Run ID: ERR4831529
Sample name:
Date: 01-04-2023 20:59:33
Number of reads: 1132552
Percentage reads mapped: 15.45
Strain: lineage2.2.1
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage2 | East-Asian | Beijing | RD105 | 1.0 |
lineage2.2 | East-Asian (Beijing) | Beijing-RD207 | RD105;RD207 | 1.0 |
lineage2.2.1 | East-Asian (Beijing) | Beijing-RD181 | RD105;RD207;RD181 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7582 | p.Asp94Ala | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rpoB | 761196 | p.Leu464Met | missense_variant | 0.17 | rifampicin |
rpoC | 764948 | p.Leu527Val | missense_variant | 0.22 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 0.97 | kanamycin, capreomycin, aminoglycosides, amikacin |
fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 1.0 | isoniazid, ethionamide |
pncA | 2288933 | p.Tyr103* | stop_gained | 0.96 | pyrazinamide |
embB | 4247429 | p.Met306Val | missense_variant | 1.0 | ethambutol |
ethR | 4327831 | p.Ala95Thr | missense_variant | 1.0 | ethionamide |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 575907 | p.Ala187Val | missense_variant | 1.0 |
mshA | 576751 | p.Lys468Asn | missense_variant | 0.13 |
ccsA | 619971 | c.81C>T | synonymous_variant | 0.14 |
ccsA | 620625 | p.Ile245Met | missense_variant | 0.93 |
rpoB | 761183 | c.1377T>C | synonymous_variant | 0.1 |
rpoB | 761189 | c.1383T>C | synonymous_variant | 0.11 |
rpoB | 761195 | c.1389G>C | synonymous_variant | 0.17 |
rpoB | 761201 | c.1395G>A | synonymous_variant | 0.16 |
rpoB | 761213 | c.1407G>C | synonymous_variant | 0.2 |
rpoB | 761218 | p.Pro471His | missense_variant | 0.17 |
rpoB | 761222 | c.1416G>C | synonymous_variant | 0.17 |
rpoB | 761228 | c.1422C>T | synonymous_variant | 0.17 |
rpoB | 761249 | c.1443A>G | synonymous_variant | 0.18 |
rpoB | 761252 | c.1446C>G | synonymous_variant | 0.18 |
rpoB | 761255 | c.1449T>G | synonymous_variant | 0.19 |
rpoB | 761261 | c.1455G>A | synonymous_variant | 0.14 |
rpoB | 761264 | c.1458C>G | synonymous_variant | 0.15 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 763486 | c.117T>C | synonymous_variant | 0.47 |
rpoC | 763498 | c.129G>A | synonymous_variant | 0.45 |
rpoC | 763501 | p.Asp44Glu | missense_variant | 0.45 |
rpoC | 763504 | c.135C>T | synonymous_variant | 0.46 |
rpoC | 763507 | c.138G>C | synonymous_variant | 0.45 |
rpoC | 763528 | c.159G>A | synonymous_variant | 0.45 |
rpoC | 763534 | c.165T>C | synonymous_variant | 0.47 |
rpoC | 763535 | p.Arg56Lys | missense_variant | 0.47 |
rpoC | 763546 | c.177A>G | synonymous_variant | 0.45 |
rpoC | 763550 | p.Tyr61His | missense_variant | 0.47 |
rpoC | 763555 | c.186C>T | synonymous_variant | 0.41 |
rpoC | 763570 | c.201G>C | synonymous_variant | 0.62 |
rpoC | 763578 | p.Phe70Tyr | missense_variant | 0.5 |
rpoC | 763582 | c.213G>A | synonymous_variant | 0.46 |
rpoC | 763586 | p.Ile73Val | missense_variant | 0.43 |
rpoC | 763589 | p.Ile74Val | missense_variant | 0.45 |
rpoC | 763597 | p.Glu76Asp | missense_variant | 0.49 |
rpoC | 763609 | c.240C>A | synonymous_variant | 0.47 |
rpoC | 763612 | c.243G>A | synonymous_variant | 0.46 |
rpoC | 763615 | c.246G>C | synonymous_variant | 0.48 |
rpoC | 763618 | c.249C>T | synonymous_variant | 0.46 |
rpoC | 763627 | c.258G>A | synonymous_variant | 0.45 |
rpoC | 763630 | c.261G>C | synonymous_variant | 0.46 |
rpoC | 763633 | c.264T>C | synonymous_variant | 0.46 |
rpoC | 763636 | c.267T>C | synonymous_variant | 0.45 |
rpoC | 763651 | c.282C>T | synonymous_variant | 0.14 |
