Run ID: SRR1062932
Sample name:
Date: 02-04-2023 18:41:31
Number of reads: 2249158
Percentage reads mapped: 94.05
Strain: lineage3
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage3 | East-African-Indian | CAS | RD750 | 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 |
rrs | 1472733 | n.888G>A | non_coding_transcript_exon_variant | 0.17 | streptomycin |
katG | 2155700 | p.Asn138His | missense_variant | 1.0 | isoniazid |
embB | 4249518 | p.His1002Arg | missense_variant | 1.0 | ethambutol |
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 | 1.0 |
rpoB | 761292 | p.Val496Met | missense_variant | 1.0 |
rpoC | 762434 | c.-936T>G | upstream_gene_variant | 1.0 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
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 |
Rv1258c | 1407059 | p.Trp94Cys | missense_variant | 0.14 |
embR | 1417150 | c.198G>C | synonymous_variant | 0.17 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472530 | n.685G>A | non_coding_transcript_exon_variant | 0.18 |
rrs | 1472537 | n.692C>T | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472544 | n.699C>A | non_coding_transcript_exon_variant | 0.16 |
rrs | 1472545 | n.700A>T | non_coding_transcript_exon_variant | 0.16 |
rrs | 1472557 | n.712G>A | non_coding_transcript_exon_variant | 0.23 |
rrs | 1472571 | n.726G>C | non_coding_transcript_exon_variant | 0.24 |
rrs | 1472579 | n.734G>T | non_coding_transcript_exon_variant | 0.27 |
rrs | 1472581 | n.736A>T | non_coding_transcript_exon_variant | 0.27 |
rrs | 1472598 | n.753A>C | non_coding_transcript_exon_variant | 0.3 |
rrs | 1472599 | n.754G>T | non_coding_transcript_exon_variant | 0.28 |
rrs | 1472713 | n.868T>C | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472742 | n.897C>T | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472744 | n.899A>G | non_coding_transcript_exon_variant | 0.14 |
rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.14 |
rrs | 1472793 | n.948A>T | non_coding_transcript_exon_variant | 0.14 |
rrs | 1473352 | n.1507C>T | non_coding_transcript_exon_variant | 0.17 |
rrl | 1474218 | n.561T>A | non_coding_transcript_exon_variant | 0.17 |
rrl | 1474283 | n.626A>G | non_coding_transcript_exon_variant | 0.12 |
rrl | 1474812 | n.1155G>A | non_coding_transcript_exon_variant | 0.13 |
rrl | 1474823 | n.1166C>G | non_coding_transcript_exon_variant | 0.12 |
rrl | 1474824 | n.1167A>G | non_coding_transcript_exon_variant | 0.11 |
rrl | 1474831 | n.1174A>C | non_coding_transcript_exon_variant | 0.11 |
rrl | 1474844 | n.1187G>T | non_coding_transcript_exon_variant | 0.14 |
rrl | 1475765 | n.2108A>C | non_coding_transcript_exon_variant | 0.14 |
rrl | 1475783 | n.2126T>G | non_coding_transcript_exon_variant | 0.12 |
rrl | 1475803 | n.2146T>C | non_coding_transcript_exon_variant | 0.19 |
rrl | 1475804 | n.2147G>C | non_coding_transcript_exon_variant | 0.19 |
rrl | 1475816 | n.2159C>G | non_coding_transcript_exon_variant | 0.2 |
rrl | 1475817 | n.2160A>G | non_coding_transcript_exon_variant | 0.2 |
rrl | 1475858 | n.2201T>C | non_coding_transcript_exon_variant | 0.14 |
rrl | 1475866 | n.2209T>A | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476332 | n.2675G>C | non_coding_transcript_exon_variant | 0.33 |
rrl | 1476338 | n.2681C>T | non_coding_transcript_exon_variant | 0.45 |
rrl | 1476353 | n.2696G>T | non_coding_transcript_exon_variant | 0.71 |
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.71 |
rrl | 1476372 | n.2715T>C | non_coding_transcript_exon_variant | 0.71 |
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.68 |
rrl | 1476383 | n.2726T>A | non_coding_transcript_exon_variant | 0.7 |
rrl | 1476425 | n.2768G>T | non_coding_transcript_exon_variant | 0.54 |
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.52 |
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.52 |
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.31 |
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.27 |
rrl | 1476514 | n.2857C>T | non_coding_transcript_exon_variant | 0.23 |
rrl | 1476519 | n.2862C>G | non_coding_transcript_exon_variant | 0.23 |
rrl | 1476524 | n.2867C>T | non_coding_transcript_exon_variant | 0.21 |
rrl | 1476525 | n.2868A>G | non_coding_transcript_exon_variant | 0.2 |
rrl | 1476530 | n.2873C>T | non_coding_transcript_exon_variant | 0.22 |
rrl | 1476536 | n.2879G>A | non_coding_transcript_exon_variant | 0.24 |
rrl | 1476537 | n.2880A>G | non_coding_transcript_exon_variant | 0.24 |
rrl | 1476538 | n.2881A>G | non_coding_transcript_exon_variant | 0.25 |
rrl | 1476540 | n.2883C>G | non_coding_transcript_exon_variant | 0.27 |
rrl | 1476547 | n.2890C>T | non_coding_transcript_exon_variant | 0.29 |
rrl | 1476567 | n.2910C>T | non_coding_transcript_exon_variant | 0.2 |
rrl | 1476577 | n.2920T>G | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476712 | n.3055C>T | non_coding_transcript_exon_variant | 0.25 |
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 | 2168480 | c.2133C>G | synonymous_variant | 0.11 |
PPE35 | 2168505 | p.Gly703Ala | missense_variant | 0.11 |
PPE35 | 2170635 | c.-23C>G | upstream_gene_variant | 0.13 |
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 | 2726117 | c.-76T>A | upstream_gene_variant | 1.0 |
pepQ | 2860119 | p.His100Gln | missense_variant | 0.11 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.97 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fbiB | 3642877 | p.Lys448Arg | missense_variant | 1.0 |
rpoA | 3878483 | p.Leu9Met | missense_variant | 0.13 |
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 |