
rpoC 764212 c.843C>T synonymous_variant 0.11
rpoC 764398 c.1029G>C synonymous_variant 0.1
rpoC 764405 c.1036A>C synonymous_variant 0.1
rpoC 765089 c.1720T>C synonymous_variant 0.4
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765321 p.Phe651Tyr missense_variant 0.17
rpoC 767004 p.Lys1212Arg missense_variant 0.4
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775962 p.Val840Asp missense_variant 0.2
mmpL5 776669 c.1812C>T synonymous_variant 0.15
mmpL5 776964 c.1514_1516delGCA disruptive_inframe_deletion 0.1
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781507 c.-53G>T upstream_gene_variant 0.29
rplC 800791 c.-18A>T upstream_gene_variant 0.14
fbiC 1302954 c.24G>A synonymous_variant 1.0
fbiC 1303292 p.Thr121Arg missense_variant 0.15
fbiC 1303790 p.Ile287Asn missense_variant 0.13
fbiC 1304129 c.1204_1207delGGCG frameshift_variant 0.2
fbiC 1304800 c.1873delG frameshift_variant 0.5
embR 1416305 p.Asn348Ser missense_variant 0.15
embR 1416768 p.Leu194Val missense_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472326 n.481T>C non_coding_transcript_exon_variant 0.15
rrs 1472492 n.648delT non_coding_transcript_exon_variant 0.11
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.25
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.31
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.23
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.23
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.22
rrs 1472669 n.824_825insTGG non_coding_transcript_exon_variant 0.23
rrs 1472677 n.832C>A non_coding_transcript_exon_variant 0.21
rrs 1472678 n.833T>A non_coding_transcript_exon_variant 0.21
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.17
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.17
rrs 1472708 n.863T>A non_coding_transcript_exon_variant 0.16
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.16
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.17
rrs 1472733 n.888G>C non_coding_transcript_exon_variant 0.14
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.14
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.14
rrs 1472742 n.897C>G non_coding_transcript_exon_variant 0.15
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.17
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.16
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.11
rrs 1472953 n.1108G>A non_coding_transcript_exon_variant 0.24
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.24
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.24
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.24
rrs 1472969 n.1125_1126delCG non_coding_transcript_exon_variant 0.25
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.25
rrs 1472974 n.1129A>C non_coding_transcript_exon_variant 0.25
rrs 1472975 n.1130T>A non_coding_transcript_exon_variant 0.25
rrs 1472977 n.1132G>T non_coding_transcript_exon_variant 0.29
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.31
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.29
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.29
rrs 1473001 n.1156G>T non_coding_transcript_exon_variant 0.29
rrs 1473002 n.1157G>C non_coding_transcript_exon_variant 0.29
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.29
rrs 1473008 n.1163C>G non_coding_transcript_exon_variant 0.29
rrs 1473009 n.1164T>A non_coding_transcript_exon_variant 0.29
rrs 1473020 n.1175T>C non_coding_transcript_exon_variant 0.29
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.29
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.19
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.11
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.11
rrl 1473652 n.-6T>C upstream_gene_variant 0.17
rrl 1474228 n.571T>C non_coding_transcript_exon_variant 0.2
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.2
rrl 1474269 n.612C>T non_coding_transcript_exon_variant 0.17
rrl 1475343 n.1686A>T non_coding_transcript_exon_variant 0.25
rrl 1475699 n.2042C>T non_coding_transcript_exon_variant 0.2
rrl 1475722 n.2065G>T non_coding_transcript_exon_variant 0.2
rrl 1475747 n.2090A>G non_coding_transcript_exon_variant 0.2
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.25
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.23
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.5
rrl 1475866 n.2209T>A non_coding_transcript_exon_variant 0.5
rrl 1476128 n.2471T>A non_coding_transcript_exon_variant 0.2
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.2
rrl 1476135 n.2478T>C non_coding_transcript_exon_variant 0.2
rrl 1476141 n.2484A>G non_coding_transcript_exon_variant 0.33
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.33
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.38
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.38
rrl 1476195 n.2538C>A non_coding_transcript_exon_variant 0.38
rrl 1476196 n.2539C>A non_coding_transcript_exon_variant 0.38
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.38
rrl 1476204 n.2547C>A non_coding_transcript_exon_variant 0.38
rrl 1476210 n.2553G>T non_coding_transcript_exon_variant 0.36
rrl 1476211 n.2554G>T non_coding_transcript_exon_variant 0.31
rrl 1476212 n.2555T>C non_coding_transcript_exon_variant 0.31
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.33
rrl 1476215 n.2558C>A non_coding_transcript_exon_variant 0.33
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.37
rrl 1476229 n.2572C>G non_coding_transcript_exon_variant 0.43
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.56
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.54
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.56
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.52
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.5
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.5
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.5
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.5
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.5
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.5
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.5