rpoC | 764428 | c.1059G>T | synonymous_variant | 0.17 |
rpoC | 764434 | c.1065A>G | synonymous_variant | 0.18 |
rpoC | 764435 | c.1066_1068delAGGinsCGC | synonymous_variant | 0.18 |
rpoC | 764441 | p.Ile358Leu | missense_variant | 0.18 |
rpoC | 764446 | c.1077T>C | synonymous_variant | 0.21 |
rpoC | 764449 | c.1080G>T | synonymous_variant | 0.2 |
rpoC | 764452 | c.1083T>C | synonymous_variant | 0.18 |
rpoC | 764461 | p.Glu364Asp | missense_variant | 0.19 |
rpoC | 764464 | c.1095C>T | synonymous_variant | 0.19 |
rpoC | 764470 | c.1101C>A | synonymous_variant | 0.14 |
rpoC | 764471 | p.Asn368Gln | missense_variant | 0.14 |
rpoC | 764498 | p.Ser377Ala | missense_variant | 0.35 |
rpoC | 764503 | c.1134G>C | synonymous_variant | 0.38 |
rpoC | 764506 | c.1137C>T | synonymous_variant | 0.33 |
rpoC | 764509 | c.1140G>C | synonymous_variant | 0.33 |
rpoC | 764512 | c.1143G>C | synonymous_variant | 0.33 |
rpoC | 764513 | p.Phe382Ile | missense_variant | 0.33 |
rpoC | 764521 | c.1152T>C | synonymous_variant | 0.3 |
rpoC | 764536 | c.1167G>T | synonymous_variant | 0.35 |
rpoC | 764539 | c.1170C>G | synonymous_variant | 0.38 |
rpoC | 764548 | c.1179G>A | synonymous_variant | 0.35 |
rpoC | 764566 | c.1197C>G | synonymous_variant | 0.25 |
rpoC | 764572 | c.1203G>C | synonymous_variant | 0.18 |
rpoC | 764644 | c.1275G>C | synonymous_variant | 0.27 |
rpoC | 764650 | c.1281G>T | synonymous_variant | 0.28 |
rpoC | 764656 | c.1287C>T | synonymous_variant | 0.32 |
rpoC | 764662 | c.1293G>C | synonymous_variant | 0.31 |
rpoC | 764672 | p.Gln435Asn | missense_variant | 0.33 |
rpoC | 764677 | c.1308C>G | synonymous_variant | 0.32 |
rpoC | 764681 | p.Leu438Met | missense_variant | 0.3 |
rpoC | 764684 | p.His439Tyr | missense_variant | 0.31 |
rpoC | 764689 | c.1320G>A | synonymous_variant | 0.32 |
rpoC | 764698 | c.1329G>T | synonymous_variant | 0.33 |
rpoC | 764701 | c.1332C>G | synonymous_variant | 0.35 |
rpoC | 764705 | p.Leu446Glu | missense_variant | 0.35 |
rpoC | 764731 | c.1362G>T | synonymous_variant | 0.21 |
rpoC | 764737 | c.1368G>C | synonymous_variant | 0.14 |
rpoC | 764819 | p.Trp484Gly | missense_variant | 0.77 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 1.0 |
mmpS5 | 778979 | c.-74G>T | upstream_gene_variant | 1.0 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472570 | n.725G>A | non_coding_transcript_exon_variant | 0.11 |
rrs | 1472573 | n.728C>T | non_coding_transcript_exon_variant | 0.11 |
rrs | 1472598 | n.753A>C | non_coding_transcript_exon_variant | 0.14 |
rrs | 1472616 | n.771G>A | non_coding_transcript_exon_variant | 0.18 |
rrs | 1472733 | n.888G>C | non_coding_transcript_exon_variant | 0.32 |
rrs | 1472734 | n.889C>T | non_coding_transcript_exon_variant | 0.31 |
rrs | 1472741 | n.896G>A | non_coding_transcript_exon_variant | 0.31 |
rrs | 1472742 | n.897C>G | non_coding_transcript_exon_variant | 0.3 |
rrs | 1472744 | n.899A>G | non_coding_transcript_exon_variant | 0.32 |
rrs | 1472767 | n.922G>A | non_coding_transcript_exon_variant | 0.42 |
rrs | 1472779 | n.934G>A | non_coding_transcript_exon_variant | 0.39 |
rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.37 |
rrs | 1472786 | n.941C>T | non_coding_transcript_exon_variant | 0.37 |
rrs | 1472793 | n.948A>T | non_coding_transcript_exon_variant | 0.37 |
rrs | 1472803 | n.958T>A | non_coding_transcript_exon_variant | 0.32 |
rrs | 1472895 | n.1050C>T | non_coding_transcript_exon_variant | 0.36 |
rrs | 1472958 | n.1114delT | non_coding_transcript_exon_variant | 0.29 |
