Run ID: SRR3743477
Sample name:
Date: 04-04-2023 05:45:54
Number of reads: 4812138
Percentage reads mapped: 76.76
Strain: lineage4.2.1
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage4 | Euro-American | LAM;T;S;X;H | None | 1.0 |
lineage4.2 | Euro-American | H;T;LAM | None | 1.0 |
lineage4.2.1 | Euro-American (TUR) | H3;H4 | None | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7581 | p.Asp94Tyr | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rpsL | 781822 | p.Lys88Arg | missense_variant | 1.0 | streptomycin |
fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 1.0 | isoniazid, ethionamide |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2288832 | p.His137Arg | missense_variant | 0.99 | pyrazinamide |
eis | 2715344 | c.-12C>T | upstream_gene_variant | 1.0 | kanamycin |
embA | 4243217 | c.-16C>T | upstream_gene_variant | 1.0 | ethambutol |
embB | 4247402 | p.Ser297Ala | 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 | 491247 | c.465C>T | synonymous_variant | 1.0 |
ccsA | 619969 | p.Val27Ile | missense_variant | 1.0 |
rpoC | 764817 | p.Val483Gly | missense_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 0.99 |
rrs | 1472150 | n.305T>A | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472172 | n.327T>C | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472557 | n.712G>A | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472570 | n.725G>A | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472571 | n.726G>C | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472573 | n.728C>T | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472579 | n.734G>C | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472598 | n.753A>C | non_coding_transcript_exon_variant | 0.13 |
rrs | 1472734 | n.889C>T | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472741 | n.896G>A | non_coding_transcript_exon_variant | 0.14 |
rrs | 1472744 | n.899A>G | non_coding_transcript_exon_variant | 0.14 |
rrs | 1472767 | n.922G>A | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472779 | n.934G>A | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472786 | n.941C>T | non_coding_transcript_exon_variant | 0.14 |
rrs | 1472793 | n.948A>T | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472803 | n.958T>A | non_coding_transcript_exon_variant | 0.12 |
rrs | 1473161 | n.1316A>C | non_coding_transcript_exon_variant | 0.1 |
rrs | 1473177 | n.1332G>A | non_coding_transcript_exon_variant | 0.11 |
rrs | 1473179 | n.1334C>T | non_coding_transcript_exon_variant | 0.11 |
rrs | 1473192 | n.1347A>G | non_coding_transcript_exon_variant | 0.13 |
rrs | 1473205 | n.1360T>C | non_coding_transcript_exon_variant | 0.12 |
rrl | 1474790 | n.1133C>T | non_coding_transcript_exon_variant | 0.13 |
rrl | 1474798 | n.1141C>T | non_coding_transcript_exon_variant | 0.16 |
rrl | 1474804 | n.1147C>T | non_coding_transcript_exon_variant | 0.18 |
rrl | 1474823 | n.1166C>G | non_coding_transcript_exon_variant | 0.25 |
rrl | 1474827 | n.1170C>T | non_coding_transcript_exon_variant | 0.25 |
rrl | 1474844 | n.1187G>T | non_coding_transcript_exon_variant | 0.29 |
rrl | 1474866 | n.1209C>A | non_coding_transcript_exon_variant | 0.25 |
rrl | 1474869 | n.1212G>T | non_coding_transcript_exon_variant | 0.23 |
rrl | 1474896 | n.1239A>G | non_coding_transcript_exon_variant | 0.17 |
rrl | 1474902 | n.1245T>C | non_coding_transcript_exon_variant | 0.14 |
rrl | 1474904 | n.1247G>C | non_coding_transcript_exon_variant | 0.14 |
rrl | 1474913 | n.1256T>A | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476338 | n.2681C>T | non_coding_transcript_exon_variant | 0.13 |
rrl | 1476353 | n.2696G>T | non_coding_transcript_exon_variant | 0.18 |
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.23 |
rrl | 1476372 | n.2715T>C | non_coding_transcript_exon_variant | 0.24 |
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.26 |
rrl | 1476383 | n.2726T>A | non_coding_transcript_exon_variant | 0.26 |
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.3 |
rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.31 |
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.32 |
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.23 |
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.27 |
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.23 |
rrl | 1476512 | n.2855C>T | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476514 | n.2857C>T | non_coding_transcript_exon_variant | 0.13 |
rrl | 1476519 | n.2862C>G | non_coding_transcript_exon_variant | 0.13 |
rrl | 1476525 | n.2868A>G | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476530 | n.2873C>T | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476537 | n.2880A>G | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476538 | n.2881A>G | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476540 | n.2883C>G | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476567 | n.2910C>T | non_coding_transcript_exon_variant | 0.14 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
PPE35 | 2169879 | p.Phe245Cys | missense_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
ald | 3086742 | c.-78A>C | upstream_gene_variant | 1.0 |
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 |
embB | 4249594 | c.3081G>A | synonymous_variant | 1.0 |
ethA | 4326632 | p.His281Pro | missense_variant | 1.0 |
ethA | 4328376 | c.-903G>C | upstream_gene_variant | 1.0 |
whiB6 | 4338593 | c.-73delT | upstream_gene_variant | 1.0 |
whiB6 | 4338596 | c.-75G>C | upstream_gene_variant | 1.0 |