Run ID: ERR4819012
Sample name:
Date: 01-04-2023 15:52:30
Number of reads: 480449
Percentage reads mapped: 67.3
Strain: lineage1.1.2
Drug-resistance: Other
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage1 | Indo-Oceanic | EAI | RD239 | 1.0 |
lineage1.1 | Indo-Oceanic | EAI3;EAI4;EAI5;EAI6 | RD239 | 0.99 |
lineage1.1.2 | Indo-Oceanic | EAI3;EAI5 | RD239 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5534 | p.Val99Met | missense_variant | 0.17 |
gyrB | 6112 | p.Met291Ile | missense_variant | 1.0 |
gyrB | 6124 | c.885C>T | synonymous_variant | 1.0 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 8150 | c.849C>T | synonymous_variant | 1.0 |
gyrA | 8452 | p.Ala384Val | missense_variant | 1.0 |
gyrA | 8622 | p.Arg441Trp | missense_variant | 0.15 |
gyrA | 9143 | c.1842T>C | synonymous_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
rpoB | 760490 | c.684C>T | synonymous_variant | 1.0 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 763884 | p.Ala172Val | missense_variant | 1.0 |
rpoC | 763886 | c.517C>A | synonymous_variant | 1.0 |
rpoC | 765171 | p.Pro601Leu | missense_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 776395 | p.Phe696Leu | missense_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rplC | 800848 | p.Thr14Ser | missense_variant | 0.22 |
fbiC | 1303051 | p.Val41Met | missense_variant | 1.0 |
embR | 1417019 | p.Cys110Tyr | missense_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1471934 | n.89A>G | non_coding_transcript_exon_variant | 0.25 |
rrs | 1472122 | n.277G>T | non_coding_transcript_exon_variant | 0.33 |
rrs | 1472123 | n.278A>T | non_coding_transcript_exon_variant | 0.33 |
rrs | 1472124 | n.279C>T | non_coding_transcript_exon_variant | 0.33 |
rrs | 1472150 | n.305T>A | non_coding_transcript_exon_variant | 0.71 |
rrs | 1472155 | n.310C>T | non_coding_transcript_exon_variant | 0.56 |
rrs | 1472160 | n.315C>T | non_coding_transcript_exon_variant | 0.56 |
rrs | 1472172 | n.327T>C | non_coding_transcript_exon_variant | 0.22 |
rrs | 1472225 | n.380C>A | non_coding_transcript_exon_variant | 1.0 |
rrs | 1472507 | n.662C>G | non_coding_transcript_exon_variant | 0.92 |
rrs | 1472517 | n.672T>A | non_coding_transcript_exon_variant | 0.93 |
rrs | 1472518 | n.673G>T | non_coding_transcript_exon_variant | 0.93 |
rrs | 1472530 | n.685G>A | non_coding_transcript_exon_variant | 1.0 |
rrs | 1472537 | n.692C>T | non_coding_transcript_exon_variant | 1.0 |
rrs | 1472544 | n.699C>A | non_coding_transcript_exon_variant | 1.0 |
rrs | 1472545 | n.700A>T | non_coding_transcript_exon_variant | 1.0 |
rrs | 1472566 | n.721G>A | non_coding_transcript_exon_variant | 1.0 |
rrs | 1472571 | n.726G>C | non_coding_transcript_exon_variant | 1.0 |
rrs | 1472579 | n.734G>C | non_coding_transcript_exon_variant | 1.0 |
rrs | 1472579 | n.734G>T | non_coding_transcript_exon_variant | 1.0 |
rrs | 1472580 | n.735C>T | non_coding_transcript_exon_variant | 0.81 |
rrs | 1472581 | n.736A>T | non_coding_transcript_exon_variant | 1.0 |
rrs | 1472598 | n.753A>C | non_coding_transcript_exon_variant | 1.0 |
rrs | 1472599 | n.754G>T | non_coding_transcript_exon_variant | 1.0 |
rrs | 1472616 | n.771G>A | non_coding_transcript_exon_variant | 0.81 |
