Run ID: SRR12199396
Sample name:
Date: 03-04-2023 06:37:13
Number of reads: 124624
Percentage reads mapped: 92.36
Strain: lineage4.9
Drug-resistance: HR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage4 | Euro-American | LAM;T;S;X;H | None | 0.8 |
lineage4.9 | Euro-American (H37Rv-like) | T1 | None | 0.91 |
lineage1.2.2 | Indo-Oceanic | EAI1 | RD239 | 0.95 |
lineage1.2.2.2 | Indo-Oceanic | NA | RD239 | 0.38 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5075 | c.-165C>T | upstream_gene_variant | 1.0 |
gyrA | 7268 | c.-34C>T | upstream_gene_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 |
fgd1 | 491742 | c.960T>C | synonymous_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 |
fbiC | 1303480 | p.Gln184* | stop_gained | 0.25 |
embR | 1417019 | p.Cys110Tyr | missense_variant | 1.0 |
atpE | 1460985 | c.-60G>T | upstream_gene_variant | 0.5 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472598 | n.753A>C | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472599 | n.754G>T | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472616 | n.771G>A | non_coding_transcript_exon_variant | 0.14 |
rrs | 1473056 | n.1211A>G | non_coding_transcript_exon_variant | 0.2 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
tlyA | 1918162 | p.Glu75Lys | missense_variant | 1.0 |
katG | 2156200 | c.-89G>A | upstream_gene_variant | 0.29 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2168742 | p.Gly624Asp | missense_variant | 1.0 |
PPE35 | 2170048 | p.Leu189Val | missense_variant | 0.67 |
PPE35 | 2170053 | p.Thr187Ser | missense_variant | 0.5 |
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 |
ahpC | 2726051 | c.-142G>A | 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 |
fprA | 3474597 | c.591C>A | synonymous_variant | 1.0 |
fprA | 3475159 | p.Asn385Asp | missense_variant | 1.0 |
Rv3236c | 3612984 | p.Asn45His | missense_variant | 1.0 |
fbiB | 3640686 | c.-849C>A | upstream_gene_variant | 0.29 |
alr | 3841612 | c.-193_-192insC | upstream_gene_variant | 0.36 |
clpC1 | 4040517 | p.Val63Ala | missense_variant | 1.0 |
panD | 4044433 | c.-152A>G | upstream_gene_variant | 0.29 |
embC | 4240671 | p.Thr270Ile | missense_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 | 4247646 | p.Glu378Ala | missense_variant | 1.0 |
embB | 4247926 | c.1413C>T | synonymous_variant | 0.29 |
embB | 4249300 | p.Trp929* | stop_gained | 0.4 |
embB | 4249339 | c.2826T>C | synonymous_variant | 1.0 |
aftB | 4268030 | c.807G>T | synonymous_variant | 0.4 |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 1.0 |
aftB | 4269606 | c.-770T>C | upstream_gene_variant | 1.0 |
ethA | 4326148 | c.1326G>T | synonymous_variant | 0.71 |
ethA | 4326439 | p.Asn345Lys | missense_variant | 1.0 |
ethA | 4327076 | p.Phe133Ser | missense_variant | 1.0 |
ethR | 4327694 | p.Asp49Ala | missense_variant | 1.0 |
whiB6 | 4338203 | p.Arg107Cys | missense_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
whiB6 | 4338603 | c.-82C>T | upstream_gene_variant | 1.0 |
whiB6 | 4338636 | c.-115C>T | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407873 | c.330G>T | synonymous_variant | 1.0 |