Run ID: ERR4798898
Sample name:
Date: 01-04-2023 08:43:09
Number of reads: 2180610
Percentage reads mapped: 88.83
Strain: lineage3.1.2.1
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage3 | East-African-Indian | CAS | RD750 | 0.98 |
lineage3.1 | East-African-Indian | Non-CAS1-Delhi | RD750 | 0.98 |
lineage3.1.2 | East-African-Indian | CAS;CAS2 | RD750 | 0.98 |
lineage3.1.2.1 | East-African-Indian | CAS2 | RD750 | 0.98 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761139 | p.His445Asp | missense_variant | 0.9 | rifampicin |
katG | 2155168 | p.Ser315Asn | missense_variant | 0.98 | isoniazid |
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 |
rpoB | 759746 | c.-61C>T | upstream_gene_variant | 0.97 |
rpoB | 760139 | c.333A>G | synonymous_variant | 0.12 |
rpoB | 760571 | c.765G>C | synonymous_variant | 0.12 |
rpoB | 761027 | c.1221A>C | synonymous_variant | 0.11 |
rpoB | 761036 | c.1230G>C | synonymous_variant | 0.11 |
rpoB | 761037 | c.1231T>C | synonymous_variant | 0.11 |
rpoB | 761051 | c.1245G>T | synonymous_variant | 0.12 |
rpoB | 761054 | c.1248G>C | synonymous_variant | 0.12 |
rpoB | 761057 | c.1251G>C | synonymous_variant | 0.12 |
rpoB | 761060 | c.1254C>G | synonymous_variant | 0.12 |
rpoB | 761063 | c.1257C>G | synonymous_variant | 0.12 |
rpoB | 761084 | c.1278C>A | synonymous_variant | 0.14 |
rpoB | 762101 | c.2295C>G | synonymous_variant | 0.11 |
rpoB | 762158 | c.2352G>C | synonymous_variant | 0.11 |
rpoB | 762167 | c.2361T>C | synonymous_variant | 0.12 |
rpoB | 762185 | c.2379G>C | synonymous_variant | 0.12 |
rpoC | 762434 | c.-936T>G | upstream_gene_variant | 0.94 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 0.99 |
rpoC | 763492 | c.123G>C | synonymous_variant | 0.11 |
rpoC | 763528 | c.159G>A | synonymous_variant | 0.14 |
rpoC | 763546 | c.177A>G | synonymous_variant | 0.12 |
rpoC | 763570 | c.201G>C | synonymous_variant | 0.12 |
rpoC | 764452 | c.1083T>C | synonymous_variant | 0.12 |
rpoC | 764458 | c.1089G>C | synonymous_variant | 0.12 |
rpoC | 764461 | c.1092A>G | synonymous_variant | 0.12 |
rpoC | 764497 | c.1128A>G | synonymous_variant | 0.13 |
rpoC | 764521 | c.1152T>C | synonymous_variant | 0.14 |
rpoC | 764527 | c.1158C>T | synonymous_variant | 0.13 |
rpoC | 764530 | c.1161C>T | synonymous_variant | 0.14 |
rpoC | 764533 | c.1164C>A | synonymous_variant | 0.13 |
rpoC | 764536 | c.1167G>T | synonymous_variant | 0.13 |
rpoC | 764539 | c.1170C>G | synonymous_variant | 0.13 |
rpoC | 764548 | c.1179G>A | synonymous_variant | 0.15 |
rpoC | 764554 | c.1185C>T | synonymous_variant | 0.18 |
rpoC | 764566 | c.1197C>G | synonymous_variant | 0.2 |
rpoC | 764575 | c.1206T>G | synonymous_variant | 0.19 |
rpoC | 764605 | c.1236G>C | synonymous_variant | 0.16 |
rpoC | 764611 | c.1242G>T | synonymous_variant | 0.18 |
rpoC | 764623 | c.1254C>T | synonymous_variant | 0.17 |
rpoC | 764626 | c.1257C>T | synonymous_variant | 0.17 |
rpoC | 764632 | c.1263T>C | synonymous_variant | 0.15 |
rpoC | 764650 | c.1281G>T | synonymous_variant | 0.13 |
rpoC | 764716 | c.1347G>C | synonymous_variant | 0.11 |
rpoC | 764746 | c.1377G>T | synonymous_variant | 0.11 |
rpoC | 764752 | c.1383G>C | synonymous_variant | 0.13 |
rpoC | 764758 | c.1389C>G | synonymous_variant | 0.12 |
rpoC | 764764 | c.1395T>C | synonymous_variant | 0.14 |
rpoC | 764803 | c.1434C>T | synonymous_variant | 0.12 |
rpoC | 764810 | p.Pro481Ala | missense_variant | 0.12 |
rpoC | 764815 | c.1446A>G | synonymous_variant | 0.12 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472150 | n.305T>A | non_coding_transcript_exon_variant | 0.11 |
rrs | 1472380 | n.535G>C | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472446 | n.601T>A | non_coding_transcript_exon_variant | 0.27 |
rrs | 1472452 | n.607G>A | non_coding_transcript_exon_variant | 0.27 |
rrs | 1472464 | n.619A>G | non_coding_transcript_exon_variant | 0.27 |
rrs | 1472612 | n.767G>T | non_coding_transcript_exon_variant | 0.25 |
