Run ID: ERR4596906
Sample name:
Date: 01-04-2023 06:28:41
Number of reads: 766258
Percentage reads mapped: 16.78
Strain: lineage1.1.2
Drug-resistance: Sensitive
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 | 1.0 |
lineage1.1.2 | Indo-Oceanic | EAI3;EAI5 | RD239 | 0.99 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
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 | 8452 | p.Ala384Val | missense_variant | 1.0 |
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 |
mshA | 576108 | p.Ala254Gly | missense_variant | 0.22 |
ccsA | 620065 | p.Ala59Ser | missense_variant | 0.14 |
ccsA | 620634 | c.744C>A | synonymous_variant | 0.15 |
rpoB | 762522 | p.Pro906Thr | missense_variant | 0.14 |
rpoB | 762694 | p.Asn963Ser | missense_variant | 0.11 |
rpoB | 762699 | p.Ile965Val | missense_variant | 0.12 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 763710 | c.345delG | frameshift_variant | 0.13 |
rpoC | 763884 | p.Ala172Val | missense_variant | 1.0 |
rpoC | 763886 | c.517C>A | synonymous_variant | 1.0 |
rpoC | 764348 | p.Met327Leu | missense_variant | 0.14 |
rpoC | 764605 | c.1236G>T | synonymous_variant | 0.13 |
rpoC | 764611 | c.1242G>T | synonymous_variant | 0.12 |
rpoC | 764623 | c.1254C>G | synonymous_variant | 0.13 |
rpoC | 764632 | c.1263T>C | synonymous_variant | 0.27 |
rpoC | 764635 | c.1266C>G | synonymous_variant | 0.22 |
rpoC | 764650 | c.1281G>T | synonymous_variant | 0.24 |
rpoC | 764665 | c.1296C>G | synonymous_variant | 0.22 |
rpoC | 764672 | p.Gln435Thr | missense_variant | 0.22 |
rpoC | 764677 | c.1308C>G | synonymous_variant | 0.21 |
rpoC | 764686 | c.1317C>T | synonymous_variant | 0.17 |
rpoC | 764695 | c.1326T>C | synonymous_variant | 0.2 |
rpoC | 764716 | c.1347G>C | synonymous_variant | 0.16 |
rpoC | 765171 | p.Pro601Leu | missense_variant | 1.0 |
rpoC | 766590 | p.Glu1074Ala | missense_variant | 0.11 |
rpoC | 767317 | c.3948C>T | synonymous_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 777589 | p.Ala298Thr | missense_variant | 0.17 |
mmpL5 | 777691 | p.Asn264Tyr | missense_variant | 0.18 |
mmpS5 | 778875 | p.Pro11Ser | missense_variant | 0.12 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rplC | 800851 | c.44delA | frameshift_variant | 0.12 |
fbiC | 1304142 | c.1212G>A | synonymous_variant | 0.15 |
embR | 1417019 | p.Cys110Tyr | missense_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472172 | n.327T>C | non_coding_transcript_exon_variant | 0.23 |
rrs | 1472210 | n.365A>T | non_coding_transcript_exon_variant | 0.29 |
rrs | 1472214 | n.369C>G | non_coding_transcript_exon_variant | 0.28 |
rrs | 1472225 | n.380C>A | non_coding_transcript_exon_variant | 0.29 |
rrs | 1472235 | n.390G>C | non_coding_transcript_exon_variant | 0.23 |
rrs | 1472240 | n.395G>A | non_coding_transcript_exon_variant | 0.21 |
rrs | 1472242 | n.397C>T | non_coding_transcript_exon_variant | 0.22 |
rrs | 1472251 | n.406G>T | non_coding_transcript_exon_variant | 0.16 |
rrs | 1472256 | n.411T>A | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472259 | n.414C>A | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472767 | n.922G>A | non_coding_transcript_exon_variant | 0.16 |
rrs | 1472786 | n.941C>G | non_coding_transcript_exon_variant | 0.13 |
rrs | 1472887 | n.1042G>C | non_coding_transcript_exon_variant | 0.24 |
rrs | 1472958 | n.1113A>T | non_coding_transcript_exon_variant | 0.57 |