rrs | 1472975 | n.1130T>G | non_coding_transcript_exon_variant | 0.28 |
rrs | 1472982 | n.1137G>C | non_coding_transcript_exon_variant | 0.22 |
rrs | 1473020 | n.1175T>C | non_coding_transcript_exon_variant | 0.19 |
rrs | 1473035 | n.1190G>A | non_coding_transcript_exon_variant | 0.34 |
rrs | 1473053 | n.1208T>A | non_coding_transcript_exon_variant | 0.84 |
rrs | 1473056 | n.1211A>T | non_coding_transcript_exon_variant | 0.85 |
rrs | 1473062 | n.1217T>A | non_coding_transcript_exon_variant | 0.85 |
rrs | 1473068 | n.1223A>G | non_coding_transcript_exon_variant | 0.85 |
rrs | 1473070 | n.1225G>A | non_coding_transcript_exon_variant | 0.85 |
rrs | 1473089 | n.1244A>C | non_coding_transcript_exon_variant | 0.85 |
rrs | 1473094 | n.1249T>C | non_coding_transcript_exon_variant | 0.85 |
rrs | 1473099 | n.1254T>A | non_coding_transcript_exon_variant | 0.85 |
rrs | 1473109 | n.1264T>C | non_coding_transcript_exon_variant | 0.84 |
rrs | 1473110 | n.1265T>G | non_coding_transcript_exon_variant | 0.84 |
rrs | 1473111 | n.1266A>G | non_coding_transcript_exon_variant | 0.83 |
rrs | 1473115 | n.1270G>C | non_coding_transcript_exon_variant | 0.84 |
rrs | 1473145 | n.1300C>T | non_coding_transcript_exon_variant | 0.57 |
rrs | 1473147 | n.1302G>C | non_coding_transcript_exon_variant | 0.41 |
rrs | 1473148 | n.1303G>A | non_coding_transcript_exon_variant | 0.41 |
rrs | 1473150 | n.1305T>G | non_coding_transcript_exon_variant | 0.41 |
rrs | 1473161 | n.1316A>C | non_coding_transcript_exon_variant | 0.42 |
rrs | 1473163 | n.1318C>T | non_coding_transcript_exon_variant | 0.42 |
rrs | 1473164 | n.1319C>G | non_coding_transcript_exon_variant | 0.43 |
rrs | 1473166 | n.1321G>A | non_coding_transcript_exon_variant | 0.43 |
rrs | 1473177 | n.1332G>A | non_coding_transcript_exon_variant | 0.44 |
rrs | 1473179 | n.1334C>T | non_coding_transcript_exon_variant | 0.45 |
rrs | 1473192 | n.1347A>G | non_coding_transcript_exon_variant | 0.42 |
rrs | 1473205 | n.1360T>C | non_coding_transcript_exon_variant | 0.39 |
rrl | 1473731 | n.74T>G | non_coding_transcript_exon_variant | 0.13 |
rrl | 1473746 | n.90delC | non_coding_transcript_exon_variant | 0.15 |
rrl | 1473750 | n.93C>G | non_coding_transcript_exon_variant | 0.16 |
rrl | 1473752 | n.95G>A | non_coding_transcript_exon_variant | 0.15 |
rrl | 1473758 | n.101G>T | non_coding_transcript_exon_variant | 0.16 |
rrl | 1473765 | n.108A>G | non_coding_transcript_exon_variant | 0.16 |
rrl | 1475687 | n.2030C>T | non_coding_transcript_exon_variant | 0.14 |
rrl | 1475696 | n.2039T>C | non_coding_transcript_exon_variant | 0.16 |
rrl | 1475703 | n.2046A>G | non_coding_transcript_exon_variant | 0.13 |
rrl | 1475707 | n.2050T>A | non_coding_transcript_exon_variant | 0.14 |
rrl | 1475716 | n.2059A>G | non_coding_transcript_exon_variant | 0.12 |
rrl | 1475803 | n.2146T>C | non_coding_transcript_exon_variant | 0.15 |
rrl | 1475804 | n.2147G>C | non_coding_transcript_exon_variant | 0.15 |
rrl | 1475816 | n.2159C>G | non_coding_transcript_exon_variant | 0.17 |
rrl | 1475817 | n.2160A>G | non_coding_transcript_exon_variant | 0.18 |
rrl | 1475843 | n.2186G>A | non_coding_transcript_exon_variant | 0.19 |
rrl | 1475849 | n.2192G>A | non_coding_transcript_exon_variant | 0.19 |
rrl | 1475853 | n.2196C>T | non_coding_transcript_exon_variant | 0.19 |
rrl | 1475858 | n.2201T>C | non_coding_transcript_exon_variant | 0.17 |
rrl | 1476332 | n.2675G>C | non_coding_transcript_exon_variant | 0.14 |