rrs | 1472655 | n.810G>A | non_coding_transcript_exon_variant | 0.71 |
rrs | 1472658 | n.813G>A | non_coding_transcript_exon_variant | 0.57 |
rrs | 1472660 | n.815T>C | non_coding_transcript_exon_variant | 0.29 |
rrs | 1472661 | n.816A>G | non_coding_transcript_exon_variant | 0.6 |
rrs | 1472670 | n.825G>T | non_coding_transcript_exon_variant | 0.4 |
rrs | 1472697 | n.852T>C | non_coding_transcript_exon_variant | 0.83 |
rrs | 1472713 | n.868T>C | non_coding_transcript_exon_variant | 0.97 |
rrs | 1472716 | n.871C>T | non_coding_transcript_exon_variant | 0.95 |
rrs | 1472742 | n.897C>T | non_coding_transcript_exon_variant | 0.96 |
rrs | 1472744 | n.899A>G | non_coding_transcript_exon_variant | 0.96 |
rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.97 |
rrs | 1472793 | n.948A>T | non_coding_transcript_exon_variant | 0.97 |
rrs | 1472803 | n.958T>A | non_coding_transcript_exon_variant | 0.97 |
rrs | 1472824 | n.979T>A | non_coding_transcript_exon_variant | 0.96 |
rrs | 1472827 | n.982G>T | non_coding_transcript_exon_variant | 0.91 |
rrs | 1472828 | n.983T>C | non_coding_transcript_exon_variant | 0.91 |
rrs | 1472952 | n.1107T>C | non_coding_transcript_exon_variant | 0.6 |
rrs | 1472955 | n.1110C>T | non_coding_transcript_exon_variant | 0.6 |
rrs | 1472956 | n.1111T>C | non_coding_transcript_exon_variant | 0.8 |
rrs | 1472957 | n.1112C>T | non_coding_transcript_exon_variant | 0.8 |
rrs | 1472973 | n.1128A>G | non_coding_transcript_exon_variant | 0.67 |
rrs | 1472973 | n.1128A>T | non_coding_transcript_exon_variant | 0.8 |
rrs | 1472987 | n.1142G>A | non_coding_transcript_exon_variant | 0.5 |
rrs | 1472989 | n.1144G>A | non_coding_transcript_exon_variant | 0.5 |
rrs | 1472990 | n.1145A>G | non_coding_transcript_exon_variant | 0.83 |
rrs | 1472992 | n.1147A>G | non_coding_transcript_exon_variant | 0.33 |
rrs | 1473005 | n.1160C>T | non_coding_transcript_exon_variant | 0.4 |
rrs | 1473008 | n.1164delT | non_coding_transcript_exon_variant | 0.25 |
rrs | 1473035 | n.1190G>A | non_coding_transcript_exon_variant | 1.0 |
rrs | 1473055 | n.1210C>T | non_coding_transcript_exon_variant | 0.75 |
rrs | 1473056 | n.1211A>T | non_coding_transcript_exon_variant | 1.0 |
rrs | 1473066 | n.1221A>G | non_coding_transcript_exon_variant | 1.0 |
rrs | 1473080 | n.1235C>T | non_coding_transcript_exon_variant | 0.8 |
rrs | 1473081 | n.1236C>T | non_coding_transcript_exon_variant | 0.8 |
rrs | 1473088 | n.1243A>G | non_coding_transcript_exon_variant | 1.0 |
rrs | 1473093 | n.1248C>T | non_coding_transcript_exon_variant | 1.0 |
rrs | 1473100 | n.1255G>A | non_coding_transcript_exon_variant | 1.0 |
rrs | 1473104 | n.1259C>T | non_coding_transcript_exon_variant | 1.0 |
rrs | 1473110 | n.1265T>G | non_coding_transcript_exon_variant | 1.0 |
rrs | 1473111 | n.1266A>G | non_coding_transcript_exon_variant | 1.0 |
rrs | 1473121 | n.1276T>C | non_coding_transcript_exon_variant | 0.83 |
rrs | 1473123 | n.1278A>T | non_coding_transcript_exon_variant | 0.6 |
rrs | 1473130 | n.1285G>A | non_coding_transcript_exon_variant | 0.6 |
rrs | 1473145 | n.1300C>T | non_coding_transcript_exon_variant | 1.0 |
rrs | 1473147 | n.1302G>T | non_coding_transcript_exon_variant | 0.33 |
rrs | 1473148 | n.1303G>A | non_coding_transcript_exon_variant | 0.33 |
