Run ID: SRR9971082
Sample name:
Date: 04-04-2023 23:10:10
Number of reads: 5071873
Percentage reads mapped: 93.5
Strain: lineage1.2.2.1
Drug-resistance: RR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage1 | Indo-Oceanic | EAI | RD239 | 1.0 |
lineage1.2.2 | Indo-Oceanic | EAI1 | RD239 | 1.0 |
lineage1.2.2.1 | Indo-Oceanic | NA | RD239 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5075 | c.-165C>T | upstream_gene_variant | 1.0 |
gyrB | 6112 | p.Met291Ile | missense_variant | 1.0 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 8452 | p.Ala384Val | missense_variant | 1.0 |
gyrA | 9143 | c.1842T>C | synonymous_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491060 | p.Met93Thr | missense_variant | 1.0 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 576108 | p.Ala254Gly | missense_variant | 0.37 |
ccsA | 620659 | p.Arg257Cys | missense_variant | 1.0 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 763884 | p.Ala172Val | missense_variant | 1.0 |
rpoC | 763886 | c.517C>A | synonymous_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpR5 | 778991 | p.Val1Ala | missense_variant | 0.61 |
mmpR5 | 779099 | c.110delG | frameshift_variant | 0.12 |
mmpR5 | 779254 | p.Arg89Trp | missense_variant | 0.14 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rplC | 800899 | p.Ala31Thr | missense_variant | 1.0 |
embR | 1417019 | p.Cys110Tyr | missense_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1471842 | n.-4T>G | upstream_gene_variant | 0.99 |
rrs | 1472655 | n.810G>A | non_coding_transcript_exon_variant | 0.13 |
rrs | 1472661 | n.816A>G | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476332 | n.2675G>C | non_coding_transcript_exon_variant | 0.1 |
rrl | 1476338 | n.2681C>T | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476353 | n.2696G>T | non_coding_transcript_exon_variant | 0.19 |
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.21 |
rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.24 |
rrl | 1476372 | n.2715T>C | non_coding_transcript_exon_variant | 0.24 |
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.25 |
rrl | 1476383 | n.2726T>A | non_coding_transcript_exon_variant | 0.23 |
rrl | 1476425 | n.2768G>T | non_coding_transcript_exon_variant | 0.2 |
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.23 |
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.21 |
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.19 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
katG | 2156004 | c.108G>A | synonymous_variant | 1.0 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2518132 | c.18C>T | synonymous_variant | 1.0 |
kasA | 2518306 | c.192C>G | synonymous_variant | 1.0 |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 1.0 |
thyX | 3068115 | c.-170C>T | upstream_gene_variant | 1.0 |
thyA | 3074034 | c.438T>C | synonymous_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fbiD | 3339734 | p.Ala206Gly | missense_variant | 0.2 |
Rv3083 | 3448714 | p.Asp71His | missense_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474597 | c.591C>A | synonymous_variant | 1.0 |
fprA | 3475159 | p.Asn385Asp | missense_variant | 1.0 |
clpC1 | 4040517 | p.Val63Ala | missense_variant | 1.0 |
embC | 4240671 | p.Thr270Ile | missense_variant | 1.0 |
embC | 4240750 | c.888C>T | synonymous_variant | 1.0 |
embC | 4241042 | p.Asn394Asp | missense_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4245969 | p.Pro913Ser | missense_variant | 1.0 |
embB | 4246584 | p.Arg24Pro | missense_variant | 0.18 |
embB | 4247028 | p.Leu172Arg | missense_variant | 0.24 |
embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 1.0 |
aftB | 4269606 | c.-770T>C | upstream_gene_variant | 1.0 |
ethA | 4326439 | p.Asn345Lys | missense_variant | 1.0 |
ethR | 4327450 | c.-99G>A | upstream_gene_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
whiB6 | 4338603 | c.-82C>T | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407873 | c.330G>T | synonymous_variant | 1.0 |