Run ID: ERR6336765
Sample name:
Date: 02-04-2023 02:02:32
Number of reads: 1066646
Percentage reads mapped: 98.12
Strain:
Drug-resistance: HR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage1 | Indo-Oceanic | EAI | RD239 | 1.0 |
lineage1.2.1.2.1 | Indo-Oceanic | NA | RD239 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpsL | 781822 | p.Lys88Arg | missense_variant | 1.0 | streptomycin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5511 | p.Ser91Phe | missense_variant | 0.25 |
gyrB | 5520 | p.Pro94Arg | missense_variant | 0.22 |
gyrB | 6112 | p.Met291Ile | missense_variant | 1.0 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 8414 | c.1113C>T | synonymous_variant | 0.2 |
gyrA | 8452 | p.Ala384Val | missense_variant | 1.0 |
gyrA | 8535 | p.Glu412Lys | missense_variant | 0.15 |
gyrA | 8843 | c.1542G>A | synonymous_variant | 0.17 |
gyrA | 9143 | c.1842T>C | synonymous_variant | 1.0 |
gyrA | 9144 | p.Arg615Cys | missense_variant | 0.17 |
gyrA | 9158 | c.1857C>T | synonymous_variant | 0.17 |
gyrA | 9260 | c.1959G>C | synonymous_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
gyrA | 9358 | p.Thr686Ile | missense_variant | 0.29 |
gyrA | 9562 | p.Met754Thr | missense_variant | 0.12 |
gyrA | 9569 | p.Asp756Glu | missense_variant | 0.18 |
fgd1 | 490885 | p.Ala35Thr | missense_variant | 0.14 |
fgd1 | 490993 | p.Gly71Ser | missense_variant | 0.29 |
fgd1 | 491129 | p.Thr116Asn | missense_variant | 0.25 |
fgd1 | 491131 | p.Gly117Arg | missense_variant | 0.2 |
fgd1 | 491227 | p.Asp149Asn | missense_variant | 0.15 |
fgd1 | 491262 | c.480C>T | synonymous_variant | 0.17 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 575368 | c.21T>C | synonymous_variant | 1.0 |
mshA | 576239 | p.Ala298Pro | missense_variant | 0.33 |
ccsA | 619791 | c.-100G>A | upstream_gene_variant | 0.18 |
ccsA | 620014 | p.Arg42Cys | missense_variant | 0.4 |
ccsA | 620085 | c.195G>A | synonymous_variant | 0.4 |
ccsA | 620371 | p.Ala161Ser | missense_variant | 0.18 |
rpoB | 759979 | p.Leu58Pro | missense_variant | 0.11 |
rpoB | 760008 | p.Ala68Thr | missense_variant | 0.18 |
rpoB | 760572 | p.Leu256Met | missense_variant | 0.15 |
rpoB | 760604 | c.798G>A | synonymous_variant | 0.14 |
rpoB | 760605 | p.Ala267Thr | missense_variant | 0.14 |
rpoB | 761133 | c.1327T>C | synonymous_variant | 0.15 |
rpoB | 761152 | p.Leu449Gln | missense_variant | 0.57 |
rpoB | 761162 | c.1356G>T | synonymous_variant | 0.4 |
rpoB | 761710 | p.Val635Asp | missense_variant | 0.6 |
rpoB | 761713 | p.Val636Asp | missense_variant | 0.6 |
rpoB | 761828 | c.2022C>T | synonymous_variant | 0.13 |
rpoB | 762307 | p.Pro834Gln | missense_variant | 0.5 |
rpoB | 762631 | p.Ala942Val | missense_variant | 0.22 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 763531 | c.162G>C | synonymous_variant | 1.0 |
rpoC | 763595 | p.Glu76Lys | missense_variant | 0.18 |
rpoC | 763884 | p.Ala172Val | missense_variant | 1.0 |
rpoC | 763886 | c.517C>A | synonymous_variant | 1.0 |
rpoC | 764560 | c.1191T>C | synonymous_variant | 0.33 |
rpoC | 765608 | p.Asp747Asn | missense_variant | 0.12 |
