Run ID: ERR4832002
Sample name:
Date: 01-04-2023 21:15:53
Number of reads: 738572
Percentage reads mapped: 90.42
Strain: lineage2.1
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage2 | East-Asian | Beijing | RD105 | 0.98 |
lineage2.1 | East-Asian (non-Beijing) | None | None | 0.93 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7570 | p.Ala90Val | missense_variant | 0.67 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.85 | rifampicin |
rpoC | 764724 | p.Phe452Ser | missense_variant | 0.76 | rifampicin |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.91 | isoniazid |
pncA | 2289204 | p.Phe13Ser | missense_variant | 1.0 | pyrazinamide |
embB | 4247431 | p.Met306Ile | missense_variant | 0.97 | ethambutol |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5806 | c.567C>A | synonymous_variant | 0.18 |
gyrB | 6342 | c.1106delG | frameshift_variant | 0.13 |
gyrB | 6651 | p.Arg471Leu | missense_variant | 0.2 |
gyrA | 7078 | c.-224A>G | upstream_gene_variant | 0.12 |
gyrA | 7081 | c.-221T>C | upstream_gene_variant | 0.12 |
gyrA | 7084 | c.-218A>G | upstream_gene_variant | 0.13 |
gyrA | 7090 | c.-212C>T | upstream_gene_variant | 0.12 |
gyrA | 7093 | c.-209T>C | upstream_gene_variant | 0.12 |
gyrA | 7100 | c.-202T>C | upstream_gene_variant | 0.13 |
gyrA | 7123 | c.-179C>G | upstream_gene_variant | 0.25 |
gyrA | 7126 | c.-176G>C | upstream_gene_variant | 0.25 |
gyrA | 7129 | c.-173T>G | upstream_gene_variant | 0.25 |
gyrA | 7132 | c.-170T>C | upstream_gene_variant | 0.25 |
gyrA | 7135 | c.-167G>A | upstream_gene_variant | 0.25 |
gyrA | 7136 | c.-166T>C | upstream_gene_variant | 0.25 |
gyrA | 7141 | c.-161T>G | upstream_gene_variant | 0.25 |
gyrA | 7144 | c.-158A>G | upstream_gene_variant | 0.25 |
gyrA | 7153 | c.-149G>C | upstream_gene_variant | 0.25 |
gyrA | 7156 | c.-146C>T | upstream_gene_variant | 0.25 |
gyrA | 7168 | c.-134C>G | upstream_gene_variant | 0.25 |
gyrA | 7178 | c.-124T>C | upstream_gene_variant | 0.25 |
gyrA | 7186 | c.-116C>G | upstream_gene_variant | 0.25 |
gyrA | 7189 | c.-113C>T | upstream_gene_variant | 0.25 |
gyrA | 7198 | c.-104C>T | upstream_gene_variant | 0.25 |
gyrB | 7210 | p.Asp657Glu | missense_variant | 0.2 |
gyrA | 7213 | c.-89G>A | upstream_gene_variant | 0.2 |
gyrA | 7216 | c.-86G>C | upstream_gene_variant | 0.2 |
gyrA | 7225 | c.-77T>C | upstream_gene_variant | 0.25 |
gyrA | 7234 | c.-68C>A | upstream_gene_variant | 0.25 |
gyrA | 7286 | c.-16T>C | upstream_gene_variant | 0.14 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7391 | c.90C>T | synonymous_variant | 0.12 |
gyrA | 7394 | c.93T>C | synonymous_variant | 0.12 |
gyrA | 7397 | c.96G>C | synonymous_variant | 0.12 |
gyrA | 7402 | p.Ser34Asn | missense_variant | 0.12 |
gyrA | 7412 | c.111C>G | synonymous_variant | 0.12 |
gyrA | 7421 | c.120G>C | synonymous_variant | 0.12 |
gyrA | 7424 | c.123G>C | synonymous_variant | 0.12 |
gyrA | 7427 | c.126G>C | synonymous_variant | 0.12 |
gyrA | 7433 | c.132G>C | synonymous_variant | 0.12 |
gyrA | 7442 | c.141G>C | synonymous_variant | 0.1 |
gyrA | 7475 | c.174A>G | synonymous_variant | 0.11 |
gyrA | 7480 | p.Phe60Tyr | missense_variant | 0.19 |
gyrA | 7484 | c.183T>C | synonymous_variant | 0.19 |
gyrA | 7499 | c.198G>C | synonymous_variant | 0.21 |
gyrA | 7516 | p.Lys72Arg | missense_variant | 0.11 |
gyrA | 7526 | c.225G>C | synonymous_variant | 0.21 |
gyrA | 7532 | c.231T>G | synonymous_variant | 0.11 |
gyrA | 7541 | c.240C>G | synonymous_variant | 0.11 |
gyrA | 7547 | c.246C>T | synonymous_variant | 0.21 |
gyrA | 7559 | c.258G>C | synonymous_variant | 0.14 |
gyrA | 7565 | c.264C>T | synonymous_variant | 0.19 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 0.95 |
gyrA | 7613 | c.312G>A | synonymous_variant | 0.15 |
gyrA | 7622 | c.321C>T | synonymous_variant | 0.17 |
gyrA | 8378 | p.Asp359Glu | missense_variant | 0.15 |
gyrA | 8897 | c.1596T>C | synonymous_variant | 0.12 |
gyrA | 8903 | c.1602T>C | synonymous_variant | 0.11 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491741 | p.Phe320Tyr | missense_variant | 0.13 |
rpoB | 760566 | p.Ser254Pro | missense_variant | 0.7 |
rpoB | 761027 | c.1221A>C | synonymous_variant | 0.14 |
rpoB | 761036 | c.1230G>C | synonymous_variant | 0.13 |
rpoB | 761037 | c.1231T>C | synonymous_variant | 0.13 |
rpoB | 761051 | c.1245G>T | synonymous_variant | 0.13 |
rpoB | 761054 | c.1248G>C | synonymous_variant | 0.13 |
rpoB | 761057 | c.1251G>C | synonymous_variant | 0.13 |
rpoB | 761060 | c.1254C>G | synonymous_variant | 0.13 |
rpoB | 761063 | c.1257C>G | synonymous_variant | 0.13 |
rpoB | 761084 | c.1278C>A | synonymous_variant | 0.13 |
rpoC | 762920 | c.-450C>T | upstream_gene_variant | 0.13 |
rpoC | 762929 | c.-441G>C | upstream_gene_variant | 0.13 |
rpoC | 762959 | c.-411G>C | upstream_gene_variant | 0.12 |
rpoC | 762995 | c.-375G>T | upstream_gene_variant | 0.14 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 763070 | c.-300T>C | upstream_gene_variant | 0.1 |
rpoC | 764752 | c.1383G>C | synonymous_variant | 0.13 |
rpoC | 764758 | c.1389C>G | synonymous_variant | 0.17 |
rpoC | 764764 | c.1395T>C | synonymous_variant | 0.2 |
rpoC | 764791 | c.1422C>G | synonymous_variant | 0.18 |
rpoC | 764803 | c.1434C>T | synonymous_variant | 0.2 |
rpoC | 764809 | c.1440C>T | synonymous_variant | 0.18 |
rpoC | 764810 | p.Pro481Ala | missense_variant | 0.18 |
rpoC | 764815 | c.1446A>G | synonymous_variant | 0.17 |
rpoC | 764824 | c.1455T>C | synonymous_variant | 0.18 |
rpoC | 764827 | c.1458G>C | synonymous_variant | 0.31 |
rpoC | 764858 | c.1489T>C | synonymous_variant | 0.17 |
rpoC | 764869 | c.1500C>T | synonymous_variant | 0.17 |
rpoC | 766448 | p.Gly1027Cys | missense_variant | 0.14 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.95 |
mmpS5 | 778490 | p.Val139Ala | missense_variant | 0.11 |
mmpS5 | 778748 | p.Pro53His | missense_variant | 0.14 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
fbiC | 1304443 | p.Ala505Thr | missense_variant | 1.0 |
embR | 1416446 | p.Tyr301Ser | missense_variant | 0.11 |
embR | 1417264 | c.84G>A | synonymous_variant | 0.22 |
atpE | 1461033 | c.-11delA | upstream_gene_variant | 0.17 |
atpE | 1461114 | p.Ala24Ser | missense_variant | 0.29 |
atpE | 1461197 | c.153A>C | synonymous_variant | 0.25 |
atpE | 1461219 | c.175T>C | synonymous_variant | 0.12 |
atpE | 1461224 | c.180T>G | synonymous_variant | 0.12 |
atpE | 1461227 | c.183G>A | synonymous_variant | 0.12 |
atpE | 1461230 | c.186G>C | synonymous_variant | 0.11 |
atpE | 1461233 | c.189A>G | synonymous_variant | 0.11 |
atpE | 1461251 | c.207G>C | synonymous_variant | 0.11 |
atpE | 1461254 | c.210T>C | synonymous_variant | 0.11 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1471925 | n.80T>C | non_coding_transcript_exon_variant | 0.33 |
rrs | 1472116 | n.271C>A | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472380 | n.535G>C | non_coding_transcript_exon_variant | 0.29 |
rrs | 1472612 | n.767G>T | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472633 | n.788C>A | non_coding_transcript_exon_variant | 0.25 |
rrs | 1472790 | n.945T>C | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472846 | n.1001C>A | non_coding_transcript_exon_variant | 0.2 |
rrs | 1472847 | n.1002G>C | non_coding_transcript_exon_variant | 0.2 |
rrs | 1472849 | n.1004C>G | non_coding_transcript_exon_variant | 0.2 |
rrs | 1472850 | n.1005T>C | non_coding_transcript_exon_variant | 0.2 |
rrs | 1472857 | n.1012A>G | non_coding_transcript_exon_variant | 0.18 |
rrs | 1472858 | n.1013G>T | non_coding_transcript_exon_variant | 0.18 |
rrs | 1472860 | n.1015C>G | non_coding_transcript_exon_variant | 0.18 |
rrs | 1472861 | n.1016G>T | non_coding_transcript_exon_variant | 0.18 |
rrl | 1473594 | n.-64A>G | upstream_gene_variant | 0.15 |
rrl | 1474249 | n.592G>T | non_coding_transcript_exon_variant | 0.67 |
rrl | 1474266 | n.609T>C | non_coding_transcript_exon_variant | 0.5 |
rrl | 1474269 | n.612C>T | non_coding_transcript_exon_variant | 0.5 |
rrl | 1474626 | n.969T>C | non_coding_transcript_exon_variant | 0.5 |
rrl | 1474632 | n.975G>T | non_coding_transcript_exon_variant | 0.4 |
rrl | 1474636 | n.979A>T | non_coding_transcript_exon_variant | 0.4 |
rrl | 1474637 | n.980C>T | non_coding_transcript_exon_variant | 0.4 |
