Run ID: ERR6336744
Sample name:
Date: 02-04-2023 02:01:46
Number of reads: 611767
Percentage reads mapped: 98.87
Strain:
Drug-resistance: HR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage1 | Indo-Oceanic | EAI | RD239 | 1.0 |
lineage1.2.1 | Indo-Oceanic | EAI2 | RD239 | 1.0 |
lineage1.2.1.2.1 | Indo-Oceanic | NA | RD239 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
katG | 2156024 | c.87delC | frameshift_variant | 0.11 | isoniazid, isoniazid |
pncA | 2289213 | p.Gln10Arg | missense_variant | 0.15 | pyrazinamide |
kasA | 2519274 | p.Gly387Asp | missense_variant | 0.25 | isoniazid |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5149 | c.-91G>A | upstream_gene_variant | 0.2 |
gyrB | 5175 | c.-65T>C | upstream_gene_variant | 0.25 |
gyrB | 6112 | p.Met291Ile | missense_variant | 1.0 |
gyrB | 6723 | p.Arg495Gln | missense_variant | 0.18 |
gyrB | 6846 | p.Asp536Val | missense_variant | 0.5 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7434 | c.134delG | frameshift_variant | 0.12 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 7884 | p.Arg195Cys | missense_variant | 0.33 |
gyrA | 8281 | p.Val327Ala | missense_variant | 0.25 |
gyrA | 8452 | p.Ala384Val | missense_variant | 1.0 |
gyrA | 8510 | c.1209G>A | synonymous_variant | 0.22 |
gyrA | 8616 | p.Gln439Lys | missense_variant | 0.18 |
gyrA | 8659 | p.Asp453Ala | missense_variant | 0.17 |
gyrA | 8699 | p.Glu466Asp | missense_variant | 0.13 |
gyrA | 8701 | c.1401delC | frameshift_variant | 0.15 |
gyrA | 9143 | c.1842T>C | synonymous_variant | 1.0 |
gyrA | 9162 | p.Pro621Ser | missense_variant | 0.2 |
gyrA | 9260 | c.1959G>C | synonymous_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
gyrA | 9657 | p.Thr786Ala | missense_variant | 0.4 |
fgd1 | 490630 | c.-153G>A | upstream_gene_variant | 0.25 |
fgd1 | 490921 | p.Gln47* | stop_gained | 0.22 |
fgd1 | 491036 | p.Val85Ala | missense_variant | 0.5 |
fgd1 | 491709 | c.927A>G | synonymous_variant | 0.1 |
fgd1 | 491714 | p.His311Arg | missense_variant | 0.11 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 575193 | c.-155G>A | upstream_gene_variant | 0.22 |
mshA | 575202 | c.-145delC | upstream_gene_variant | 0.29 |
mshA | 575368 | c.21T>C | synonymous_variant | 1.0 |
mshA | 575416 | c.69T>G | synonymous_variant | 0.11 |
mshA | 575916 | p.Asp190Gly | missense_variant | 0.15 |
mshA | 575980 | p.Asp211Glu | missense_variant | 0.29 |
mshA | 576108 | p.Ala254Gly | missense_variant | 0.67 |
mshA | 576351 | p.Asp335Val | missense_variant | 0.2 |
mshA | 576388 | c.1041G>A | synonymous_variant | 0.29 |
ccsA | 620600 | p.Phe237Ser | missense_variant | 0.5 |
ccsA | 620825 | p.Leu312Gln | missense_variant | 0.25 |
rpoB | 759812 | c.6A>G | synonymous_variant | 0.18 |
rpoB | 760817 | p.Glu337Asp | missense_variant | 0.22 |
rpoB | 761355 | p.Val517Met | missense_variant | 0.25 |
rpoB | 761611 | p.Gly602Glu | missense_variant | 0.17 |
rpoB | 761685 | p.Arg627Cys | missense_variant | 0.2 |
rpoB | 762030 | p.Thr742Ser | missense_variant | 0.29 |
rpoB | 762996 | p.Glu1064* | stop_gained | 0.33 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoB | 763060 | p.Ile1085Ser | missense_variant | 0.14 |
rpoC | 763531 | c.162G>C | synonymous_variant | 1.0 |
rpoC | 763884 | p.Ala172Val | missense_variant | 1.0 |