rpoC | 765941 | p.Lys858Glu | missense_variant | 0.13 |
rpoC | 765966 | p.Arg866His | missense_variant | 0.29 |
rpoC | 766073 | c.2706delC | frameshift_variant | 0.14 |
rpoC | 766163 | p.Glu932Lys | missense_variant | 0.25 |
rpoC | 766171 | c.2802C>T | synonymous_variant | 0.2 |
rpoC | 766199 | c.2830C>T | synonymous_variant | 0.15 |
rpoC | 766782 | p.Val1138Ala | missense_variant | 0.15 |
rpoC | 766912 | c.3543C>T | synonymous_variant | 0.18 |
rpoC | 766919 | p.Ala1184Thr | missense_variant | 0.22 |
rpoC | 767205 | p.Arg1279His | missense_variant | 0.13 |
rpoC | 767271 | p.Thr1301Ser | missense_variant | 0.18 |
rpoC | 767320 | c.3951G>A | splice_region_variant&stop_retained_variant | 0.15 |
mmpL5 | 775633 | p.Gln950* | stop_gained | 0.4 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 775925 | c.2556G>T | synonymous_variant | 0.12 |
mmpL5 | 775931 | c.2550C>T | synonymous_variant | 0.13 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 777410 | c.1071A>T | synonymous_variant | 0.25 |
mmpL5 | 777418 | p.Pro355Thr | missense_variant | 0.22 |
mmpL5 | 777479 | c.1002C>T | synonymous_variant | 0.15 |
mmpL5 | 777722 | c.759C>T | synonymous_variant | 0.25 |
rpsL | 781361 | c.-199G>A | upstream_gene_variant | 0.2 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rplC | 800991 | c.183G>A | synonymous_variant | 0.17 |
fbiC | 1302879 | c.-52T>C | upstream_gene_variant | 0.13 |
fbiC | 1303591 | p.Arg221Gly | missense_variant | 0.2 |
fbiC | 1303678 | p.Arg250Trp | missense_variant | 0.15 |
fbiC | 1304016 | c.1086C>T | synonymous_variant | 0.15 |
fbiC | 1304197 | p.Gly423Ser | missense_variant | 0.67 |
fbiC | 1304791 | p.Val621Ile | missense_variant | 0.25 |
fbiC | 1305280 | p.Ile784Phe | missense_variant | 0.13 |
Rv1258c | 1406200 | p.Leu381Phe | missense_variant | 0.15 |
Rv1258c | 1406312 | c.1029T>C | synonymous_variant | 1.0 |
Rv1258c | 1406471 | c.870C>A | synonymous_variant | 0.17 |
Rv1258c | 1406704 | p.Ala213Thr | missense_variant | 0.17 |
embR | 1416490 | c.858G>A | synonymous_variant | 0.25 |
embR | 1417019 | p.Cys110Tyr | missense_variant | 1.0 |
atpE | 1460907 | c.-138T>C | upstream_gene_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1474425 | n.768A>G | non_coding_transcript_exon_variant | 0.13 |
rrl | 1474639 | n.982G>A | non_coding_transcript_exon_variant | 1.0 |
fabG1 | 1674010 | p.Thr191Ser | missense_variant | 0.12 |
fabG1 | 1674059 | p.Pro207Leu | missense_variant | 0.18 |
inhA | 1674162 | c.-40C>T | upstream_gene_variant | 1.0 |
inhA | 1674687 | c.486G>A | synonymous_variant | 0.2 |
rpsA | 1834040 | p.Lys167Glu | missense_variant | 0.29 |
rpsA | 1834562 | p.Gly341Ser | missense_variant | 0.22 |
tlyA | 1917825 | c.-115G>A | upstream_gene_variant | 0.17 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
tlyA | 1918102 | p.Val55Met | missense_variant | 0.25 |
tlyA | 1918426 | p.Val163Met | missense_variant | 0.13 |
tlyA | 1918710 | c.771G>A | synonymous_variant | 0.17 |
ndh | 2102079 | p.Asp322Asn | missense_variant | 0.17 |
ndh | 2102127 | p.Leu306Met | missense_variant | 0.2 |
ndh | 2102308 | c.735G>C | synonymous_variant | 0.18 |