rrl | 1476338 | n.2681C>T | non_coding_transcript_exon_variant | 0.14 |
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476372 | n.2715T>C | non_coding_transcript_exon_variant | 0.14 |
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.24 |
rrl | 1476383 | n.2726T>A | non_coding_transcript_exon_variant | 0.24 |
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.65 |
rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.67 |
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.67 |
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.53 |
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.51 |
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.28 |
rrl | 1476567 | n.2910C>T | non_coding_transcript_exon_variant | 0.59 |
rrl | 1476573 | n.2916A>T | non_coding_transcript_exon_variant | 0.6 |
rrl | 1476577 | n.2920T>G | non_coding_transcript_exon_variant | 0.61 |
rrl | 1476584 | n.2927C>T | non_coding_transcript_exon_variant | 0.62 |
rrl | 1476594 | n.2937C>T | non_coding_transcript_exon_variant | 0.57 |
rrl | 1476603 | n.2946G>A | non_coding_transcript_exon_variant | 0.57 |
rrl | 1476614 | n.2957A>G | non_coding_transcript_exon_variant | 0.54 |
rrl | 1476619 | n.2962C>T | non_coding_transcript_exon_variant | 0.52 |
rrl | 1476624 | n.2967T>A | non_coding_transcript_exon_variant | 0.55 |
rrl | 1476628 | n.2971T>A | non_coding_transcript_exon_variant | 0.56 |
rrl | 1476630 | n.2973A>G | non_coding_transcript_exon_variant | 0.54 |
rrl | 1476637 | n.2980C>G | non_coding_transcript_exon_variant | 0.52 |
inhA | 1674952 | p.Pro251Ala | missense_variant | 0.18 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
tlyA | 1918582 | p.Ala215Thr | missense_variant | 0.12 |
katG | 2153933 | p.Ala727Ser | missense_variant | 0.35 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
katG | 2155139 | p.Pro325Ser | missense_variant | 1.0 |
katG | 2155698 | c.414C>T | synonymous_variant | 0.12 |
katG | 2155997 | p.Trp39Arg | missense_variant | 0.12 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2169320 | p.Leu431Phe | missense_variant | 0.28 |
PPE35 | 2169866 | c.747G>C | synonymous_variant | 0.17 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
ribD | 2987307 | p.Ala157Pro | missense_variant | 0.13 |
thyX | 3067431 | p.Arg172His | missense_variant | 0.13 |
thyA | 3073806 | c.666C>G | synonymous_variant | 0.15 |
thyA | 3074394 | c.78C>A | synonymous_variant | 0.12 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.93 |
rpoA | 3878641 | c.-134C>G | upstream_gene_variant | 0.15 |
clpC1 | 4038795 | p.Ser637Ile | missense_variant | 0.14 |
clpC1 | 4038803 | p.Ile634Val | missense_variant | 0.14 |
clpC1 | 4038806 | c.1899G>A | synonymous_variant | 0.15 |
clpC1 | 4038810 | p.Gln632Pro | missense_variant | 0.24 |
clpC1 | 4038835 | p.Phe624Leu | missense_variant | 0.32 |
clpC1 | 4038839 | c.1866G>C | synonymous_variant | 0.32 |
clpC1 | 4038842 | c.1863G>C | synonymous_variant | 0.3 |
clpC1 | 4038845 | c.1860G>C | synonymous_variant | 0.3 |
clpC1 | 4038849 | p.Phe619Tyr | missense_variant | 0.3 |
clpC1 | 4038860 | c.1845G>C | synonymous_variant | 0.5 |
clpC1 | 4038875 | c.1830C>G | synonymous_variant | 0.38 |
clpC1 | 4038878 | c.1827A>G | synonymous_variant | 0.43 |
clpC1 | 4038890 | c.1815G>A | synonymous_variant | 0.32 |
clpC1 | 4038893 | c.1812C>T | synonymous_variant | 0.33 |
clpC1 | 4038896 | c.1809C>T | synonymous_variant | 0.28 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407927 | p.Glu92Asp | missense_variant | 1.0 |