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
Drug | Resistance | Supporting mutations |
---|
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 |
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 |
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 |