Run ID: SRR21677894
Sample name:
Date: 04-04-2023 02:49:42
Number of reads: 310233
Percentage reads mapped: 97.45
Strain: lineage4.1.1.3
Drug-resistance: Other
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 |
---|---|---|---|---|---|
ethA | 4327282 | c.191delT | frameshift_variant | 0.17 | ethionamide |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5500 | c.261C>T | synonymous_variant | 0.2 |
gyrB | 5558 | p.Gly107Ser | missense_variant | 0.18 |
gyrB | 6059 | c.821delG | frameshift_variant | 0.18 |
gyrB | 6070 | p.Asp277Glu | missense_variant | 0.18 |
gyrB | 6099 | p.Val287Ala | missense_variant | 0.12 |
gyrA | 7210 | c.-92C>T | upstream_gene_variant | 1.0 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7552 | p.Tyr84Cys | missense_variant | 0.4 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 7598 | p.Met99Ile | missense_variant | 0.5 |
gyrA | 8023 | p.Ala241Gly | missense_variant | 0.33 |
gyrA | 8107 | p.Leu269Pro | missense_variant | 0.25 |
gyrA | 8309 | p.Gln336His | missense_variant | 0.25 |
gyrA | 9013 | p.Thr571Ile | missense_variant | 0.17 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
gyrA | 9532 | c.2233delC | frameshift_variant | 0.15 |
gyrA | 9652 | p.Ile784Thr | missense_variant | 0.25 |
fgd1 | 491732 | p.Gln317Arg | missense_variant | 0.18 |
fgd1 | 491749 | p.Leu323Ile | missense_variant | 0.22 |
mshA | 575414 | p.Gly23Cys | missense_variant | 0.14 |
mshA | 575441 | p.Gly32Arg | missense_variant | 0.13 |
mshA | 575657 | p.Ala104Pro | missense_variant | 0.15 |
ccsA | 620034 | c.144C>T | synonymous_variant | 0.2 |
ccsA | 620655 | p.Trp255* | stop_gained | 0.11 |
rpoB | 760070 | c.264T>C | synonymous_variant | 0.14 |
rpoB | 760745 | p.Lys313Asn | missense_variant | 0.12 |
rpoB | 761154 | p.Ser450Pro | missense_variant | 0.33 |
rpoB | 762768 | p.Pro988Thr | missense_variant | 0.17 |
rpoB | 763197 | p.Val1131Leu | missense_variant | 0.14 |
rpoC | 763659 | p.Leu97Pro | missense_variant | 0.4 |
rpoC | 765150 | p.Gly594Glu | missense_variant | 1.0 |
rpoC | 765451 | c.2082C>T | synonymous_variant | 0.13 |
rpoC | 765552 | p.Gly728Asp | missense_variant | 0.12 |
rpoC | 765618 | p.Glu750Gly | missense_variant | 0.22 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776146 | p.Ala779Ser | missense_variant | 0.18 |
mmpL5 | 776906 | c.1575G>A | synonymous_variant | 0.11 |
mmpL5 | 778171 | p.Ala104Thr | missense_variant | 0.25 |
mmpL5 | 778411 | p.Ile24Leu | missense_variant | 0.22 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rpsL | 781435 | c.-125G>C | upstream_gene_variant | 1.0 |
rpsL | 781753 | p.Ala65Glu | missense_variant | 0.29 |
fbiC | 1303400 | p.Gln157Leu | missense_variant | 0.17 |
fbiC | 1303831 | p.Thr301Pro | missense_variant | 0.13 |
fbiC | 1304231 | p.Pro434Arg | missense_variant | 0.15 |
Rv1258c | 1406492 | c.849C>T | synonymous_variant | 0.18 |
Rv1258c | 1406607 | p.Val245Glu | missense_variant | 0.15 |
Rv1258c | 1407322 | p.Gly7Ser | missense_variant | 0.22 |
atpE | 1460855 | c.-189delC | upstream_gene_variant | 0.12 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472068 | n.226delG | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472301 | n.456C>A | non_coding_transcript_exon_variant | 0.11 |
rrs | 1473124 | n.1279A>G | non_coding_transcript_exon_variant | 0.15 |
rrs | 1473279 | n.1434G>A | non_coding_transcript_exon_variant | 0.18 |
rrl | 1474868 | n.1211T>C | non_coding_transcript_exon_variant | 0.14 |
rrl | 1475231 | n.1574C>T | non_coding_transcript_exon_variant | 0.11 |
rrl | 1475238 | n.1581A>C | non_coding_transcript_exon_variant | 0.12 |
rrl | 1475673 | n.2020_2021delAA | non_coding_transcript_exon_variant | 0.15 |
rrl | 1475703 | n.2046A>T | non_coding_transcript_exon_variant | 0.13 |
rrl | 1476174 | n.2520_2521delGC | non_coding_transcript_exon_variant | 0.17 |
