Run ID: SRR1173727
Sample name:
Date: 03-04-2023 03:30:39
Number of reads: 855988
Percentage reads mapped: 72.56
Strain: lineage3
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage3 | East-African-Indian | CAS | RD750 | 0.99 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761139 | p.His445Ser | missense_variant | 1.0 | rifampicin |
katG | 2154007 | c.2101_2104dupAACT | frameshift_variant&stop_gained | 1.0 | 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 |
mshA | 576136 | c.789T>C | synonymous_variant | 0.17 |
rpoB | 759746 | c.-61C>T | upstream_gene_variant | 1.0 |
rpoC | 762434 | c.-936T>G | upstream_gene_variant | 1.0 |
rpoB | 762911 | p.Ile1035Met | missense_variant | 0.12 |
rpoC | 762920 | c.-450C>T | upstream_gene_variant | 0.11 |
rpoC | 762923 | c.-447C>G | upstream_gene_variant | 0.1 |
rpoB | 762939 | p.Met1045Leu | missense_variant | 0.11 |
rpoB | 762942 | p.Ile1046Val | missense_variant | 0.11 |
rpoC | 762965 | c.-405T>C | upstream_gene_variant | 0.13 |
rpoC | 762989 | c.-381G>C | upstream_gene_variant | 0.11 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 764665 | c.1296C>G | synonymous_variant | 0.12 |
rpoC | 764668 | c.1299C>T | synonymous_variant | 0.12 |
rpoC | 764695 | c.1326T>C | synonymous_variant | 0.12 |
rpoC | 764713 | c.1344G>C | synonymous_variant | 0.13 |
rpoC | 764719 | c.1350G>A | 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 |
fbiC | 1305134 | p.Gly735Val | missense_variant | 0.13 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472172 | n.327T>C | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472177 | n.332C>T | non_coding_transcript_exon_variant | 0.16 |
rrs | 1472214 | n.369C>G | non_coding_transcript_exon_variant | 0.19 |
rrs | 1472235 | n.390G>C | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472240 | n.395G>C | non_coding_transcript_exon_variant | 0.18 |
rrs | 1472242 | n.397C>T | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472243 | n.398G>A | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472253 | n.408G>T | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472256 | n.411T>A | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472259 | n.414C>A | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472332 | n.487_488insT | non_coding_transcript_exon_variant | 1.0 |
rrs | 1472714 | n.869A>T | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472716 | n.871C>G | non_coding_transcript_exon_variant | 0.14 |
rrs | 1472734 | n.889C>T | non_coding_transcript_exon_variant | 0.38 |
rrs | 1472741 | n.896G>A | non_coding_transcript_exon_variant | 0.39 |
rrs | 1472744 | n.899A>G | non_coding_transcript_exon_variant | 0.37 |
rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.39 |
rrs | 1472786 | n.941C>T | non_coding_transcript_exon_variant | 0.38 |
rrs | 1472793 | n.948A>T | non_coding_transcript_exon_variant | 0.37 |
rrs | 1472956 | n.1111T>C | non_coding_transcript_exon_variant | 0.14 |
rrs | 1472957 | n.1112C>T | non_coding_transcript_exon_variant | 0.13 |
rrs | 1472958 | n.1113A>T | non_coding_transcript_exon_variant | 0.12 |
rrs | 1473145 | n.1300C>T | non_coding_transcript_exon_variant | 0.12 |
rrs | 1473148 | n.1303G>A | non_coding_transcript_exon_variant | 0.12 |
rrs | 1473163 | n.1318C>T | non_coding_transcript_exon_variant | 0.18 |
rrs | 1473166 | n.1321G>A | non_coding_transcript_exon_variant | 0.18 |
rrs | 1473177 | n.1332G>A | non_coding_transcript_exon_variant | 0.18 |
rrs | 1473201 | n.1356A>T | non_coding_transcript_exon_variant | 0.18 |
rrs | 1473202 | n.1357C>T | non_coding_transcript_exon_variant | 0.18 |
rrl | 1476336 | n.2679C>T | non_coding_transcript_exon_variant | 0.3 |
rrl | 1476356 | n.2699C>A | non_coding_transcript_exon_variant | 0.42 |
rrl | 1476357 | n.2700T>C | non_coding_transcript_exon_variant | 0.41 |
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.41 |
rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.4 |
rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.37 |
rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.35 |
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.35 |
rrl | 1476383 | n.2726T>G | non_coding_transcript_exon_variant | 0.35 |
rrl | 1476384 | n.2727G>T | non_coding_transcript_exon_variant | 0.36 |
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.43 |
rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.33 |
rrl | 1476425 | n.2768G>T | non_coding_transcript_exon_variant | 0.37 |
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.25 |
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.4 |
rrl | 1476442 | n.2785T>A | non_coding_transcript_exon_variant | 0.26 |
rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.23 |
rrl | 1476455 | n.2798C>A | non_coding_transcript_exon_variant | 0.23 |
rrl | 1476456 | n.2799A>T | non_coding_transcript_exon_variant | 0.23 |
rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.19 |
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.31 |
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.15 |
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 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289365 | c.-125delC | upstream_gene_variant | 1.0 |
ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 1.0 |
ahpC | 2726115 | c.-77delT | upstream_gene_variant | 1.0 |
thyA | 3073806 | c.666C>G | synonymous_variant | 0.19 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3613012 | c.105G>T | synonymous_variant | 0.14 |
fbiB | 3642877 | p.Lys448Arg | missense_variant | 1.0 |
embC | 4242075 | p.Arg738Gln | missense_variant | 0.94 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4244491 | p.Thr420Met | missense_variant | 0.13 |
embB | 4245629 | c.-885C>T | upstream_gene_variant | 0.12 |
embB | 4247990 | p.Val493Leu | missense_variant | 0.83 |
ubiA | 4268972 | p.Ala288Ser | missense_variant | 0.12 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407847 | p.Ala119Asp | missense_variant | 1.0 |