Run ID: SRR14782723
Sample name:
Date: 03-04-2023 11:36:26
Number of reads: 2658838
Percentage reads mapped: 99.6
Strain: lineage4.8;lineage4.2.1
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 |
lineage4.2 | Euro-American | H;T;LAM | None | 0.11 |
lineage4.8 | Euro-American (mainly T) | T1;T2;T3;T5 | RD219 | 0.86 |
lineage4.2.1 | Euro-American (TUR) | H3;H4 | None | 0.16 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.25 | rifampicin |
rpsL | 781822 | p.Lys88Arg | missense_variant | 0.12 | streptomycin |
fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 0.17 | isoniazid, ethionamide |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.14 | isoniazid |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 0.15 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 0.15 |
gyrA | 9647 | c.2346C>G | synonymous_variant | 0.17 |
fgd1 | 491247 | c.465C>T | synonymous_variant | 0.21 |
mshA | 576613 | c.1266A>C | synonymous_variant | 0.28 |
mshA | 576616 | c.1269G>C | synonymous_variant | 0.16 |
ccsA | 619969 | p.Val27Ile | missense_variant | 0.19 |
rpoC | 764367 | p.Gly333Ala | missense_variant | 0.18 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 777883 | p.Gly200Arg | missense_variant | 0.19 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 0.87 |
fabG1 | 1673553 | p.Asp38Glu | missense_variant | 0.23 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
PPE35 | 2168149 | p.Pro822Ser | missense_variant | 0.89 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2519071 | p.Asp319Glu | missense_variant | 0.21 |
pepQ | 2860159 | p.Ala87Gly | missense_variant | 0.16 |
ald | 3086742 | c.-78A>C | upstream_gene_variant | 0.12 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.17 |
ald | 3087818 | p.Cys333Trp | missense_variant | 0.1 |
fbiD | 3339734 | p.Ala206Gly | missense_variant | 0.62 |
fbiD | 3339749 | p.Val211Gly | missense_variant | 0.33 |
Rv3083 | 3448497 | c.-7T>A | upstream_gene_variant | 0.33 |
Rv3083 | 3448500 | c.-4A>G | upstream_gene_variant | 0.27 |
Rv3083 | 3448501 | c.-3G>T | upstream_gene_variant | 0.25 |
whiB7 | 3568425 | c.255T>G | synonymous_variant | 0.25 |
whiB7 | 3568428 | c.252A>G | synonymous_variant | 0.44 |
whiB7 | 3568431 | c.249C>G | synonymous_variant | 0.24 |
rpoA | 3878613 | c.-106A>C | upstream_gene_variant | 0.5 |
rpoA | 3878641 | c.-134C>G | upstream_gene_variant | 1.0 |
embC | 4239930 | p.Gly23Glu | missense_variant | 0.82 |
embC | 4240409 | p.Pro183Ala | missense_variant | 0.28 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embB | 4246527 | p.Ala5Gly | missense_variant | 0.45 |
embB | 4246529 | p.Ser6Arg | missense_variant | 0.33 |
embB | 4246584 | p.Arg24Pro | missense_variant | 0.23 |
embB | 4248328 | c.1815G>C | synonymous_variant | 0.22 |
embB | 4249594 | c.3081G>A | synonymous_variant | 0.21 |
ethA | 4326632 | p.His281Pro | missense_variant | 0.1 |
ethA | 4328376 | c.-903G>C | upstream_gene_variant | 0.12 |
whiB6 | 4338594 | c.-73T>G | upstream_gene_variant | 0.14 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |