Run ID: SRR4035714
Sample name:
Date: 04-04-2023 07:15:12
Number of reads: 755434
Percentage reads mapped: 99.43
Strain: lineage4.1.2
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 |
lineage4.1.2 | Euro-American | T;H | None | 0.99 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
tlyA | 1918586 | c.649delG | frameshift_variant | 0.18 | capreomycin |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5291 | p.Thr18Ala | missense_variant | 0.11 |
gyrB | 5472 | p.Ala78Val | missense_variant | 0.25 |
gyrB | 6080 | p.Lys281Glu | missense_variant | 0.25 |
gyrB | 6088 | c.849C>T | synonymous_variant | 0.25 |
gyrB | 6273 | p.Leu345His | missense_variant | 0.18 |
gyrA | 6307 | c.-995T>A | upstream_gene_variant | 0.18 |
gyrA | 6346 | c.-956C>G | upstream_gene_variant | 0.2 |
gyrB | 6567 | p.Ala443Val | missense_variant | 0.4 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 7831 | p.Gly177Glu | missense_variant | 0.29 |
gyrA | 7988 | c.688delA | frameshift_variant | 0.22 |
gyrA | 8061 | p.Arg254Cys | missense_variant | 1.0 |
gyrA | 8567 | c.1266C>T | synonymous_variant | 0.17 |
gyrA | 8682 | p.Glu461Lys | missense_variant | 0.18 |
gyrA | 8688 | p.Ala463Pro | missense_variant | 0.18 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 490971 | c.189A>G | synonymous_variant | 0.2 |
fgd1 | 490985 | p.Leu68Pro | missense_variant | 0.2 |
fgd1 | 491591 | p.Lys270Met | missense_variant | 1.0 |
fgd1 | 491607 | c.825G>A | synonymous_variant | 0.18 |
fgd1 | 491664 | c.882C>T | synonymous_variant | 0.2 |
mshA | 575168 | c.-180C>T | upstream_gene_variant | 0.22 |
mshA | 575200 | c.-148T>C | upstream_gene_variant | 0.25 |
mshA | 575238 | c.-110T>A | upstream_gene_variant | 0.18 |
mshA | 575319 | c.-29C>T | upstream_gene_variant | 0.25 |
mshA | 575379 | p.Gly11Val | missense_variant | 0.29 |
mshA | 576190 | p.Asp281Glu | missense_variant | 0.25 |
ccsA | 619709 | c.-182T>A | upstream_gene_variant | 0.22 |
ccsA | 619784 | c.-107G>T | upstream_gene_variant | 0.15 |
ccsA | 619787 | c.-104_-103insAG | upstream_gene_variant | 0.17 |
ccsA | 620606 | p.Val239Ala | missense_variant | 0.14 |
ccsA | 620657 | p.Gly256Asp | missense_variant | 0.14 |
rpoB | 760115 | c.309C>T | synonymous_variant | 1.0 |
rpoB | 760197 | p.Ala131Thr | missense_variant | 0.17 |
rpoB | 762233 | c.2427G>A | synonymous_variant | 0.15 |
rpoC | 763958 | p.Val197Ile | missense_variant | 0.2 |
rpoC | 763974 | p.Glu202Val | missense_variant | 0.18 |
rpoC | 764263 | c.894G>A | synonymous_variant | 1.0 |
rpoC | 764537 | p.Pro390Ser | missense_variant | 0.29 |
rpoC | 764717 | p.Glu450Gln | missense_variant | 0.13 |
rpoC | 764750 | p.Val461Leu | missense_variant | 0.12 |
rpoC | 765150 | p.Gly594Glu | missense_variant | 1.0 |
rpoC | 765161 | c.1794delA | frameshift_variant | 0.13 |
rpoC | 765226 | p.Ile619Met | missense_variant | 0.1 |
rpoC | 765516 | p.Leu716Pro | missense_variant | 0.18 |
rpoC | 765726 | p.Gly786Ala | missense_variant | 0.12 |