rrs | 1472959 | n.1114T>A | non_coding_transcript_exon_variant | 0.56 |
rrs | 1472972 | n.1127T>A | non_coding_transcript_exon_variant | 0.55 |
rrs | 1472974 | n.1130_1133delTGGT | non_coding_transcript_exon_variant | 0.58 |
rrs | 1472982 | n.1137G>C | non_coding_transcript_exon_variant | 0.56 |
rrs | 1472987 | n.1142G>T | non_coding_transcript_exon_variant | 0.58 |
rrs | 1472988 | n.1143T>A | non_coding_transcript_exon_variant | 0.58 |
rrs | 1473002 | n.1157G>T | non_coding_transcript_exon_variant | 0.59 |
rrs | 1473004 | n.1159T>A | non_coding_transcript_exon_variant | 0.6 |
rrs | 1473008 | n.1163C>A | non_coding_transcript_exon_variant | 0.6 |
rrs | 1473009 | n.1164T>C | non_coding_transcript_exon_variant | 0.6 |
rrs | 1473038 | n.1193A>C | non_coding_transcript_exon_variant | 0.59 |
rrs | 1473044 | n.1199C>G | non_coding_transcript_exon_variant | 0.56 |
rrs | 1473053 | n.1208T>G | non_coding_transcript_exon_variant | 0.38 |
rrs | 1473054 | n.1209C>G | non_coding_transcript_exon_variant | 0.36 |
rrs | 1473055 | n.1210C>T | non_coding_transcript_exon_variant | 0.36 |
rrs | 1473068 | n.1223A>G | non_coding_transcript_exon_variant | 0.24 |
rrs | 1473070 | n.1225G>C | non_coding_transcript_exon_variant | 0.19 |
rrs | 1473071 | n.1226C>A | non_coding_transcript_exon_variant | 0.18 |
rrs | 1473192 | n.1347A>G | non_coding_transcript_exon_variant | 0.13 |
rrs | 1473205 | n.1360T>C | non_coding_transcript_exon_variant | 0.14 |
rrs | 1473226 | n.1381C>T | non_coding_transcript_exon_variant | 0.14 |
rrl | 1475816 | n.2159C>G | non_coding_transcript_exon_variant | 0.12 |
rrl | 1475817 | n.2160A>G | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476336 | n.2679C>T | non_coding_transcript_exon_variant | 0.45 |
rrl | 1476338 | n.2681C>T | non_coding_transcript_exon_variant | 0.47 |
rrl | 1476356 | n.2699C>A | non_coding_transcript_exon_variant | 0.61 |
rrl | 1476357 | n.2700T>C | non_coding_transcript_exon_variant | 0.61 |
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.61 |
rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.63 |
rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.68 |
rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.74 |
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.74 |
rrl | 1476383 | n.2726T>G | non_coding_transcript_exon_variant | 0.74 |
rrl | 1476384 | n.2727G>T | non_coding_transcript_exon_variant | 0.72 |
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.74 |
rrl | 1476411 | n.2754G>T | non_coding_transcript_exon_variant | 0.73 |
rrl | 1476425 | n.2768G>T | non_coding_transcript_exon_variant | 0.73 |
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.74 |
rrl | 1476442 | n.2785T>A | non_coding_transcript_exon_variant | 0.72 |
rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.73 |
rrl | 1476455 | n.2798C>A | non_coding_transcript_exon_variant | 0.69 |
rrl | 1476456 | n.2799A>T | non_coding_transcript_exon_variant | 0.7 |
rrl | 1476463 | n.2806C>A | non_coding_transcript_exon_variant | 0.68 |
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.64 |
rrl | 1476470 | n.2813C>T | non_coding_transcript_exon_variant | 0.64 |
rrl | 1476483 | n.2826G>A | non_coding_transcript_exon_variant | 0.53 |
rrl | 1476501 | n.2844C>T | non_coding_transcript_exon_variant | 0.31 |
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.29 |
fabG1 | 1673283 | c.-157A>C | upstream_gene_variant | 1.0 |