rrs | 1473150 | n.1305T>G | non_coding_transcript_exon_variant | 0.33 |
rrs | 1473161 | n.1316A>C | non_coding_transcript_exon_variant | 0.5 |
rrs | 1473163 | n.1318C>T | non_coding_transcript_exon_variant | 0.5 |
rrs | 1473164 | n.1319C>A | non_coding_transcript_exon_variant | 0.5 |
rrs | 1473166 | n.1321G>A | non_coding_transcript_exon_variant | 1.0 |
rrs | 1473172 | n.1327T>G | non_coding_transcript_exon_variant | 0.21 |
rrs | 1473173 | n.1328C>T | non_coding_transcript_exon_variant | 0.15 |
rrs | 1473177 | n.1332G>A | non_coding_transcript_exon_variant | 0.62 |
rrs | 1473192 | n.1347A>G | non_coding_transcript_exon_variant | 0.65 |
rrs | 1473199 | n.1356delA | non_coding_transcript_exon_variant | 0.65 |
rrs | 1473205 | n.1360T>C | non_coding_transcript_exon_variant | 0.65 |
rrs | 1473221 | n.1376C>T | non_coding_transcript_exon_variant | 0.14 |
rrs | 1473252 | n.1407T>C | non_coding_transcript_exon_variant | 1.0 |
rrs | 1473259 | n.1414C>T | non_coding_transcript_exon_variant | 1.0 |
rrl | 1474249 | n.592G>T | non_coding_transcript_exon_variant | 1.0 |
rrl | 1474252 | n.595T>A | non_coding_transcript_exon_variant | 1.0 |
rrl | 1474275 | n.618T>C | non_coding_transcript_exon_variant | 1.0 |
rrl | 1475753 | n.2096C>T | non_coding_transcript_exon_variant | 1.0 |
rrl | 1475757 | n.2100_2101insG | non_coding_transcript_exon_variant | 1.0 |
rrl | 1475916 | n.2259C>G | non_coding_transcript_exon_variant | 0.5 |
rrl | 1475975 | n.2318C>T | non_coding_transcript_exon_variant | 0.67 |
rrl | 1475977 | n.2320A>G | non_coding_transcript_exon_variant | 0.67 |
rrl | 1476131 | n.2474C>T | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476153 | n.2496T>C | non_coding_transcript_exon_variant | 0.5 |
rrl | 1476160 | n.2503T>C | non_coding_transcript_exon_variant | 0.5 |
rrl | 1476165 | n.2508T>G | non_coding_transcript_exon_variant | 0.5 |
rrl | 1476194 | n.2537A>G | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476200 | n.2543A>T | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476201 | n.2544C>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 | 0.22 |
rrl | 1476225 | n.2568T>G | non_coding_transcript_exon_variant | 0.78 |
rrl | 1476227 | n.2570C>T | non_coding_transcript_exon_variant | 0.88 |
rrl | 1476229 | n.2572C>T | non_coding_transcript_exon_variant | 0.88 |
rrl | 1476250 | n.2593C>G | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476251 | n.2594T>C | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476257 | n.2600G>C | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476260 | n.2603A>G | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476280 | n.2623A>C | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476353 | n.2696G>T | non_coding_transcript_exon_variant | 0.75 |
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.75 |
rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.8 |
rrl | 1476372 | n.2715T>C | non_coding_transcript_exon_variant | 0.8 |
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.8 |
rrl | 1476383 | n.2726T>A | non_coding_transcript_exon_variant | 0.8 |
rrl | 1476425 | n.2768G>T | non_coding_transcript_exon_variant | 0.88 |
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 1.0 |
fabG1 | 1673560 | p.Lys41Leu | missense_variant | 0.14 |