rpoC | 765960 | p.Ala864Glu | missense_variant | 0.15 |
rpoC | 766402 | c.3033C>A | synonymous_variant | 0.13 |
rpoC | 766429 | c.3060C>A | synonymous_variant | 0.18 |
rpoC | 766434 | p.Glu1022Val | missense_variant | 0.15 |
rpoC | 766788 | p.Glu1140Gly | missense_variant | 0.18 |
rpoC | 766857 | p.Arg1163His | missense_variant | 0.15 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 775651 | c.2830C>A | synonymous_variant | 0.2 |
mmpL5 | 776283 | p.Ala733Val | missense_variant | 0.2 |
mmpL5 | 776866 | p.Met539Leu | missense_variant | 0.18 |
mmpL5 | 776877 | p.Gln535Leu | missense_variant | 0.22 |
mmpL5 | 776899 | p.Asp528His | missense_variant | 0.18 |
mmpL5 | 777130 | p.Glu451Lys | missense_variant | 0.29 |
mmpL5 | 777139 | c.1342C>T | synonymous_variant | 0.25 |
mmpL5 | 777320 | c.1161C>G | synonymous_variant | 1.0 |
mmpL5 | 777730 | c.749_750delTC | frameshift_variant | 0.25 |
mmpL5 | 777982 | p.Glu167Lys | missense_variant | 0.29 |
mmpR5 | 779348 | p.Val120Ala | missense_variant | 0.2 |
mmpR5 | 779380 | p.Gln131* | stop_gained | 0.22 |
mmpS5 | 779565 | c.-660G>A | upstream_gene_variant | 0.12 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rplC | 801003 | c.195G>A | synonymous_variant | 0.18 |
rplC | 801080 | p.Ala91Asp | missense_variant | 0.18 |
rplC | 801087 | c.279C>A | synonymous_variant | 0.2 |
rplC | 801098 | p.Val97Asp | missense_variant | 0.2 |
rplC | 801113 | p.Thr102Asn | missense_variant | 0.2 |
fbiC | 1302832 | c.-99G>C | upstream_gene_variant | 0.12 |
fbiC | 1303206 | c.276C>T | synonymous_variant | 0.15 |
fbiC | 1303341 | c.413delT | frameshift_variant | 0.15 |
fbiC | 1303545 | c.617dupC | frameshift_variant | 0.33 |
fbiC | 1304074 | p.Ala382Thr | missense_variant | 0.2 |
fbiC | 1305234 | c.2304G>C | synonymous_variant | 0.33 |
Rv1258c | 1406339 | c.1002C>T | synonymous_variant | 0.17 |
Rv1258c | 1407205 | p.Ile46Val | missense_variant | 0.13 |
Rv1258c | 1407522 | c.-182C>T | upstream_gene_variant | 0.15 |
embR | 1416822 | p.Ala176Thr | missense_variant | 0.14 |
embR | 1416887 | p.Arg154Leu | missense_variant | 0.15 |
embR | 1416938 | c.409dupC | frameshift_variant | 0.25 |
atpE | 1461026 | c.-19C>T | upstream_gene_variant | 0.15 |
atpE | 1461189 | c.145C>T | synonymous_variant | 0.17 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1471926 | n.81C>A | non_coding_transcript_exon_variant | 0.4 |
rrs | 1472129 | n.284G>A | non_coding_transcript_exon_variant | 0.22 |
rrs | 1472547 | n.703delA | non_coding_transcript_exon_variant | 0.2 |
rrl | 1473735 | n.78T>A | non_coding_transcript_exon_variant | 0.15 |
rrl | 1474955 | n.1298T>C | non_coding_transcript_exon_variant | 0.5 |
rrl | 1474963 | n.1306G>A | non_coding_transcript_exon_variant | 0.29 |
rrl | 1475490 | n.1833C>T | non_coding_transcript_exon_variant | 0.2 |
rrl | 1475751 | n.2094C>A | non_coding_transcript_exon_variant | 0.33 |
rrl | 1476509 | n.2852A>G | non_coding_transcript_exon_variant | 0.25 |
rrl | 1476517 | n.2860C>G | non_coding_transcript_exon_variant | 0.29 |
