Run ID: SRR4035746
Sample name:
Date: 04-04-2023 07:16:24
Number of reads: 965254
Percentage reads mapped: 99.51
Strain: lineage4.1.2
Drug-resistance: Sensitive
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 | 0.99 |
lineage4.1.2 | Euro-American | T;H | None | 0.99 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6228 | p.Lys330Met | missense_variant | 0.17 |
gyrA | 7174 | c.-128C>T | upstream_gene_variant | 0.25 |
gyrB | 7262 | p.Val675Phe | missense_variant | 0.12 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 8061 | p.Arg254Cys | missense_variant | 0.87 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491591 | p.Lys270Met | missense_variant | 1.0 |
mshA | 575404 | c.57C>A | synonymous_variant | 0.12 |
mshA | 576136 | c.789T>C | synonymous_variant | 0.18 |
mshA | 576402 | p.Ser352Phe | missense_variant | 0.22 |
ccsA | 620107 | p.Asp73His | missense_variant | 0.15 |
ccsA | 620493 | c.603G>A | synonymous_variant | 0.14 |
ccsA | 620516 | p.Glu209Val | missense_variant | 0.14 |
rpoB | 760115 | c.309C>T | synonymous_variant | 1.0 |
rpoB | 762474 | p.Gly890Arg | missense_variant | 0.12 |
rpoC | 764263 | c.894G>A | synonymous_variant | 1.0 |
rpoC | 764805 | p.Gln479Leu | missense_variant | 0.13 |
rpoC | 765150 | p.Gly594Glu | missense_variant | 1.0 |
rpoC | 766048 | c.2679C>A | synonymous_variant | 0.15 |
rpoC | 766063 | c.2694C>T | synonymous_variant | 0.12 |
rpoC | 766485 | p.Val1039Ala | missense_variant | 0.11 |
rpoC | 766622 | p.Arg1085Trp | missense_variant | 0.15 |
rpoC | 767161 | p.Ile1264Met | missense_variant | 0.17 |
rpoC | 767189 | p.Pro1274Ser | missense_variant | 0.13 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 775893 | p.His863Arg | missense_variant | 0.12 |
mmpL5 | 777320 | c.1161C>G | synonymous_variant | 1.0 |
mmpL5 | 777372 | p.Pro370Arg | missense_variant | 0.14 |
mmpL5 | 777764 | c.717G>A | synonymous_variant | 0.12 |
mmpS5 | 779587 | c.-682A>G | upstream_gene_variant | 0.14 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rpsL | 781450 | c.-110A>T | upstream_gene_variant | 0.22 |
fbiC | 1304666 | p.Leu579Pro | missense_variant | 0.13 |
fbiC | 1305306 | c.2376A>G | synonymous_variant | 0.11 |
fbiC | 1305339 | c.2409C>T | synonymous_variant | 0.13 |
Rv1258c | 1406768 | c.573G>A | synonymous_variant | 0.15 |
Rv1258c | 1406803 | p.Ala180Thr | missense_variant | 0.15 |
Rv1258c | 1406977 | p.Thr122Ser | missense_variant | 0.13 |
Rv1258c | 1407293 | c.48G>A | synonymous_variant | 0.15 |
embR | 1416870 | p.Glu160Lys | missense_variant | 0.18 |
atpE | 1460979 | c.-66G>C | upstream_gene_variant | 0.14 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1471664 | n.-182C>G | upstream_gene_variant | 0.15 |
rrs | 1472139 | n.294C>T | non_coding_transcript_exon_variant | 0.25 |
rrl | 1475885 | n.2228C>T | non_coding_transcript_exon_variant | 0.25 |
rrl | 1476256 | n.2599A>G | non_coding_transcript_exon_variant | 0.2 |
rrl | 1476381 | n.2724G>A | non_coding_transcript_exon_variant | 0.18 |
inhA | 1674936 | c.735G>A | synonymous_variant | 0.18 |
inhA | 1674951 | c.750G>C | synonymous_variant | 0.2 |
rpsA | 1834816 | c.1275C>T | synonymous_variant | 0.14 |
rpsA | 1834827 | p.Thr429Ile | missense_variant | 0.15 |
rpsA | 1834841 | p.Lys434Glu | missense_variant | 0.17 |
tlyA | 1917817 | c.-122delC | upstream_gene_variant | 0.13 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
tlyA | 1918172 | p.Ala78Val | missense_variant | 0.13 |
tlyA | 1918405 | p.Ser156Pro | missense_variant | 0.12 |
tlyA | 1918595 | p.Gly219Asp | missense_variant | 0.17 |
ndh | 2101668 | p.Ala459Thr | missense_variant | 0.15 |
ndh | 2101675 | c.1368G>A | synonymous_variant | 0.17 |
ndh | 2102342 | p.Ala234Val | missense_variant | 0.14 |
ndh | 2103237 | c.-195C>T | upstream_gene_variant | 0.13 |
katG | 2156328 | c.-217C>A | upstream_gene_variant | 0.14 |
katG | 2156423 | c.-312A>G | upstream_gene_variant | 0.2 |
PPE35 | 2167690 | p.Asn975Tyr | missense_variant | 0.29 |
PPE35 | 2168520 | p.Gln698Arg | missense_variant | 0.12 |