ndh | 2102397 | p.Ala216Ser | missense_variant | 0.29 |
ndh | 2103167 | c.-125A>G | upstream_gene_variant | 0.18 |
ndh | 2103220 | c.-178C>G | upstream_gene_variant | 0.25 |
ndh | 2103227 | c.-185T>C | upstream_gene_variant | 0.22 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
katG | 2155310 | p.Gly268Ser | missense_variant | 0.33 |
katG | 2155416 | c.696G>A | synonymous_variant | 0.18 |
katG | 2155638 | p.Lys158Asn | missense_variant | 0.18 |
katG | 2155656 | c.456G>A | synonymous_variant | 0.22 |
katG | 2156346 | c.-235T>G | upstream_gene_variant | 0.15 |
katG | 2156493 | c.-382C>T | upstream_gene_variant | 0.14 |
katG | 2156517 | c.-406C>T | upstream_gene_variant | 0.2 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2167982 | c.2631C>G | synonymous_variant | 0.13 |
PPE35 | 2169961 | p.Gly218Ser | missense_variant | 0.14 |
PPE35 | 2169986 | c.627G>A | synonymous_variant | 0.33 |
PPE35 | 2170048 | p.Leu189Val | missense_variant | 0.75 |
PPE35 | 2170053 | p.Thr187Ser | missense_variant | 0.75 |
PPE35 | 2170300 | p.Val105Ile | missense_variant | 0.15 |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2288699 | c.543G>A | synonymous_variant | 0.33 |
pncA | 2288799 | p.Arg148His | missense_variant | 0.15 |
pncA | 2289350 | c.-109G>T | upstream_gene_variant | 0.12 |
pncA | 2289529 | c.-288G>T | upstream_gene_variant | 0.13 |
pncA | 2289815 | c.-574C>T | upstream_gene_variant | 0.33 |
pncA | 2289884 | c.-643G>A | upstream_gene_variant | 0.4 |
pncA | 2290109 | c.-868C>T | upstream_gene_variant | 0.12 |
kasA | 2518132 | c.18C>T | synonymous_variant | 1.0 |
kasA | 2518390 | c.276A>G | synonymous_variant | 0.13 |
kasA | 2518392 | p.Gln93Arg | missense_variant | 0.13 |
kasA | 2519048 | p.Gly312Ser | missense_variant | 1.0 |
kasA | 2519321 | p.Gly403Arg | missense_variant | 0.2 |
eis | 2714408 | p.Gly309Ser | missense_variant | 0.2 |
eis | 2714970 | c.363C>T | synonymous_variant | 0.29 |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 1.0 |
ahpC | 2726694 | p.Leu168Phe | missense_variant | 0.18 |
folC | 2746625 | p.Ala325Val | missense_variant | 0.22 |
folC | 2747118 | p.Ala161Pro | missense_variant | 0.67 |
folC | 2747135 | p.Leu155His | missense_variant | 0.67 |
pepQ | 2859399 | p.Asp340Glu | missense_variant | 0.11 |
pepQ | 2859592 | p.Ala276Val | missense_variant | 0.22 |
pepQ | 2860048 | p.Ala124Val | missense_variant | 0.17 |
ribD | 2986711 | c.-128G>T | upstream_gene_variant | 0.2 |
ribD | 2986790 | c.-49G>A | upstream_gene_variant | 0.14 |
ribD | 2987528 | c.693delC | frameshift_variant | 0.17 |
Rv2752c | 3064922 | p.Glu424Lys | missense_variant | 0.12 |
Rv2752c | 3065336 | p.Leu286Phe | missense_variant | 0.14 |
Rv2752c | 3065492 | p.Ile234Val | missense_variant | 0.12 |
Rv2752c | 3065533 | p.Pro220Leu | missense_variant | 0.2 |
Rv2752c | 3066135 | c.57C>T | synonymous_variant | 0.18 |
Rv2752c | 3066171 | c.20delC | frameshift_variant | 0.14 |
Rv2752c | 3066240 | c.-49G>A | upstream_gene_variant | 0.14 |
Rv2752c | 3067134 | c.-943C>T | upstream_gene_variant | 0.2 |
thyA | 3074038 | p.Pro145Leu | missense_variant | 0.17 |