inhA | 1673366 | c.-836G>A | upstream_gene_variant | 0.25 |
fabG1 | 1673464 | p.Ala9Thr | missense_variant | 0.33 |
fabG1 | 1673733 | p.Met98Ile | missense_variant | 0.22 |
fabG1 | 1673837 | p.Gly133Asp | missense_variant | 0.4 |
fabG1 | 1673845 | p.Ile136Leu | missense_variant | 0.29 |
inhA | 1673919 | c.-283G>A | upstream_gene_variant | 0.18 |
inhA | 1674273 | c.72C>T | synonymous_variant | 0.15 |
inhA | 1674287 | p.Ala29Val | missense_variant | 0.14 |
inhA | 1674468 | c.271dupG | frameshift_variant | 0.18 |
inhA | 1674523 | p.Phe108Leu | missense_variant | 0.18 |
inhA | 1674790 | c.589C>T | synonymous_variant | 0.3 |
inhA | 1674855 | c.654C>A | synonymous_variant | 0.25 |
rpsA | 1833447 | c.-95C>T | upstream_gene_variant | 0.25 |
rpsA | 1833473 | c.-69C>T | upstream_gene_variant | 0.25 |
rpsA | 1833507 | c.-35C>T | upstream_gene_variant | 0.29 |
rpsA | 1833516 | c.-26A>C | upstream_gene_variant | 0.29 |
rpsA | 1833524 | c.-18C>T | upstream_gene_variant | 0.29 |
rpsA | 1833786 | p.Val82Ala | missense_variant | 0.13 |
rpsA | 1833791 | p.Asp84Asn | missense_variant | 0.13 |
rpsA | 1833797 | p.Val86Leu | missense_variant | 0.12 |
rpsA | 1833800 | p.Glu87* | stop_gained | 0.13 |
rpsA | 1833899 | p.Lys120* | stop_gained | 0.14 |
rpsA | 1833964 | c.423C>T | synonymous_variant | 0.17 |
rpsA | 1833992 | p.Ser151Thr | missense_variant | 0.2 |
rpsA | 1834217 | p.Val226Ile | missense_variant | 0.25 |
rpsA | 1834309 | c.768C>T | synonymous_variant | 0.14 |
rpsA | 1834559 | p.Val340Ile | missense_variant | 0.18 |
rpsA | 1834813 | c.1272G>A | synonymous_variant | 0.2 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
tlyA | 1918565 | p.Leu209His | missense_variant | 0.13 |
ndh | 2102213 | p.Ser277* | stop_gained | 0.22 |
ndh | 2102228 | p.Ala272Val | missense_variant | 0.2 |
ndh | 2102238 | p.Ile269Val | missense_variant | 0.18 |
ndh | 2102272 | c.771C>T | synonymous_variant | 0.17 |
ndh | 2102290 | c.753C>T | synonymous_variant | 0.18 |
ndh | 2102345 | p.Ala233Gly | missense_variant | 0.17 |
ndh | 2102364 | p.Lys227* | stop_gained | 0.15 |
ndh | 2102678 | p.Gly122Ala | missense_variant | 0.17 |
ndh | 2102696 | p.Ile116Thr | missense_variant | 0.14 |
ndh | 2102956 | c.87G>A | synonymous_variant | 0.18 |
ndh | 2103224 | c.-182C>T | upstream_gene_variant | 0.4 |
katG | 2154100 | p.Ser671Leu | missense_variant | 0.25 |
katG | 2154297 | c.1815G>A | synonymous_variant | 0.18 |
katG | 2156159 | c.-48C>A | upstream_gene_variant | 0.5 |
PPE35 | 2167671 | p.Phe981Ser | missense_variant | 0.22 |
PPE35 | 2167690 | p.Asn975Tyr | missense_variant | 0.2 |
PPE35 | 2169055 | c.1557delA | frameshift_variant | 0.18 |
PPE35 | 2169106 | p.Leu503Met | missense_variant | 0.29 |
PPE35 | 2169236 | p.Asp459Glu | missense_variant | 0.12 |
PPE35 | 2170304 | c.309G>T | synonymous_variant | 0.15 |
Rv1979c | 2222039 | p.Gly376Ser | missense_variant | 0.13 |
Rv1979c | 2222798 | p.Pro123Ala | missense_variant | 0.22 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