inhA | 1674503 | p.Thr101Ile | missense_variant | 0.12 |
rpsA | 1833818 | p.Lys93Glu | missense_variant | 0.1 |
rpsA | 1834316 | p.Thr259Ala | missense_variant | 0.14 |
tlyA | 1917777 | c.-163A>G | upstream_gene_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
tlyA | 1918106 | p.Thr56Ile | missense_variant | 1.0 |
ndh | 2101702 | c.1341G>A | synonymous_variant | 0.13 |
ndh | 2102785 | p.Leu86Phe | missense_variant | 0.13 |
katG | 2154102 | c.2010C>A | synonymous_variant | 0.13 |
katG | 2154467 | p.Cys549Gly | missense_variant | 0.12 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
katG | 2155346 | p.Ala256Thr | missense_variant | 0.12 |
katG | 2155514 | p.Lys200Gln | missense_variant | 0.13 |
katG | 2155557 | c.555C>T | synonymous_variant | 1.0 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2167983 | p.Gly877Asp | missense_variant | 1.0 |
PPE35 | 2170378 | p.Ala79Thr | missense_variant | 1.0 |
Rv1979c | 2221783 | p.Ala461Glu | missense_variant | 1.0 |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2518132 | c.18C>T | synonymous_variant | 1.0 |
eis | 2714199 | p.Lys378Asn | missense_variant | 1.0 |
ahpC | 2725931 | c.-262_-261insG | upstream_gene_variant | 1.0 |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 1.0 |
ahpC | 2726672 | c.480G>A | synonymous_variant | 1.0 |
folC | 2746317 | p.Asp428Asn | missense_variant | 0.12 |
pepQ | 2859931 | p.Leu163Pro | missense_variant | 0.11 |
Rv2752c | 3064632 | c.1560C>T | synonymous_variant | 1.0 |
thyX | 3068121 | c.-176G>T | upstream_gene_variant | 0.12 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
Rv3083 | 3448442 | c.-62A>C | upstream_gene_variant | 1.0 |
Rv3083 | 3448566 | c.63T>C | synonymous_variant | 0.18 |
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 |
Rv3236c | 3611976 | p.Ala381Ser | missense_variant | 0.14 |
Rv3236c | 3612069 | p.Gly350Trp | missense_variant | 0.17 |
Rv3236c | 3612866 | p.Ser84Asn | missense_variant | 0.15 |
Rv3236c | 3613012 | c.105G>A | synonymous_variant | 1.0 |
fbiA | 3640453 | c.-90C>T | upstream_gene_variant | 0.15 |
fbiB | 3641996 | c.462C>T | synonymous_variant | 0.14 |
alr | 3840262 | p.His387Tyr | missense_variant | 1.0 |
rpoA | 3878458 | p.Asn17Ile | missense_variant | 0.18 |
rpoA | 3878476 | c.26_31delTGTCCG | disruptive_inframe_deletion | 0.17 |
clpC1 | 4039289 | c.1416T>C | synonymous_variant | 0.12 |
clpC1 | 4040517 | p.Val63Ala | missense_variant | 1.0 |
clpC1 | 4040605 | p.Leu34Ile | missense_variant | 0.3 |
embC | 4240671 | p.Thr270Ile | missense_variant | 1.0 |
embC | 4240803 | p.Tyr314Cys | missense_variant | 0.11 |
embC | 4241042 | p.Asn394Asp | missense_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embC | 4242812 | p.Asp984Asn | missense_variant | 0.13 |
embA | 4243848 | p.Val206Met | missense_variant | 1.0 |
embA | 4245166 | p.Pro645Gln | missense_variant | 1.0 |
embA | 4245969 | p.Pro913Ser | missense_variant | 1.0 |
embB | 4247276 | p.Pro255Ser | missense_variant | 0.12 |
embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 |
embB | 4248038 | p.Arg509Ser | missense_variant | 0.15 |
embB | 4248826 | c.2313G>T | synonymous_variant | 0.12 |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 1.0 |
aftB | 4269606 | c.-770T>C | upstream_gene_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 | 4407873 | c.330G>T | synonymous_variant | 1.0 |