Run ID: ERR3077968
Sample name:
Date: 01-04-2023 00:13:02
Number of reads: 846208
Percentage reads mapped: 96.47
Strain: lineage4.1.2.1
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage4 | Euro-American | LAM;T;S;X;H | None | 1.0 |
lineage4.1 | Euro-American | T;X;H | None | 1.0 |
lineage4.1.2 | Euro-American | T;H | None | 1.0 |
lineage4.1.2.1 | Euro-American (Haarlem) | T1;H1 | RD182 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761139 | p.His445Tyr | missense_variant | 0.96 | rifampicin |
katG | 2155168 | p.Ser315Thr | missense_variant | 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 | 491591 | p.Lys270Met | missense_variant | 1.0 |
mshA | 575679 | p.Asn111Ser | missense_variant | 1.0 |
rpoB | 760115 | c.309C>T | synonymous_variant | 1.0 |
rpoB | 761352 | p.Gly516Cys | missense_variant | 0.12 |
rpoB | 761364 | p.Asp520Tyr | missense_variant | 0.12 |
rpoC | 765150 | p.Gly594Glu | missense_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776311 | p.Gly724Cys | missense_variant | 0.12 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
Rv1258c | 1407079 | c.261delC | frameshift_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472655 | n.810G>A | non_coding_transcript_exon_variant | 0.11 |
rrs | 1472658 | n.813G>A | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472661 | n.816A>G | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472665 | n.820G>A | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472678 | n.833T>G | non_coding_transcript_exon_variant | 0.11 |
rrs | 1472679 | n.834T>C | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472682 | n.839_843delGGGAT | non_coding_transcript_exon_variant | 0.13 |
rrs | 1472689 | n.844C>T | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472690 | n.845C>A | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472695 | n.850C>T | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472697 | n.852T>A | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472700 | n.855C>T | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472713 | n.868T>C | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472716 | n.871C>T | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472744 | n.899A>G | non_coding_transcript_exon_variant | 0.1 |
rrl | 1474777 | n.1120T>C | non_coding_transcript_exon_variant | 0.17 |
rrl | 1474782 | n.1125G>A | non_coding_transcript_exon_variant | 0.17 |
rrl | 1474790 | n.1133C>T | non_coding_transcript_exon_variant | 0.15 |
rrl | 1474794 | n.1137C>A | non_coding_transcript_exon_variant | 0.16 |
rrl | 1474798 | n.1141C>T | non_coding_transcript_exon_variant | 0.16 |
rrl | 1474803 | n.1146G>A | non_coding_transcript_exon_variant | 0.14 |
rrl | 1474804 | n.1147C>T | non_coding_transcript_exon_variant | 0.14 |
rrl | 1474812 | n.1155G>A | non_coding_transcript_exon_variant | 0.14 |
rrl | 1474823 | n.1166C>G | non_coding_transcript_exon_variant | 0.15 |
rrl | 1474827 | n.1170C>T | non_coding_transcript_exon_variant | 0.16 |
rrl | 1474830 | n.1173A>T | non_coding_transcript_exon_variant | 0.16 |
rrl | 1474831 | n.1174A>T | non_coding_transcript_exon_variant | 0.16 |
rrl | 1474839 | n.1182C>T | non_coding_transcript_exon_variant | 0.17 |
rrl | 1474844 | n.1187G>T | non_coding_transcript_exon_variant | 0.16 |
rrl | 1474866 | n.1209C>A | non_coding_transcript_exon_variant | 0.14 |
rrl | 1474869 | n.1212G>T | non_coding_transcript_exon_variant | 0.14 |
rrl | 1474896 | n.1239A>G | non_coding_transcript_exon_variant | 0.11 |
rrl | 1474902 | n.1245T>C | non_coding_transcript_exon_variant | 0.11 |
rrl | 1474904 | n.1247G>C | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476251 | n.2594T>C | non_coding_transcript_exon_variant | 0.15 |
rrl | 1476260 | n.2603A>G | non_coding_transcript_exon_variant | 0.23 |
rrl | 1476280 | n.2623A>C | non_coding_transcript_exon_variant | 0.28 |
rrl | 1476293 | n.2636C>T | non_coding_transcript_exon_variant | 0.3 |
rrl | 1476294 | n.2637A>G | non_coding_transcript_exon_variant | 0.3 |
rrl | 1476295 | n.2638C>G | non_coding_transcript_exon_variant | 0.3 |
rrl | 1476296 | n.2639C>T | non_coding_transcript_exon_variant | 0.3 |
rrl | 1476297 | n.2640C>T | non_coding_transcript_exon_variant | 0.3 |
rrl | 1476301 | n.2644A>C | non_coding_transcript_exon_variant | 0.32 |
rrl | 1476302 | n.2645G>A | non_coding_transcript_exon_variant | 0.32 |
rrl | 1476311 | n.2654G>C | non_coding_transcript_exon_variant | 0.32 |
rrl | 1476312 | n.2655T>C | non_coding_transcript_exon_variant | 0.32 |
rrl | 1476313 | n.2656G>A | non_coding_transcript_exon_variant | 0.29 |
rrl | 1476332 | n.2675G>C | non_coding_transcript_exon_variant | 0.32 |
rrl | 1476353 | n.2696G>T | non_coding_transcript_exon_variant | 0.39 |
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.43 |
rrl | 1476372 | n.2715T>C | non_coding_transcript_exon_variant | 0.43 |
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.4 |
rrl | 1476383 | n.2726T>A | non_coding_transcript_exon_variant | 0.4 |
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.34 |
rrl | 1476425 | n.2768G>T | non_coding_transcript_exon_variant | 0.35 |
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.35 |
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.35 |
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.33 |
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.27 |
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.13 |
rrl | 1476514 | n.2857C>T | non_coding_transcript_exon_variant | 0.13 |
rrl | 1476519 | n.2862C>G | non_coding_transcript_exon_variant | 0.1 |
rrl | 1476525 | n.2868A>G | non_coding_transcript_exon_variant | 0.1 |
rrl | 1476537 | n.2880A>G | non_coding_transcript_exon_variant | 0.1 |
rrl | 1476538 | n.2881A>G | non_coding_transcript_exon_variant | 0.1 |
rrl | 1476540 | n.2883C>G | non_coding_transcript_exon_variant | 0.1 |
rrl | 1476573 | n.2916A>C | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476577 | n.2920T>G | non_coding_transcript_exon_variant | 0.11 |
inhA | 1673904 | c.-298C>A | upstream_gene_variant | 0.13 |
tlyA | 1917966 | c.27C>T | synonymous_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2155011 | c.1101G>A | synonymous_variant | 1.0 |
PPE35 | 2169298 | p.Asn439Asp | missense_variant | 0.12 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2518076 | c.-39C>T | upstream_gene_variant | 1.0 |
eis | 2714488 | p.Thr282Ile | missense_variant | 0.14 |
ahpC | 2726265 | p.Lys25Gln | missense_variant | 0.19 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embC | 4242803 | p.Val981Leu | missense_variant | 1.0 |
embB | 4249197 | p.Gly895Glu | missense_variant | 0.13 |
embB | 4249701 | p.Ser1063Phe | missense_variant | 0.14 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
Rv1258c | 1404072 | c.541_*2008del | stop_lost&conservative_inframe_deletion&splice_region_variant | 1.0 |