rrl | 1476311 | n.2654G>C | non_coding_transcript_exon_variant | 0.17 |
rrl | 1476312 | n.2655T>C | non_coding_transcript_exon_variant | 0.17 |
rrl | 1476313 | n.2656G>A | non_coding_transcript_exon_variant | 0.17 |
rrl | 1476324 | n.2667G>A | non_coding_transcript_exon_variant | 0.18 |
rrl | 1476336 | n.2679C>T | non_coding_transcript_exon_variant | 0.25 |
rrl | 1476338 | n.2681C>T | non_coding_transcript_exon_variant | 0.29 |
rrl | 1476339 | n.2682G>A | non_coding_transcript_exon_variant | 0.29 |
rrl | 1476356 | n.2699C>T | non_coding_transcript_exon_variant | 0.17 |
rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.15 |
rrl | 1476366 | n.2709A>C | non_coding_transcript_exon_variant | 0.15 |
rrl | 1476372 | n.2715T>C | non_coding_transcript_exon_variant | 0.15 |
rrl | 1476374 | n.2717T>G | non_coding_transcript_exon_variant | 0.15 |
rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.17 |
rrl | 1476383 | n.2726T>A | non_coding_transcript_exon_variant | 0.17 |
rrl | 1476384 | n.2727G>A | non_coding_transcript_exon_variant | 0.17 |
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.15 |
rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.15 |
rrl | 1476443 | n.2786G>C | non_coding_transcript_exon_variant | 0.14 |
rrl | 1476455 | n.2798C>G | non_coding_transcript_exon_variant | 0.13 |
rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.13 |
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.17 |
rrl | 1476470 | n.2813C>T | non_coding_transcript_exon_variant | 0.17 |
inhA | 1674114 | c.-88T>A | upstream_gene_variant | 0.25 |
inhA | 1674675 | c.474C>T | synonymous_variant | 0.13 |
rpsA | 1833650 | p.Asp37Asn | missense_variant | 0.11 |
rpsA | 1833839 | p.Leu100Phe | missense_variant | 0.17 |
rpsA | 1834211 | p.Ala224Thr | missense_variant | 0.33 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
tlyA | 1918097 | p.Thr53Asn | missense_variant | 0.22 |
tlyA | 1918527 | c.588G>T | synonymous_variant | 0.12 |
tlyA | 1918688 | p.Ala250Glu | missense_variant | 0.2 |
ndh | 2101767 | p.Arg426Cys | missense_variant | 0.33 |
ndh | 2102413 | c.630G>T | synonymous_variant | 0.15 |
ndh | 2102414 | c.628delC | frameshift_variant | 0.15 |
katG | 2154281 | p.Leu611Ile | missense_variant | 0.33 |
katG | 2155479 | p.Ser211Arg | missense_variant | 0.14 |
katG | 2156188 | c.-77T>A | upstream_gene_variant | 0.2 |
katG | 2156332 | c.-221C>T | upstream_gene_variant | 0.14 |
katG | 2156488 | c.-377C>A | upstream_gene_variant | 0.17 |
PPE35 | 2168269 | p.Gly782Arg | missense_variant | 0.17 |
PPE35 | 2168320 | p.Thr765Ala | missense_variant | 0.12 |
PPE35 | 2168357 | c.2256T>C | synonymous_variant | 0.14 |
PPE35 | 2168375 | c.2238T>C | synonymous_variant | 0.12 |
PPE35 | 2168806 | p.Gly603Ser | missense_variant | 0.25 |
PPE35 | 2169650 | p.Leu321Phe | missense_variant | 0.13 |
PPE35 | 2169713 | c.900C>T | synonymous_variant | 0.17 |
Rv1979c | 2221870 | p.Tyr432Cys | missense_variant | 0.18 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2288824 | p.Arg140Cys | missense_variant | 0.17 |
pncA | 2290065 | c.-824G>A | upstream_gene_variant | 0.29 |
kasA | 2517962 | c.-153C>A | upstream_gene_variant | 0.25 |
kasA | 2517976 | c.-139C>T | upstream_gene_variant | 0.25 |
kasA | 2518476 | p.Arg121Met | missense_variant | 0.18 |
kasA | 2519159 | p.Ala349Thr | missense_variant | 0.33 |
kasA | 2519197 | c.1083G>T | synonymous_variant | 0.4 |
eis | 2714341 | p.Leu331Pro | missense_variant | 0.13 |
eis | 2715164 | p.Glu57* | stop_gained | 0.2 |
ahpC | 2725966 | c.-227C>T | upstream_gene_variant | 0.15 |
ahpC | 2726115 | c.-77delT | upstream_gene_variant | 0.17 |
ahpC | 2726215 | p.Asp8Gly | missense_variant | 0.15 |
ahpC | 2726480 | p.Trp96Cys | missense_variant | 0.33 |