Rv1979c | 2223325 | c.-161G>T | upstream_gene_variant | 0.14 |
Rv1979c | 2223336 | c.-172G>A | upstream_gene_variant | 0.15 |
pncA | 2289098 | p.Lys48Asn | missense_variant | 0.29 |
pncA | 2289331 | c.-90C>T | upstream_gene_variant | 0.2 |
pncA | 2289367 | c.-126C>T | upstream_gene_variant | 0.29 |
kasA | 2518040 | c.-75G>A | upstream_gene_variant | 0.18 |
kasA | 2518076 | c.-39C>T | upstream_gene_variant | 1.0 |
kasA | 2518574 | p.Ile154Val | missense_variant | 0.18 |
kasA | 2518581 | p.Leu156Gln | missense_variant | 0.18 |
kasA | 2518590 | p.Gly159Glu | missense_variant | 0.2 |
eis | 2714206 | p.Arg376His | missense_variant | 0.2 |
eis | 2714827 | p.Thr169Ile | missense_variant | 0.18 |
eis | 2715433 | c.-101T>C | upstream_gene_variant | 0.22 |
ahpC | 2726541 | p.Glu117Gln | missense_variant | 0.2 |
folC | 2747344 | c.255G>A | synonymous_variant | 0.25 |
pepQ | 2860155 | c.264C>T | synonymous_variant | 0.29 |
pepQ | 2860254 | c.165C>T | synonymous_variant | 0.25 |
pepQ | 2860339 | p.Leu27Pro | missense_variant | 0.17 |
pepQ | 2860489 | c.-71G>A | upstream_gene_variant | 0.15 |
pepQ | 2860556 | c.-138C>T | upstream_gene_variant | 0.18 |
ribD | 2986884 | c.46C>T | synonymous_variant | 0.15 |
ribD | 2987121 | p.Gly95Cys | missense_variant | 0.2 |
Rv2752c | 3064729 | p.Ala488Val | missense_variant | 0.14 |
Rv2752c | 3066133 | p.Ala20Val | missense_variant | 0.17 |
Rv2752c | 3066377 | c.-186G>A | upstream_gene_variant | 0.17 |
thyX | 3067438 | p.Ala170Thr | missense_variant | 0.29 |
thyX | 3067707 | p.Phe80Ser | missense_variant | 0.22 |
thyX | 3067730 | c.216G>A | synonymous_variant | 0.18 |
thyX | 3067760 | c.186G>A | synonymous_variant | 0.23 |
thyX | 3067800 | p.Lys49Met | missense_variant | 0.13 |
thyA | 3074509 | c.-38G>A | upstream_gene_variant | 0.2 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fbiD | 3338923 | c.-195T>A | upstream_gene_variant | 0.18 |
fbiD | 3338927 | c.-191C>T | upstream_gene_variant | 0.18 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474628 | p.Thr208Ala | missense_variant | 0.29 |
fprA | 3474635 | p.Leu210* | stop_gained | 0.2 |
fprA | 3474645 | c.639C>T | synonymous_variant | 0.22 |
Rv3236c | 3611974 | c.1143A>C | synonymous_variant | 1.0 |
Rv3236c | 3612355 | p.Glu254Asp | missense_variant | 0.18 |
Rv3236c | 3612688 | c.429C>A | synonymous_variant | 0.25 |
Rv3236c | 3613135 | c.-19G>A | upstream_gene_variant | 0.17 |
Rv3236c | 3613269 | c.-153C>T | upstream_gene_variant | 0.25 |
fbiA | 3640346 | c.-197G>T | upstream_gene_variant | 0.18 |
fbiA | 3640484 | c.-59T>C | upstream_gene_variant | 0.2 |
fbiA | 3640573 | p.Gly11Arg | missense_variant | 0.33 |
fbiB | 3641642 | c.108G>A | synonymous_variant | 0.17 |
fbiB | 3642100 | p.Val189Ala | missense_variant | 0.22 |
fbiB | 3642174 | p.Val214Leu | missense_variant | 0.17 |
fbiB | 3642413 | c.879G>A | synonymous_variant | 0.18 |
fbiB | 3642534 | c.1000C>A | synonymous_variant | 0.15 |