thyA | 3074044 | p.Leu143Arg | missense_variant | 0.17 |
thyA | 3074471 | p.Val1Met | missense_variant | 0.2 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
ald | 3087725 | c.907delG | frameshift_variant | 0.22 |
fbiD | 3339090 | c.-28C>T | upstream_gene_variant | 0.4 |
fbiD | 3339238 | p.Ala41Pro | missense_variant | 0.25 |
fbiD | 3339284 | c.170_171delGC | frameshift_variant | 0.25 |
fbiD | 3339290 | p.Ser58Leu | missense_variant | 0.33 |
fbiD | 3339417 | c.300A>G | synonymous_variant | 1.0 |
Rv3083 | 3448358 | c.-146G>T | upstream_gene_variant | 0.29 |
Rv3083 | 3448361 | c.-143G>T | upstream_gene_variant | 0.22 |
Rv3083 | 3448588 | c.87_88delCA | frameshift_variant | 0.15 |
Rv3083 | 3448714 | p.Asp71His | missense_variant | 1.0 |
Rv3083 | 3448858 | p.Ala119Thr | missense_variant | 0.15 |
Rv3083 | 3449937 | p.Ile478Met | missense_variant | 0.29 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474033 | c.27G>A | synonymous_variant | 0.5 |
fprA | 3474355 | c.350delA | frameshift_variant | 0.18 |
fprA | 3474363 | c.357G>A | synonymous_variant | 0.15 |
fprA | 3474597 | c.591C>A | synonymous_variant | 1.0 |
fprA | 3474600 | c.594G>A | synonymous_variant | 0.17 |
fprA | 3475090 | p.Arg362Cys | missense_variant | 0.13 |
fprA | 3475159 | p.Asn385Asp | missense_variant | 1.0 |
fprA | 3475344 | p.Ser446Arg | missense_variant | 0.22 |
fprA | 3475351 | p.Glu449Lys | missense_variant | 0.22 |
fprA | 3475356 | c.1350G>A | synonymous_variant | 0.22 |
whiB7 | 3568488 | c.191delG | frameshift_variant | 1.0 |
whiB7 | 3568561 | p.Lys40Arg | missense_variant | 0.12 |
Rv3236c | 3613161 | c.-45A>T | upstream_gene_variant | 0.12 |
Rv3236c | 3613297 | c.-181C>T | upstream_gene_variant | 0.18 |
fbiB | 3640557 | c.-978T>C | upstream_gene_variant | 1.0 |
fbiA | 3640616 | p.Leu25Pro | missense_variant | 0.17 |
fbiB | 3640879 | c.-656C>T | upstream_gene_variant | 0.13 |
fbiB | 3642543 | p.Arg337Cys | missense_variant | 0.15 |
rpoA | 3877626 | c.882C>T | synonymous_variant | 0.17 |
rpoA | 3877881 | c.627G>A | synonymous_variant | 0.17 |
rpoA | 3877885 | p.Leu208Arg | missense_variant | 0.13 |
rpoA | 3877891 | p.Asp206Val | missense_variant | 0.13 |
rpoA | 3877897 | p.Pro204Gln | missense_variant | 0.14 |
rpoA | 3878086 | p.Glu141Gly | missense_variant | 0.12 |
rpoA | 3878567 | c.-60C>G | upstream_gene_variant | 0.23 |
clpC1 | 4038899 | c.1806C>G | synonymous_variant | 0.25 |
clpC1 | 4039251 | p.Ala485Val | missense_variant | 0.17 |
clpC1 | 4040002 | p.His235Asn | missense_variant | 0.17 |
clpC1 | 4040051 | c.654C>T | synonymous_variant | 0.29 |
clpC1 | 4040057 | c.648C>T | synonymous_variant | 0.29 |
clpC1 | 4040170 | p.Thr179Ala | missense_variant | 0.13 |
clpC1 | 4040517 | p.Val63Ala | missense_variant | 1.0 |
embC | 4239694 | c.-168delA | upstream_gene_variant | 0.2 |
embC | 4239725 | c.-138G>A | upstream_gene_variant | 0.18 |
embC | 4240360 | c.498C>T | synonymous_variant | 0.22 |
embC | 4240671 | p.Thr270Ile | missense_variant | 1.0 |
embC | 4241042 | p.Asn394Asp | missense_variant | 1.0 |
embC | 4241212 | c.1350G>A | synonymous_variant | 0.22 |