folC | 2746376 | p.Ser408Leu | missense_variant | 0.29 |
folC | 2746393 | c.1206C>A | synonymous_variant | 0.4 |
folC | 2746636 | c.963C>T | synonymous_variant | 0.25 |
folC | 2746699 | p.His300Gln | missense_variant | 0.33 |
pepQ | 2859363 | c.1056T>C | synonymous_variant | 0.17 |
pepQ | 2860488 | c.-70C>A | upstream_gene_variant | 0.14 |
ribD | 2986863 | p.Ala9Ser | missense_variant | 0.12 |
Rv2752c | 3064999 | p.Gly398Glu | missense_variant | 0.14 |
Rv2752c | 3065155 | p.Glu346Gly | missense_variant | 0.11 |
Rv2752c | 3065298 | p.Asp298Glu | missense_variant | 0.15 |
thyX | 3067351 | p.Arg199Trp | missense_variant | 0.13 |
thyA | 3073981 | p.Tyr164Cys | missense_variant | 0.17 |
thyA | 3074424 | c.48G>A | synonymous_variant | 0.14 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
ald | 3087130 | p.Thr104Ile | missense_variant | 0.18 |
ald | 3087369 | p.Ala184Ser | missense_variant | 0.2 |
fbiD | 3339194 | p.Leu26Arg | missense_variant | 0.22 |
fbiD | 3339326 | p.Ala70Val | missense_variant | 0.15 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474453 | c.447G>A | synonymous_variant | 0.13 |
fprA | 3475113 | c.1107G>A | synonymous_variant | 0.15 |
whiB7 | 3568516 | p.Ala55Val | missense_variant | 0.2 |
whiB7 | 3568687 | c.-8A>G | upstream_gene_variant | 0.18 |
Rv3236c | 3612564 | p.Met185Leu | missense_variant | 0.17 |
fbiA | 3640504 | c.-39A>T | upstream_gene_variant | 0.2 |
fbiB | 3641124 | c.-411C>T | upstream_gene_variant | 0.12 |
fbiB | 3642566 | c.1032A>G | synonymous_variant | 0.15 |
fbiB | 3642728 | c.1194C>T | synonymous_variant | 0.18 |
alr | 3840299 | c.1122C>A | synonymous_variant | 0.18 |
alr | 3841100 | c.321A>C | synonymous_variant | 0.14 |
alr | 3841111 | p.Gly104Cys | missense_variant | 0.15 |
alr | 3841347 | p.Met25Thr | missense_variant | 0.29 |
alr | 3841571 | c.-151A>T | upstream_gene_variant | 0.15 |
rpoA | 3877876 | p.Ala211Val | missense_variant | 0.33 |
rpoA | 3878541 | c.-34C>T | upstream_gene_variant | 0.5 |
clpC1 | 4038548 | p.Phe719Leu | missense_variant | 0.11 |
clpC1 | 4038805 | p.Ile634Phe | missense_variant | 0.33 |
clpC1 | 4039388 | c.1315_1316delAT | frameshift_variant | 0.17 |
clpC1 | 4039498 | p.Ile403Val | missense_variant | 0.2 |
clpC1 | 4039971 | p.Lys245Thr | missense_variant | 0.15 |
clpC1 | 4040475 | p.His77Arg | missense_variant | 0.2 |
clpC1 | 4040722 | c.-18G>T | upstream_gene_variant | 0.2 |
clpC1 | 4040866 | c.-162T>A | upstream_gene_variant | 0.13 |
clpC1 | 4040901 | c.-197C>T | upstream_gene_variant | 0.13 |
embC | 4239928 | c.66G>A | synonymous_variant | 0.12 |
embC | 4241090 | p.Trp410Arg | missense_variant | 0.13 |
embC | 4241136 | p.Val425Ala | missense_variant | 0.13 |
embC | 4241295 | p.Ala478Val | missense_variant | 0.14 |
embC | 4241491 | c.1629G>T | synonymous_variant | 0.33 |
embC | 4241603 | p.Phe581Ile | missense_variant | 0.15 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embC | 4242803 | p.Val981Leu | missense_variant | 1.0 |
embA | 4243293 | p.Gly21* | stop_gained | 0.12 |
embA | 4244860 | p.Gly543Glu | missense_variant | 1.0 |
embB | 4248032 | p.Arg507Trp | missense_variant | 0.17 |
embB | 4248495 | p.Pro661Leu | missense_variant | 0.12 |
embB | 4249174 | p.Ser887Arg | missense_variant | 0.12 |
embB | 4249315 | p.Phe934Leu | missense_variant | 0.29 |
embB | 4249362 | p.Ala950Asp | missense_variant | 0.29 |
embB | 4249408 | c.2895G>A | synonymous_variant | 1.0 |
embB | 4249520 | p.Ala1003Thr | missense_variant | 0.17 |
aftB | 4266993 | p.Leu615Pro | missense_variant | 0.18 |
aftB | 4267741 | p.Glu366* | stop_gained | 0.17 |
aftB | 4268952 | c.-116G>C | upstream_gene_variant | 0.14 |
ethA | 4327521 | c.-48G>T | upstream_gene_variant | 0.14 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407798 | c.405G>T | synonymous_variant | 1.0 |