rpsA | 1834027 | p.Gln162His | missense_variant | 0.22 |
rpsA | 1834189 | c.648G>C | synonymous_variant | 0.29 |
rpsA | 1834195 | c.654G>C | synonymous_variant | 0.38 |
rpsA | 1834210 | c.669C>T | synonymous_variant | 0.25 |
rpsA | 1834213 | c.672G>A | synonymous_variant | 0.38 |
rpsA | 1834219 | c.678C>G | synonymous_variant | 0.29 |
rpsA | 1834222 | c.681T>C | synonymous_variant | 0.33 |
rpsA | 1834225 | c.684C>G | synonymous_variant | 0.33 |
rpsA | 1834231 | c.690T>C | synonymous_variant | 0.33 |
rpsA | 1834246 | c.705G>T | synonymous_variant | 0.43 |
rpsA | 1834249 | c.708T>C | synonymous_variant | 0.43 |
rpsA | 1834252 | c.711C>T | synonymous_variant | 0.29 |
rpsA | 1834261 | c.720A>G | synonymous_variant | 0.33 |
rpsA | 1834264 | c.723G>C | synonymous_variant | 0.33 |
rpsA | 1834285 | c.744G>C | synonymous_variant | 0.25 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
PPE35 | 2167862 | c.2751G>A | synonymous_variant | 1.0 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2167983 | p.Gly877Asp | missense_variant | 1.0 |
PPE35 | 2169961 | p.Gly218Ser | missense_variant | 0.29 |
PPE35 | 2170696 | c.-84A>G | upstream_gene_variant | 0.13 |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 1.0 |
Rv1979c | 2223136 | p.Ala10Val | missense_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2518132 | c.18C>T | synonymous_variant | 1.0 |
eis | 2714956 | p.Tyr126Cys | missense_variant | 0.29 |
eis | 2715322 | p.Thr4Ser | missense_variant | 0.15 |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 1.0 |
pepQ | 2859504 | c.915G>A | synonymous_variant | 0.14 |
Rv2752c | 3064632 | c.1560C>T | synonymous_variant | 1.0 |
Rv2752c | 3066256 | c.-65C>T | upstream_gene_variant | 0.11 |
thyA | 3074206 | p.Glu89Val | missense_variant | 0.22 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
Rv3083 | 3448714 | p.Asp71His | missense_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474597 | c.591C>A | synonymous_variant | 1.0 |
fprA | 3475159 | p.Asn385Asp | missense_variant | 1.0 |
whiB7 | 3568675 | p.Ser2Leu | missense_variant | 0.12 |
alr | 3840302 | c.1119G>A | synonymous_variant | 0.13 |
alr | 3841602 | c.-182C>A | upstream_gene_variant | 0.4 |
rpoA | 3877929 | c.579C>T | synonymous_variant | 0.15 |
rpoA | 3878163 | c.344delG | frameshift_variant | 0.29 |
clpC1 | 4040517 | p.Val63Ala | missense_variant | 1.0 |
embC | 4240671 | p.Thr270Ile | missense_variant | 1.0 |
embC | 4241042 | p.Asn394Asp | missense_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243848 | p.Val206Met | missense_variant | 1.0 |
embA | 4244167 | p.Ala312Val | missense_variant | 1.0 |
embA | 4244408 | c.1176G>A | synonymous_variant | 1.0 |
embA | 4245969 | p.Pro913Ser | missense_variant | 1.0 |
embA | 4246464 | p.Val1078Met | missense_variant | 0.12 |
embB | 4247022 | p.Ala170Glu | missense_variant | 0.18 |
embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 1.0 |
aftB | 4269606 | c.-770T>C | upstream_gene_variant | 1.0 |
ubiA | 4269690 | p.Tyr48* | stop_gained | 0.11 |
ethA | 4326432 | p.Leu348Phe | missense_variant | 1.0 |
ethA | 4326685 | p.Met263Ile | missense_variant | 0.2 |
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 | 4407873 | c.330G>T | synonymous_variant | 1.0 |