rpoC | 763886 | c.517C>A | synonymous_variant | 1.0 |
rpoC | 764149 | c.780G>A | synonymous_variant | 0.18 |
rpoC | 765646 | p.Gln759His | missense_variant | 0.29 |
rpoC | 765898 | c.2529C>A | synonymous_variant | 0.12 |
rpoC | 765902 | p.Thr845Ala | missense_variant | 0.13 |
rpoC | 765967 | c.2598C>T | synonymous_variant | 0.13 |
rpoC | 766084 | c.2718dupC | frameshift_variant | 0.13 |
rpoC | 766113 | p.Tyr915Ser | missense_variant | 0.15 |
rpoC | 766119 | p.Glu917Ala | missense_variant | 0.15 |
rpoC | 766321 | c.2952C>G | synonymous_variant | 0.33 |
rpoC | 767189 | p.Pro1274Ala | missense_variant | 0.12 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 775806 | p.Met892Thr | missense_variant | 0.14 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 776386 | p.Pro699Ser | missense_variant | 0.22 |
mmpL5 | 776880 | p.Asp534Ala | missense_variant | 0.15 |
mmpL5 | 776884 | p.Ile533Val | missense_variant | 0.15 |
mmpL5 | 777010 | p.Pro491Ser | missense_variant | 0.13 |
mmpL5 | 777337 | p.Val382Ile | missense_variant | 0.18 |
mmpS5 | 778486 | p.Lys140Asn | missense_variant | 0.18 |
mmpL5 | 778953 | c.-473A>T | upstream_gene_variant | 0.2 |
mmpL5 | 779094 | c.-614C>T | upstream_gene_variant | 0.22 |
mmpL5 | 779106 | c.-626C>T | upstream_gene_variant | 0.22 |
mmpS5 | 779673 | c.-768A>G | upstream_gene_variant | 0.17 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rpsL | 781421 | c.-139C>T | upstream_gene_variant | 0.17 |
fbiC | 1303063 | c.135delC | frameshift_variant | 0.2 |
fbiC | 1303253 | p.Val108Ala | missense_variant | 0.29 |
fbiC | 1303556 | p.Pro209Leu | missense_variant | 0.22 |
fbiC | 1304010 | c.1080G>A | synonymous_variant | 0.17 |
fbiC | 1304059 | c.1129C>T | synonymous_variant | 0.15 |
Rv1258c | 1406312 | c.1029T>C | synonymous_variant | 1.0 |
Rv1258c | 1406365 | p.Gly326Arg | missense_variant | 0.17 |
embR | 1416565 | c.783T>C | synonymous_variant | 0.22 |
embR | 1417019 | p.Cys110Tyr | missense_variant | 1.0 |
embR | 1417098 | p.Gly84Ser | missense_variant | 0.18 |
atpE | 1460907 | c.-138T>C | upstream_gene_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1471748 | n.-98C>G | upstream_gene_variant | 0.18 |
rrl | 1473500 | n.-158C>T | upstream_gene_variant | 0.22 |
rrl | 1473590 | n.-68A>G | upstream_gene_variant | 0.17 |
rrl | 1473605 | n.-53G>A | upstream_gene_variant | 0.17 |
rrl | 1474639 | n.982G>A | non_coding_transcript_exon_variant | 1.0 |
fabG1 | 1673367 | c.-73G>C | upstream_gene_variant | 0.25 |
fabG1 | 1673553 | p.Asp38Glu | missense_variant | 0.3 |
inhA | 1674162 | c.-40C>T | upstream_gene_variant | 1.0 |
rpsA | 1833358 | c.-184C>A | upstream_gene_variant | 0.17 |
rpsA | 1833622 | c.81C>T | synonymous_variant | 0.15 |
rpsA | 1834525 | c.984G>A | synonymous_variant | 0.13 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
ndh | 2103124 | c.-82T>C | upstream_gene_variant | 0.29 |
katG | 2154227 | p.Gly629Arg | missense_variant | 0.29 |
katG | 2154240 | p.Met624Ile | missense_variant | 0.4 |
katG | 2154343 | p.Lys590Arg | missense_variant | 0.18 |
katG | 2154601 | p.Gly504Glu | missense_variant | 0.2 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
katG | 2155512 | c.600G>A | synonymous_variant | 0.5 |
katG | 2156277 | c.-166G>A | upstream_gene_variant | 0.14 |