fbiB | 3642570 | p.Glu346* | stop_gained | 0.17 |
fbiB | 3642623 | c.1089C>T | synonymous_variant | 0.29 |
alr | 3840660 | p.Gly254Asp | missense_variant | 0.2 |
alr | 3840940 | c.480delC | frameshift_variant | 0.22 |
alr | 3840983 | c.438C>T | synonymous_variant | 0.14 |
alr | 3841154 | c.267C>T | synonymous_variant | 0.25 |
alr | 3841309 | p.Ala38Thr | missense_variant | 0.15 |
alr | 3841488 | c.-68C>T | upstream_gene_variant | 0.33 |
rpoA | 3878421 | c.86delG | frameshift_variant | 0.2 |
clpC1 | 4038432 | p.Leu758Gln | missense_variant | 0.18 |
clpC1 | 4038536 | c.2169C>T | synonymous_variant | 0.22 |
clpC1 | 4040196 | p.Val170Ala | missense_variant | 0.17 |
clpC1 | 4040626 | p.Tyr27His | missense_variant | 0.33 |
embC | 4239958 | c.96C>T | synonymous_variant | 0.2 |
embC | 4240102 | c.243_247delCTTGA | frameshift_variant | 0.29 |
embC | 4240379 | p.Gln173* | stop_gained | 0.25 |
embC | 4241058 | p.Glu399Val | missense_variant | 0.22 |
embC | 4241401 | p.Phe513Leu | missense_variant | 0.29 |
embC | 4241585 | c.1725dupC | frameshift_variant | 0.12 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embC | 4242803 | p.Val981Leu | missense_variant | 1.0 |
embC | 4242910 | p.Phe1016Leu | missense_variant | 0.25 |
embC | 4243139 | p.Arg1093Ser | missense_variant | 0.15 |
embA | 4243400 | c.168C>A | synonymous_variant | 0.15 |
embA | 4244296 | p.Ala355Val | missense_variant | 0.29 |
embA | 4244462 | c.1230A>G | synonymous_variant | 0.17 |
embA | 4245382 | p.Thr717Asn | missense_variant | 0.18 |
embA | 4245481 | p.Leu750Gln | missense_variant | 0.22 |
embA | 4245942 | p.Arg904Ser | missense_variant | 0.22 |
embB | 4245954 | c.-560C>T | upstream_gene_variant | 0.17 |
embB | 4246001 | c.-513C>A | upstream_gene_variant | 0.14 |
embB | 4248519 | p.Ser669Ile | missense_variant | 0.2 |
embB | 4249427 | p.Arg972Cys | missense_variant | 0.5 |
aftB | 4267186 | p.Pro551Ser | missense_variant | 0.29 |
aftB | 4267990 | p.Ala283Thr | missense_variant | 0.29 |
aftB | 4268868 | c.-32G>T | upstream_gene_variant | 0.18 |
ubiA | 4269160 | p.Ser225Leu | missense_variant | 0.12 |
aftB | 4269348 | c.-512C>T | upstream_gene_variant | 0.15 |
ubiA | 4269855 | c.-22G>T | upstream_gene_variant | 0.4 |
ethA | 4326229 | c.1245C>T | synonymous_variant | 0.18 |
ethA | 4326983 | p.Pro164Arg | missense_variant | 0.5 |
ethA | 4327541 | c.-68G>T | upstream_gene_variant | 0.15 |
whiB6 | 4338198 | c.324C>T | synonymous_variant | 0.25 |
whiB6 | 4338229 | p.Leu98Pro | missense_variant | 0.25 |
whiB6 | 4338556 | c.-35A>T | upstream_gene_variant | 0.15 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
whiB6 | 4338602 | c.-81A>G | upstream_gene_variant | 0.15 |
whiB6 | 4338676 | c.-155T>G | upstream_gene_variant | 0.12 |
gid | 4407743 | p.Arg154Trp | missense_variant | 0.13 |
gid | 4407830 | p.Gln125Glu | missense_variant | 0.11 |
gid | 4408035 | c.168T>C | synonymous_variant | 0.15 |
gid | 4408207 | c.-5G>T | upstream_gene_variant | 0.17 |