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.5
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.5
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.55
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.55
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.6
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.6
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.52
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.52
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.52
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.61
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.5
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.46
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.64
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.64
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.64
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.55
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.55
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.55
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.55
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.55
rrl 1476529 n.2872A>G non_coding_transcript_exon_variant 0.6
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.6
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.6
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.6
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.6
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.58
rrl 1476573 n.2916A>C non_coding_transcript_exon_variant 0.58
rrl 1476577 n.2920T>G non_coding_transcript_exon_variant 0.64
rrl 1476595 n.2938C>A non_coding_transcript_exon_variant 0.58
rrl 1476602 n.2945G>T non_coding_transcript_exon_variant 0.58
rrl 1476608 n.2951C>A non_coding_transcript_exon_variant 0.58
rrl 1476614 n.2957A>G non_coding_transcript_exon_variant 0.58
rrl 1476619 n.2962C>T non_coding_transcript_exon_variant 0.56
rrl 1476621 n.2964C>T non_coding_transcript_exon_variant 0.5
rrl 1476624 n.2967T>G non_coding_transcript_exon_variant 0.5
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.67
rrl 1476630 n.2973A>G non_coding_transcript_exon_variant 0.67
rrl 1476637 n.2980C>G non_coding_transcript_exon_variant 0.67
rrl 1476657 n.3000G>T non_coding_transcript_exon_variant 0.5
rrl 1476661 n.3004A>G non_coding_transcript_exon_variant 0.5
tlyA 1917811 c.-129T>C upstream_gene_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1917984 c.45C>T synonymous_variant 0.12
ndh 2101720 c.1323G>T synonymous_variant 0.12
ndh 2101767 p.Arg426Cys missense_variant 0.17
ndh 2102792 p.Val84Ala missense_variant 0.22
katG 2153934 c.2178T>C synonymous_variant 0.29
katG 2154206 p.Ala636Thr missense_variant 0.17
katG 2154302 c.1810T>C synonymous_variant 0.14
katG 2154678 c.1434G>C synonymous_variant 1.0
katG 2155267 p.Asp282Gly missense_variant 0.29
katG 2155442 p.Gln224* stop_gained 0.12
PPE35 2167867 c.2745delA frameshift_variant 0.17
PPE35 2168085 p.Glu843Val missense_variant 0.25
PPE35 2169405 p.Asn403Ser missense_variant 1.0
PPE35 2169509 p.Asn368Lys missense_variant 0.2
PPE35 2169857 c.755delT frameshift_variant 0.11
Rv1979c 2222455 p.Ser237Trp missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289827 c.-586A>G upstream_gene_variant 0.29
eis 2715076 p.Ala86Val missense_variant 0.25
ahpC 2726409 p.Asp73His missense_variant 1.0
folC 2747119 c.480C>T synonymous_variant 0.18
pepQ 2859409 p.Arg337His missense_variant 0.14
Rv2752c 3064857 c.1334delG frameshift_variant 0.12
Rv2752c 3065461 c.729_730delTC frameshift_variant 0.12
Rv2752c 3067031 c.-840G>A upstream_gene_variant 0.17
thyX 3067870 p.Thr26Ser missense_variant 0.17
thyX 3068036 c.-92delC upstream_gene_variant 0.13
ald 3086752 c.-68C>A upstream_gene_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087004 p.Asp62Gly missense_variant 0.2
ald 3087036 p.Lys73Glu missense_variant 0.18
ald 3087055 p.Ala79Glu missense_variant 0.18
ald 3087812 c.993G>A synonymous_variant 0.18
ald 3087849 p.Ser344Thr missense_variant 0.15
fbiD 3339243 p.Met42Ile missense_variant 0.33
fbiD 3339386 c.272delC frameshift_variant 0.22
Rv3083 3448422 c.-82T>G upstream_gene_variant 0.4
Rv3083 3448765 p.Thr88Ala missense_variant 0.13
Rv3083 3449082 c.579T>C synonymous_variant 0.4
Rv3083 3449701 p.Asp400Tyr missense_variant 0.18
Rv3083 3449951 p.Leu483Pro missense_variant 0.29
fprA 3473896 c.-111T>C upstream_gene_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474685 p.Pro227Ser missense_variant 0.33
Rv3236c 3612855 p.His88Asp missense_variant 0.13
fbiA 3640718 c.179delC frameshift_variant 0.14
fbiA 3640783 p.Gln81* stop_gained 0.12
fbiB 3642637 c.1104_1105delCG frameshift_variant 0.4
fbiB 3642749 c.1215T>G synonymous_variant 0.2
alr 3841132 p.Ala97Thr missense_variant 0.17
alr 3841164 p.Ala86Val missense_variant 0.14
rpoA 3878536 c.-29G>A upstream_gene_variant 0.4
clpC1 4038907 p.Gly600* stop_gained 0.22
clpC1 4039504 p.Asp401Tyr missense_variant 0.11
clpC1 4040281 c.412_423delGTGATCCAGCTG conservative_inframe_deletion 0.18
clpC1 4040323 p.Gly128Arg missense_variant 0.15
clpC1 4040556 p.Glu50Gly missense_variant 0.29
embC 4240149 c.288delA frameshift_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4244104 p.Ala291Asp missense_variant 0.25
embB 4247505 p.Gly331Asp missense_variant 0.5
embB 4248317 p.Val602Pro missense_variant 0.17
embB 4248320 p.Gly603Thr missense_variant 0.17
embB 4248578 p.Ala689Thr missense_variant 0.17
embB 4249408 c.2895G>A synonymous_variant 1.0
embB 4249458 p.Gln982Arg missense_variant 0.18
embB 4249678 c.3165C>A synonymous_variant 1.0
embB 4249766 p.Arg1085Cys missense_variant 0.4
aftB 4268281 c.556C>A synonymous_variant 0.12
aftB 4268794 p.Val15Met missense_variant 0.25
aftB 4269381 c.-545C>T upstream_gene_variant 0.17
ethR 4327087 c.-462G>T upstream_gene_variant 0.13
ethA 4327158 p.Ser106Gly missense_variant 0.17
ethR 4328161 p.His205Asp missense_variant 0.17
ethA 4328247 c.-774G>A upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338618 c.-97A>G upstream_gene_variant 0.1
gid 4408406 c.-204A>G upstream_gene_variant 0.11