PPE35 | 2167676 | c.2936dupG | frameshift_variant | 0.25 |
PPE35 | 2167714 | p.Val967Ile | missense_variant | 0.2 |
PPE35 | 2167768 | p.Gly949Ser | missense_variant | 0.29 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2168142 | p.Phe824Ser | missense_variant | 0.12 |
PPE35 | 2169691 | p.Gly308Ser | missense_variant | 0.17 |
PPE35 | 2170048 | p.Leu189Val | missense_variant | 0.67 |
PPE35 | 2170053 | p.Thr187Ser | missense_variant | 0.67 |
PPE35 | 2170266 | p.Gly116Asp | missense_variant | 0.33 |
PPE35 | 2170271 | c.342T>C | synonymous_variant | 0.29 |
Rv1979c | 2222144 | p.Ser341Thr | missense_variant | 0.5 |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 1.0 |
Rv1979c | 2222627 | p.Gly180Ser | missense_variant | 0.14 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289003 | p.Asp80Val | missense_variant | 0.15 |
pncA | 2289045 | p.Ser66Trp | missense_variant | 0.15 |
pncA | 2290003 | c.-762C>T | upstream_gene_variant | 0.4 |
pncA | 2290032 | c.-791A>G | upstream_gene_variant | 0.25 |
pncA | 2290034 | c.-794_-793delGCinsAT | upstream_gene_variant | 0.2 |
pncA | 2290106 | c.-865C>T | upstream_gene_variant | 0.22 |
kasA | 2518110 | c.-5T>G | upstream_gene_variant | 0.18 |
kasA | 2518132 | c.18C>T | synonymous_variant | 1.0 |
kasA | 2518756 | c.642G>C | synonymous_variant | 0.13 |
kasA | 2518765 | c.651G>A | synonymous_variant | 0.15 |
kasA | 2518809 | p.Lys232Arg | missense_variant | 0.15 |
kasA | 2519048 | p.Gly312Ser | missense_variant | 1.0 |
eis | 2714271 | c.1062C>T | synonymous_variant | 0.33 |
eis | 2714429 | p.Pro302Ser | missense_variant | 0.22 |
eis | 2714949 | c.384G>A | synonymous_variant | 0.15 |
eis | 2715285 | p.Met16Ile | missense_variant | 0.2 |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 1.0 |
ahpC | 2726383 | p.Glu64Gly | missense_variant | 0.4 |
folC | 2746367 | p.Ala411Val | missense_variant | 0.5 |
folC | 2746439 | p.Val387Ala | missense_variant | 0.13 |
pepQ | 2859960 | c.459G>A | synonymous_variant | 0.18 |
pepQ | 2860418 | p.Val1Met | missense_variant | 0.25 |
pepQ | 2860539 | c.-121G>A | upstream_gene_variant | 0.33 |
Rv2752c | 3065086 | p.Arg369Thr | missense_variant | 0.2 |
Rv2752c | 3065217 | c.975C>T | synonymous_variant | 0.12 |
Rv2752c | 3065315 | p.Glu293Gln | missense_variant | 0.14 |
Rv2752c | 3065366 | c.826C>T | synonymous_variant | 0.15 |
Rv2752c | 3065478 | c.714C>T | synonymous_variant | 0.18 |
Rv2752c | 3065549 | p.Glu215Lys | missense_variant | 0.18 |
Rv2752c | 3065582 | p.Thr204Ala | missense_variant | 0.17 |
Rv2752c | 3065786 | p.His136Tyr | missense_variant | 0.15 |
Rv2752c | 3066037 | p.His52Arg | missense_variant | 0.67 |
Rv2752c | 3067053 | c.-862C>G | upstream_gene_variant | 0.14 |
thyX | 3067243 | p.Leu235Met | missense_variant | 0.33 |
thyX | 3067752 | p.Ile65Thr | missense_variant | 0.25 |
thyX | 3068128 | c.-183C>T | upstream_gene_variant | 0.22 |
thyA | 3074459 | p.Glu5Lys | missense_variant | 0.14 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
ald | 3086881 | p.Ala21Asp | missense_variant | 0.22 |
ald | 3087103 | p.Leu95Trp | missense_variant | 0.11 |
fbiD | 3339417 | c.300A>G | synonymous_variant | 1.0 |
Rv3083 | 3448515 | p.His4Gln | missense_variant | 0.13 |
Rv3083 | 3448516 | p.Phe5Val | missense_variant | 0.13 |
