Run ID: SRR6479534
Sample name:
Date: 04-04-2023 14:32:28
Number of reads: 699123
Percentage reads mapped: 99.49
Strain: lineage2.2.1
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage2 | East-Asian | Beijing | RD105 | 0.99 |
lineage2.2 | East-Asian (Beijing) | Beijing-RD207 | RD105;RD207 | 1.0 |
lineage2.2.1 | East-Asian (Beijing) | Beijing-RD181 | RD105;RD207;RD181 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 1.0 | kanamycin, capreomycin, aminoglycosides, amikacin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2288859 | p.Val128Gly | missense_variant | 1.0 | pyrazinamide |
embB | 4247431 | p.Met306Ile | missense_variant | 1.0 | ethambutol |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5216 | c.-24A>T | upstream_gene_variant | 0.25 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 7812 | p.Pro171Thr | missense_variant | 0.33 |
gyrA | 8787 | p.Thr496Ala | missense_variant | 0.22 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 575907 | p.Ala187Val | missense_variant | 1.0 |
ccsA | 619826 | c.-65G>T | upstream_gene_variant | 0.14 |
ccsA | 620625 | p.Ile245Met | missense_variant | 1.0 |
rpoB | 761387 | c.1581C>T | synonymous_variant | 0.25 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 763421 | p.Glu18* | stop_gained | 0.22 |
rpoC | 764067 | p.Gln233Arg | missense_variant | 0.18 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 1.0 |
mmpL5 | 777556 | p.Val309Phe | missense_variant | 0.38 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
fbiC | 1304403 | c.1473T>C | synonymous_variant | 0.15 |
Rv1258c | 1406681 | p.Trp220Cys | missense_variant | 0.12 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1474809 | n.1152T>G | non_coding_transcript_exon_variant | 0.2 |
fabG1 | 1673278 | c.-162T>C | upstream_gene_variant | 0.2 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2170048 | p.Leu189Val | missense_variant | 1.0 |
PPE35 | 2170053 | p.Thr187Ser | missense_variant | 1.0 |
Rv1979c | 2223210 | c.-47delG | upstream_gene_variant | 0.18 |
Rv1979c | 2223248 | c.-84G>A | upstream_gene_variant | 0.18 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2288843 | c.399T>A | synonymous_variant | 0.29 |
folC | 2746231 | c.1368G>A | synonymous_variant | 0.5 |
ald | 3086731 | c.-89A>G | upstream_gene_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
ald | 3087390 | p.Gly191Cys | missense_variant | 0.29 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 |
alr | 3841120 | p.Arg101Ser | missense_variant | 0.67 |
alr | 3841235 | p.Met62Ile | missense_variant | 0.15 |
rpoA | 3877949 | p.Thr187Ala | missense_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243346 | c.114A>G | synonymous_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
embA | 4246083 | p.Glu951* | stop_gained | 0.29 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 |
ethA | 4326155 | p.Leu440Pro | missense_variant | 1.0 |
whiB6 | 4338371 | p.Thr51Pro | missense_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407927 | p.Glu92Asp | missense_variant | 1.0 |