PPE35 | 2168731 | p.Pro628Ser | missense_variant | 0.15 |
PPE35 | 2170149 | p.His155Leu | missense_variant | 0.17 |
Rv1979c | 2221727 | p.Thr480Ala | missense_variant | 0.14 |
Rv1979c | 2222006 | p.Ile387Val | missense_variant | 0.13 |
Rv1979c | 2222016 | p.Phe383Leu | missense_variant | 0.12 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289689 | c.-448A>T | upstream_gene_variant | 0.2 |
kasA | 2518076 | c.-39C>T | upstream_gene_variant | 1.0 |
eis | 2715411 | c.-79A>T | upstream_gene_variant | 0.18 |
eis | 2715439 | c.-107G>A | upstream_gene_variant | 0.17 |
ahpC | 2725913 | c.-280T>C | upstream_gene_variant | 0.12 |
ahpC | 2726441 | c.249G>A | synonymous_variant | 0.13 |
folC | 2746932 | p.Ala223Ser | missense_variant | 0.15 |
folC | 2747168 | p.Lys144Arg | missense_variant | 0.2 |
folC | 2747665 | c.-67T>G | upstream_gene_variant | 0.1 |
pepQ | 2859511 | p.His303Arg | missense_variant | 0.11 |
ribD | 2987587 | p.Tyr250Ser | missense_variant | 0.12 |
Rv2752c | 3065431 | p.Ala254Gly | missense_variant | 0.12 |
Rv2752c | 3065469 | c.723C>T | synonymous_variant | 0.18 |
Rv2752c | 3065545 | p.Ser216Asn | missense_variant | 0.18 |
Rv2752c | 3065688 | c.502_503dupAC | frameshift_variant | 0.15 |
thyX | 3067297 | p.Arg217Cys | missense_variant | 0.2 |
thyX | 3067696 | p.Gly84Arg | missense_variant | 0.17 |
thyX | 3068123 | c.-178A>G | upstream_gene_variant | 0.17 |
thyA | 3073769 | p.Arg235Trp | missense_variant | 0.17 |
thyA | 3073806 | c.666C>G | synonymous_variant | 0.3 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
Rv3083 | 3449138 | p.Arg212Gln | missense_variant | 0.12 |
Rv3083 | 3449195 | p.Gly231Ala | missense_variant | 0.11 |
Rv3083 | 3449247 | c.744C>T | synonymous_variant | 0.12 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474295 | p.Tyr97Asn | missense_variant | 0.13 |
fprA | 3474549 | p.His181Gln | missense_variant | 0.25 |
Rv3236c | 3611974 | c.1143A>C | synonymous_variant | 1.0 |
Rv3236c | 3612513 | p.Trp202Arg | missense_variant | 0.25 |
Rv3236c | 3612761 | p.Leu119His | missense_variant | 0.17 |
Rv3236c | 3612766 | c.351C>T | synonymous_variant | 0.14 |
fbiB | 3642448 | p.Ile305Thr | missense_variant | 0.12 |
fbiB | 3642470 | c.936G>A | synonymous_variant | 0.12 |
alr | 3840844 | c.576delG | frameshift_variant | 0.14 |
alr | 3840915 | p.Pro169Leu | missense_variant | 0.18 |
alr | 3841478 | c.-58C>T | upstream_gene_variant | 0.13 |
alr | 3841498 | c.-78A>G | upstream_gene_variant | 0.15 |
rpoA | 3878443 | p.Val22Ala | missense_variant | 0.18 |
clpC1 | 4038921 | p.Phe595Ser | missense_variant | 0.13 |
clpC1 | 4038925 | c.1780C>T | synonymous_variant | 0.13 |
clpC1 | 4040216 | c.489C>G | synonymous_variant | 0.12 |
embC | 4240456 | c.594C>G | synonymous_variant | 0.14 |
embC | 4240874 | p.Ser338Arg | missense_variant | 0.11 |
embC | 4242147 | p.Asn762Ile | missense_variant | 0.12 |
embC | 4242182 | p.Ala774Thr | missense_variant | 0.14 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embC | 4242803 | p.Val981Leu | missense_variant | 1.0 |
embA | 4244052 | p.Asp274Asn | missense_variant | 0.13 |
embA | 4244278 | p.Pro349Leu | missense_variant | 0.18 |
embA | 4244462 | c.1230A>G | synonymous_variant | 0.14 |
embB | 4246762 | c.249G>A | synonymous_variant | 0.15 |
embB | 4247715 | p.Gly401Asp | missense_variant | 0.13 |
embB | 4247964 | p.Ala484Val | missense_variant | 0.12 |
embB | 4248875 | p.Phe788Leu | missense_variant | 0.17 |
embB | 4248906 | p.Val798Ala | missense_variant | 0.22 |
aftB | 4268220 | p.Thr206Ile | missense_variant | 0.12 |
ubiA | 4269214 | p.Arg207Pro | missense_variant | 0.11 |
ubiA | 4269758 | p.Trp26Arg | missense_variant | 0.17 |
ethA | 4326702 | p.Arg258Trp | missense_variant | 0.14 |
ethR | 4327740 | p.Tyr64* | stop_gained | 0.12 |
ethR | 4327808 | p.Leu87Pro | missense_variant | 0.1 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
whiB6 | 4338703 | c.-182T>C | upstream_gene_variant | 0.22 |
gid | 4407577 | p.Lys209Arg | missense_variant | 0.12 |