rrl | 1474638 | n.981C>G | non_coding_transcript_exon_variant | 0.4 |
rrl | 1474639 | n.982G>T | non_coding_transcript_exon_variant | 0.4 |
rrl | 1474640 | n.983C>T | non_coding_transcript_exon_variant | 0.4 |
rrl | 1475649 | n.1992A>G | non_coding_transcript_exon_variant | 1.0 |
rrl | 1475659 | n.2002G>A | non_coding_transcript_exon_variant | 1.0 |
rrl | 1475760 | n.2105_2106delGC | non_coding_transcript_exon_variant | 0.29 |
rrl | 1475764 | n.2107A>T | non_coding_transcript_exon_variant | 0.29 |
rrl | 1475765 | n.2108A>T | non_coding_transcript_exon_variant | 0.29 |
rrl | 1475975 | n.2318C>T | non_coding_transcript_exon_variant | 0.4 |
rrl | 1475977 | n.2320A>G | non_coding_transcript_exon_variant | 0.4 |
rrl | 1475988 | n.2331A>G | non_coding_transcript_exon_variant | 0.8 |
rrl | 1475989 | n.2332T>C | non_coding_transcript_exon_variant | 0.4 |
rrl | 1475991 | n.2334T>C | non_coding_transcript_exon_variant | 0.4 |
rrl | 1475993 | n.2336C>T | non_coding_transcript_exon_variant | 0.4 |
rrl | 1475995 | n.2338G>A | non_coding_transcript_exon_variant | 0.4 |
rrl | 1475997 | n.2340A>T | non_coding_transcript_exon_variant | 0.4 |
rrl | 1476030 | n.2373A>G | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476032 | n.2375C>A | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476033 | n.2376T>G | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476034 | n.2377C>G | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476035 | n.2378G>C | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476044 | n.2387T>G | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476045 | n.2388G>T | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476046 | n.2389G>T | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476047 | n.2390G>T | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476049 | n.2392C>T | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476056 | n.2399G>A | non_coding_transcript_exon_variant | 0.5 |
rrl | 1476058 | n.2401T>C | non_coding_transcript_exon_variant | 0.5 |
rrl | 1476085 | n.2428G>A | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476086 | n.2429G>A | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476088 | n.2431A>C | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476099 | n.2442A>G | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476103 | n.2446C>G | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476105 | n.2448G>A | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476106 | n.2449A>T | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476110 | n.2453G>C | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476114 | n.2457T>C | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476115 | n.2458T>C | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476131 | n.2474C>T | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476160 | n.2503T>C | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476164 | n.2507A>G | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476165 | n.2508T>A | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476194 | n.2537A>G | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476201 | n.2544C>T | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476204 | n.2547C>T | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476214 | n.2557G>T | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476215 | n.2558C>T | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476224 | n.2567A>G | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476245 | n.2588C>T | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476252 | n.2595T>G | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476256 | n.2599A>G | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476260 | n.2603A>G | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476267 | n.2610G>T | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476276 | n.2619C>A | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476281 | n.2624T>C | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476297 | n.2640C>G | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476298 | n.2641C>G | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476300 | n.2643G>T | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476301 | n.2644A>T | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476309 | n.2652G>C | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476584 | n.2927C>T | non_coding_transcript_exon_variant | 0.5 |