embC | 4241231 | p.Arg457Gly | missense_variant | 0.18 |
embC | 4241281 | c.1419G>A | synonymous_variant | 0.2 |
embC | 4241470 | c.1608C>T | synonymous_variant | 0.13 |
embC | 4242530 | p.Arg890* | stop_gained | 0.5 |
embC | 4243121 | p.Ser1087Cys | missense_variant | 0.18 |
embA | 4243580 | c.348G>A | synonymous_variant | 1.0 |
embA | 4243608 | c.377delC | frameshift_variant | 0.5 |
embA | 4243704 | p.Gly158Ser | missense_variant | 0.33 |
embA | 4243723 | p.Pro164Leu | missense_variant | 0.29 |
embA | 4244011 | p.Thr260Ile | missense_variant | 0.4 |
embA | 4244417 | c.1185G>A | synonymous_variant | 0.5 |
embA | 4244420 | c.1188G>C | synonymous_variant | 1.0 |
embB | 4245950 | c.-564G>A | upstream_gene_variant | 0.15 |
embA | 4245969 | p.Pro913Ser | missense_variant | 1.0 |
embA | 4246105 | p.Pro958Leu | missense_variant | 0.17 |
embB | 4246430 | c.-84C>G | upstream_gene_variant | 0.22 |
embB | 4246475 | c.-39G>A | upstream_gene_variant | 0.25 |
embB | 4246544 | p.Thr11Pro | missense_variant | 0.25 |
embB | 4246548 | p.Pro12Gln | missense_variant | 0.42 |
embB | 4246555 | c.42G>C | synonymous_variant | 0.36 |
embB | 4246556 | p.Ala15Pro | missense_variant | 0.36 |
embB | 4246563 | p.Leu17Trp | missense_variant | 0.36 |
embB | 4246567 | c.54G>T | synonymous_variant | 0.5 |
embB | 4246584 | p.Arg24Pro | missense_variant | 0.4 |
embB | 4246814 | p.Thr101Ala | missense_variant | 0.22 |
embB | 4246886 | p.Val125Ile | missense_variant | 0.18 |
embB | 4247578 | c.1065G>A | synonymous_variant | 1.0 |
embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 |
embB | 4248670 | c.2157C>T | synonymous_variant | 0.14 |
embB | 4248766 | c.2253C>T | synonymous_variant | 0.13 |
embB | 4248967 | c.2454G>C | synonymous_variant | 0.13 |
embB | 4249395 | p.Ile961Thr | missense_variant | 0.18 |
embB | 4249434 | p.Leu974Pro | missense_variant | 0.13 |
embB | 4249494 | p.Phe994Ser | missense_variant | 0.12 |
aftB | 4267906 | p.Val311Met | missense_variant | 0.4 |
aftB | 4267910 | c.927G>A | synonymous_variant | 0.4 |
aftB | 4268925 | c.-89G>A | upstream_gene_variant | 0.18 |
ubiA | 4268944 | c.889dupG | frameshift_variant | 0.18 |
ubiA | 4269115 | p.Arg240Pro | missense_variant | 0.4 |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 1.0 |
ubiA | 4269498 | p.Thr112Met | missense_variant | 0.14 |
aftB | 4269606 | c.-770T>C | upstream_gene_variant | 1.0 |
ubiA | 4269864 | c.-32delG | upstream_gene_variant | 1.0 |
ubiA | 4269908 | c.-75C>T | upstream_gene_variant | 0.22 |
ubiA | 4269941 | c.-108C>T | upstream_gene_variant | 0.17 |
ethA | 4326921 | p.Ala185Pro | missense_variant | 0.2 |
ethR | 4326934 | c.-615C>T | upstream_gene_variant | 0.17 |
ethA | 4327641 | c.-168G>A | upstream_gene_variant | 0.2 |
ethA | 4328187 | c.-714G>A | upstream_gene_variant | 0.22 |
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 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407805 | p.Ala133Val | missense_variant | 0.25 |
gid | 4407873 | c.330G>T | synonymous_variant | 1.0 |
gid | 4408063 | p.Arg47Pro | missense_variant | 0.14 |
gid | 4408351 | c.-149G>A | upstream_gene_variant | 0.4 |