Rv3083 | 3448714 | p.Asp71His | missense_variant | 1.0 |
Rv3083 | 3448720 | p.Lys73* | stop_gained | 0.17 |
Rv3083 | 3448787 | p.Asp95Val | missense_variant | 0.18 |
Rv3083 | 3449196 | c.693C>T | synonymous_variant | 0.15 |
Rv3083 | 3449330 | p.Arg276His | missense_variant | 0.18 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474597 | c.591C>A | synonymous_variant | 1.0 |
fprA | 3474791 | p.Pro262Leu | missense_variant | 0.15 |
fprA | 3474914 | p.Ala303Val | missense_variant | 0.22 |
fprA | 3475159 | p.Asn385Asp | missense_variant | 1.0 |
whiB7 | 3568488 | c.191delG | frameshift_variant | 1.0 |
whiB7 | 3568571 | p.Glu37Lys | missense_variant | 0.4 |
whiB7 | 3568580 | p.Ala34Thr | missense_variant | 0.4 |
whiB7 | 3568797 | c.-118G>A | upstream_gene_variant | 0.18 |
Rv3236c | 3612193 | c.924C>T | synonymous_variant | 0.18 |
Rv3236c | 3612327 | c.789delG | frameshift_variant | 0.14 |
Rv3236c | 3612403 | c.714G>A | synonymous_variant | 0.15 |
Rv3236c | 3612536 | p.Gly194Glu | missense_variant | 0.15 |
Rv3236c | 3612895 | c.222T>A | synonymous_variant | 0.12 |
fbiA | 3640478 | c.-65G>A | upstream_gene_variant | 0.17 |
fbiB | 3640557 | c.-978T>C | upstream_gene_variant | 1.0 |
fbiA | 3640654 | p.Asp38Asn | missense_variant | 0.29 |
fbiA | 3640660 | p.Gln40* | stop_gained | 0.25 |
fbiB | 3640881 | c.-654G>A | upstream_gene_variant | 0.17 |
fbiA | 3641387 | p.Thr282Ile | missense_variant | 0.33 |
fbiB | 3641627 | c.93C>T | synonymous_variant | 0.29 |
fbiB | 3641955 | p.Gly141Ser | missense_variant | 0.2 |
fbiB | 3642269 | c.735C>T | synonymous_variant | 0.2 |
alr | 3840310 | c.1111C>A | synonymous_variant | 0.2 |
alr | 3840842 | c.579G>C | synonymous_variant | 0.29 |
rpoA | 3878334 | c.174T>A | synonymous_variant | 0.33 |
ddn | 3986935 | p.Arg31His | missense_variant | 0.13 |
clpC1 | 4039942 | c.763C>T | synonymous_variant | 0.17 |
clpC1 | 4040057 | c.648C>T | synonymous_variant | 0.18 |
clpC1 | 4040517 | p.Val63Thr | missense_variant | 1.0 |
clpC1 | 4040536 | p.Glu57Lys | missense_variant | 0.18 |
clpC1 | 4040548 | p.Gly53Arg | missense_variant | 0.15 |
panD | 4043903 | p.Asn127His | missense_variant | 0.15 |
panD | 4044172 | p.Asp37Gly | missense_variant | 0.15 |
embC | 4239822 | c.-41C>A | upstream_gene_variant | 0.17 |
embC | 4240295 | p.Ser145Gly | missense_variant | 0.15 |
embC | 4240329 | p.Thr156Ile | missense_variant | 0.15 |
embC | 4240671 | p.Thr270Ile | missense_variant | 1.0 |
embC | 4241042 | p.Asn394Asp | missense_variant | 1.0 |
embC | 4241080 | p.Ile406Met | missense_variant | 0.33 |
embC | 4241087 | p.Thr409Ala | missense_variant | 0.33 |
embC | 4241360 | p.Asn500Asp | missense_variant | 0.67 |
embC | 4241489 | p.Ala543Thr | missense_variant | 0.13 |
embC | 4241595 | p.Ala578Val | missense_variant | 0.14 |
embC | 4241988 | p.Ala709Val | missense_variant | 0.17 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embC | 4242837 | p.Pro992Leu | missense_variant | 0.17 |
embA | 4243427 | c.195G>A | synonymous_variant | 0.13 |
embA | 4243580 | c.348G>A | synonymous_variant | 1.0 |
embA | 4243898 | c.666C>T | synonymous_variant | 0.25 |
embA | 4244009 | c.777G>A | synonymous_variant | 0.12 |
embA | 4244030 | c.798C>T | synonymous_variant | 0.2 |
embA | 4244420 | c.1188G>C | synonymous_variant | 1.0 |
embA | 4244884 | p.Arg551Gln | missense_variant | 0.12 |
embA | 4245028 | p.Ser599Asn | missense_variant | 0.13 |
embA | 4245471 | p.Ala747Thr | missense_variant | 0.33 |
embA | 4245654 | p.Asp808Asn | missense_variant | 0.29 |
embB | 4245806 | c.-708G>A | upstream_gene_variant | 0.22 |
embA | 4245969 | p.Pro913Ser | missense_variant | 1.0 |
embA | 4246311 | p.Gly1027Ser | missense_variant | 0.29 |
embB | 4246584 | p.Arg24Pro | missense_variant | 0.25 |
embB | 4247087 | c.574C>T | synonymous_variant | 0.29 |
embB | 4247426 | p.Gly305Thr | missense_variant | 0.18 |
embB | 4247437 | c.924A>G | synonymous_variant | 0.2 |
embB | 4247440 | c.927C>G | synonymous_variant | 0.2 |
embB | 4247441 | p.Ala310Ser | missense_variant | 0.2 |
embB | 4247446 | p.Asp311Glu | missense_variant | 0.2 |
embB | 4247449 | c.936C>T | synonymous_variant | 0.2 |
embB | 4247452 | c.939C>G | synonymous_variant | 0.2 |
embB | 4247458 | c.945C>T | synonymous_variant | 0.2 |
embB | 4247578 | c.1065G>A | synonymous_variant | 1.0 |
embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 |
embB | 4247778 | p.Ser422Phe | missense_variant | 0.22 |
embB | 4247905 | c.1392G>A | synonymous_variant | 0.5 |
embB | 4247918 | p.Arg469Gly | missense_variant | 0.5 |
embB | 4248324 | p.Ala604Gly | missense_variant | 0.25 |
embB | 4248995 | p.Gly828Ser | missense_variant | 0.17 |
embB | 4249755 | p.Gly1081Ala | missense_variant | 0.14 |
embB | 4249761 | p.Ala1083Gly | missense_variant | 0.17 |
aftB | 4267114 | p.Leu575Phe | missense_variant | 0.15 |
aftB | 4267486 | c.1351C>T | synonymous_variant | 0.33 |
aftB | 4267491 | p.Ala449Val | missense_variant | 0.33 |
aftB | 4267496 | p.Glu447Asp | missense_variant | 0.33 |
aftB | 4267522 | p.Leu439Phe | missense_variant | 0.33 |
aftB | 4267638 | p.Thr400Ile | missense_variant | 0.13 |
aftB | 4267995 | p.Met281Thr | missense_variant | 0.2 |
aftB | 4268601 | p.Leu79Arg | missense_variant | 0.17 |
aftB | 4268607 | c.229_230insG | frameshift_variant | 0.12 |
aftB | 4268683 | p.Gly52Arg | missense_variant | 0.11 |
aftB | 4268861 | c.-25T>G | upstream_gene_variant | 0.15 |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 1.0 |
aftB | 4269606 | c.-770T>C | upstream_gene_variant | 1.0 |
ubiA | 4269635 | p.Ser67Pro | missense_variant | 0.29 |
ubiA | 4269864 | c.-32delG | upstream_gene_variant | 1.0 |
ubiA | 4269997 | c.-164C>T | upstream_gene_variant | 0.33 |
ethA | 4327629 | c.-156C>T | upstream_gene_variant | 0.22 |
ethR | 4327748 | p.Ser67Phe | missense_variant | 0.33 |
whiB6 | 4338330 | c.192C>T | synonymous_variant | 1.0 |
whiB6 | 4338361 | p.Arg54Gln | missense_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
whiB6 | 4338603 | c.-82C>T | upstream_gene_variant | 1.0 |
whiB6 | 4338664 | c.-143C>T | upstream_gene_variant | 0.18 |
whiB6 | 4338687 | c.-166G>A | upstream_gene_variant | 0.15 |
whiB6 | 4338703 | c.-182T>C | upstream_gene_variant | 0.18 |
whiB6 | 4338707 | c.-186A>C | upstream_gene_variant | 0.18 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407873 | c.330G>T | synonymous_variant | 1.0 |
gid | 4407899 | c.304C>A | synonymous_variant | 0.4 |
gid | 4407997 | p.Gly69Val | missense_variant | 1.0 |
gid | 4408194 | c.9G>A | synonymous_variant | 0.29 |