rrl | 1476594 | n.2937C>T | non_coding_transcript_exon_variant | 0.5 |
rrl | 1476597 | n.2940G>A | non_coding_transcript_exon_variant | 0.5 |
inhA | 1674300 | c.99C>A | synonymous_variant | 1.0 |
inhA | 1674427 | p.Gly76Cys | missense_variant | 0.14 |
inhA | 1674552 | c.353delA | frameshift_variant | 0.15 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.87 |
rpsA | 1834303 | c.762T>G | synonymous_variant | 0.11 |
rpsA | 1834306 | c.765T>C | synonymous_variant | 0.11 |
rpsA | 1834348 | c.807T>C | synonymous_variant | 0.11 |
rpsA | 1834361 | c.820T>C | synonymous_variant | 0.11 |
rpsA | 1834366 | c.825A>G | synonymous_variant | 0.11 |
rpsA | 1834396 | c.855G>C | synonymous_variant | 0.11 |
rpsA | 1834411 | c.870T>C | synonymous_variant | 0.1 |
rpsA | 1834666 | c.1125G>C | synonymous_variant | 0.11 |
rpsA | 1834690 | c.1149T>C | synonymous_variant | 0.12 |
rpsA | 1834700 | p.Gln387Ala | missense_variant | 0.14 |
rpsA | 1834705 | c.1164C>G | synonymous_variant | 0.14 |
rpsA | 1834720 | c.1179C>G | synonymous_variant | 0.13 |
rpsA | 1834732 | c.1191T>C | synonymous_variant | 0.13 |
rpsA | 1834738 | c.1197A>G | synonymous_variant | 0.13 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154212 | p.Leu634Ile | missense_variant | 0.16 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
katG | 2156428 | c.-317C>A | upstream_gene_variant | 1.0 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2168399 | p.Glu738Asp | missense_variant | 0.13 |
PPE35 | 2168561 | c.2052T>C | synonymous_variant | 0.22 |
PPE35 | 2168565 | p.Pro683His | missense_variant | 0.22 |
PPE35 | 2168741 | c.1872C>A | synonymous_variant | 0.13 |
PPE35 | 2169128 | p.Asn495Lys | missense_variant | 0.12 |
PPE35 | 2169256 | p.Phe453Ile | missense_variant | 0.17 |
PPE35 | 2169289 | p.Phe442Leu | missense_variant | 0.13 |
PPE35 | 2169382 | p.Trp411Arg | missense_variant | 0.15 |
PPE35 | 2169732 | p.Asn294Thr | missense_variant | 0.96 |
PPE35 | 2170048 | p.Leu189Val | missense_variant | 0.12 |
PPE35 | 2170053 | p.Thr187Ser | missense_variant | 0.12 |
Rv1979c | 2222406 | c.759G>A | synonymous_variant | 0.17 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289211 | p.Asn11Asp | missense_variant | 0.11 |
Rv2752c | 3064819 | p.Gly458Val | missense_variant | 0.14 |
Rv2752c | 3065518 | p.Leu225Pro | missense_variant | 1.0 |
thyX | 3067400 | c.546C>T | synonymous_variant | 1.0 |
thyA | 3074130 | c.342G>C | synonymous_variant | 0.11 |
ald | 3086700 | c.-120G>T | upstream_gene_variant | 0.14 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
Rv3083 | 3448991 | c.489delC | frameshift_variant | 0.18 |
Rv3083 | 3449001 | c.498G>A | synonymous_variant | 0.17 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fbiA | 3640357 | c.-186G>A | upstream_gene_variant | 0.12 |
fbiB | 3641262 | c.-273C>A | upstream_gene_variant | 0.15 |
rpoA | 3878143 | p.Gly122Val | missense_variant | 0.14 |
clpC1 | 4038755 | c.1950G>C | synonymous_variant | 0.11 |
clpC1 | 4038845 | c.1860G>C | synonymous_variant | 0.1 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embB | 4246088 | c.-426A>G | upstream_gene_variant | 0.93 |
embB | 4249314 | c.2802delC | frameshift_variant | 0.15 |
embB | 4249354 | c.2841G>T | synonymous_variant | 0.18 |
aftB | 4267087 | p.Leu584Met | missense_variant | 0.18 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 |
aftB | 4267766 | c.1071G>T | synonymous_variant | 0.15 |
aftB | 4267827 | p.Arg337Leu | missense_variant | 0.13 |
aftB | 4268456 | c.381G>A | synonymous_variant | 0.25 |
aftB | 4268830 | p.Arg3Trp | missense_variant | 0.13 |
aftB | 4268858 | c.-22G>T | upstream_gene_variant | 0.12 |
ethA | 4326309 | p.Ala389Ser | missense_variant | 0.22 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407926 | c.276dupA | frameshift_variant | 1.0 |