rrs | 1472734 | n.889C>T | non_coding_transcript_exon_variant | 0.45 |
rrs | 1472741 | n.896G>A | non_coding_transcript_exon_variant | 0.45 |
rrs | 1472846 | n.1001C>T | non_coding_transcript_exon_variant | 0.18 |
rrs | 1472847 | n.1002G>A | non_coding_transcript_exon_variant | 0.18 |
rrs | 1472860 | n.1015C>T | non_coding_transcript_exon_variant | 0.23 |
rrs | 1472861 | n.1016G>A | non_coding_transcript_exon_variant | 0.23 |
rrs | 1472956 | n.1111T>C | non_coding_transcript_exon_variant | 0.36 |
rrs | 1472957 | n.1112C>T | non_coding_transcript_exon_variant | 0.44 |
rrs | 1472969 | n.1124A>G | non_coding_transcript_exon_variant | 0.44 |
rrs | 1472970 | n.1125C>G | non_coding_transcript_exon_variant | 0.44 |
rrs | 1472977 | n.1132G>C | non_coding_transcript_exon_variant | 0.44 |
rrs | 1472978 | n.1133T>C | non_coding_transcript_exon_variant | 0.44 |
rrs | 1472989 | n.1144G>A | non_coding_transcript_exon_variant | 0.43 |
rrs | 1472990 | n.1145A>G | non_coding_transcript_exon_variant | 0.43 |
rrs | 1473082 | n.1237G>A | non_coding_transcript_exon_variant | 0.2 |
rrs | 1473088 | n.1243A>G | non_coding_transcript_exon_variant | 0.17 |
rrs | 1473166 | n.1321G>A | non_coding_transcript_exon_variant | 0.11 |
rrs | 1473290 | n.1445C>T | non_coding_transcript_exon_variant | 0.17 |
rrs | 1473291 | n.1446_1447insT | non_coding_transcript_exon_variant | 0.17 |
rrl | 1473414 | n.-244G>C | upstream_gene_variant | 1.0 |
rrl | 1474140 | n.483C>T | non_coding_transcript_exon_variant | 0.17 |
rrl | 1474151 | n.494C>T | non_coding_transcript_exon_variant | 0.18 |
rrl | 1474181 | n.524_525insT | non_coding_transcript_exon_variant | 0.2 |
rrl | 1474184 | n.527C>A | non_coding_transcript_exon_variant | 0.2 |
rrl | 1474185 | n.529delA | non_coding_transcript_exon_variant | 0.2 |
rrl | 1474249 | n.592G>T | non_coding_transcript_exon_variant | 0.17 |
rrl | 1474356 | n.699T>C | non_coding_transcript_exon_variant | 0.2 |
rrl | 1474362 | n.705A>G | non_coding_transcript_exon_variant | 0.2 |
rrl | 1474387 | n.730C>T | non_coding_transcript_exon_variant | 0.22 |
rrl | 1474413 | n.756A>C | non_coding_transcript_exon_variant | 0.25 |
rrl | 1475426 | n.1769C>A | non_coding_transcript_exon_variant | 0.29 |
rrl | 1476584 | n.2927C>T | non_coding_transcript_exon_variant | 0.29 |
rrl | 1476594 | n.2937C>T | non_coding_transcript_exon_variant | 0.17 |
rrl | 1476597 | n.2940G>A | non_coding_transcript_exon_variant | 0.14 |
rrl | 1476603 | n.2946G>A | non_coding_transcript_exon_variant | 0.13 |
rrl | 1476608 | n.2951C>G | non_coding_transcript_exon_variant | 0.11 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2168604 | p.Pro670Leu | missense_variant | 0.93 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289047 | c.195C>T | synonymous_variant | 0.97 |
pncA | 2289365 | c.-125delC | upstream_gene_variant | 0.95 |
ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 0.98 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 0.99 |
rpoA | 3878184 | c.324C>T | synonymous_variant | 0.12 |
rpoA | 3878193 | c.315T>C | synonymous_variant | 0.12 |
rpoA | 3878197 | p.Glu104Ala | missense_variant | 0.1 |
rpoA | 3878217 | c.291A>G | synonymous_variant | 0.11 |
rpoA | 3878244 | c.264G>A | synonymous_variant | 0.12 |
rpoA | 3878259 | c.249G>C | synonymous_variant | 0.12 |
rpoA | 3878271 | c.237T>C | synonymous_variant | 0.1 |
clpC1 | 4039106 | c.1599G>C | synonymous_variant | 0.1 |
clpC1 | 4039136 | c.1569C>T | synonymous_variant | 0.11 |
clpC1 | 4039145 | c.1560G>C | synonymous_variant | 0.11 |
clpC1 | 4039925 | c.780C>G | synonymous_variant | 0.13 |
clpC1 | 4039931 | c.774T>C | synonymous_variant | 0.12 |
clpC1 | 4040048 | c.657C>T | synonymous_variant | 0.12 |
clpC1 | 4040057 | c.648C>T | synonymous_variant | 0.12 |
clpC1 | 4040090 | p.Ser205Cys | missense_variant | 0.11 |
clpC1 | 4040202 | p.Ser168Phe | missense_variant | 0.94 |
embC | 4242075 | p.Arg738Gln | missense_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |