Run ID: SRR5341243
Sample name:
Date: 04-04-2023 10:10:21
Number of reads: 1617730
Percentage reads mapped: 99.38
Strain: lineage2.2.1;lineage1.2.2.2
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage2 | East-Asian | Beijing | RD105 | 0.78 |
lineage1 | Indo-Oceanic | EAI | RD239 | 0.1 |
lineage2.2 | East-Asian (Beijing) | Beijing-RD207 | RD105;RD207 | 0.79 |
lineage1.2.2 | Indo-Oceanic | EAI1 | RD239 | 0.19 |
lineage2.2.1 | East-Asian (Beijing) | Beijing-RD181 | RD105;RD207;RD181 | 0.78 |
lineage1.2.2.2 | Indo-Oceanic | NA | RD239 | 0.17 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7570 | p.Ala90Val | missense_variant | 0.19 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761161 | p.Leu452Pro | missense_variant | 0.14 | rifampicin |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.14 | isoniazid |
pncA | 2288997 | p.His82Arg | missense_variant | 0.26 | pyrazinamide |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 8452 | p.Ala384Val | missense_variant | 0.13 |
gyrA | 8685 | p.Ile462Val | missense_variant | 0.7 |
gyrA | 9143 | c.1842T>C | synonymous_variant | 0.15 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.95 |
mshA | 575907 | p.Ala187Val | missense_variant | 0.81 |
ccsA | 620625 | p.Ile245Met | missense_variant | 0.79 |
ccsA | 620748 | c.858T>G | synonymous_variant | 0.26 |
rpoB | 759615 | c.-192A>C | upstream_gene_variant | 0.31 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 763884 | p.Ala172Val | missense_variant | 0.14 |
rpoC | 763886 | c.517C>A | synonymous_variant | 0.14 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.87 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.91 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 0.98 |
fbiC | 1303016 | p.Val29Gly | missense_variant | 0.24 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 0.83 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1473694 | n.37C>T | non_coding_transcript_exon_variant | 0.12 |
rrl | 1475284 | n.1627C>T | non_coding_transcript_exon_variant | 0.13 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.79 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
tlyA | 1918645 | p.Asn236Asp | missense_variant | 0.26 |
ndh | 2102240 | p.Arg268His | missense_variant | 0.2 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2168279 | c.2334G>T | synonymous_variant | 0.12 |
PPE35 | 2168742 | p.Gly624Asp | missense_variant | 0.21 |
PPE35 | 2170048 | p.Leu189Val | missense_variant | 0.58 |
PPE35 | 2170053 | p.Thr187Ser | missense_variant | 0.56 |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 0.27 |
Rv1979c | 2222936 | p.Ala77Ser | missense_variant | 0.12 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 0.28 |
thyX | 3067467 | p.Ala160Val | missense_variant | 0.91 |
thyX | 3068145 | c.-200C>A | upstream_gene_variant | 0.66 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3475159 | p.Asn385Asp | missense_variant | 0.22 |
fprA | 3475375 | c.1360_1361insGA | frameshift_variant | 0.15 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.68 |
clpC1 | 4040517 | p.Val63Ala | missense_variant | 0.12 |
clpC1 | 4040719 | c.-15A>G | upstream_gene_variant | 0.25 |
embC | 4241042 | p.Asn394Asp | missense_variant | 0.17 |
embC | 4241551 | c.1689A>G | synonymous_variant | 0.2 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243218 | c.-15C>G | upstream_gene_variant | 0.15 |
embA | 4243460 | c.228C>T | synonymous_variant | 0.66 |
embA | 4245969 | p.Pro913Ser | missense_variant | 0.3 |
embB | 4246544 | p.Thr11Pro | missense_variant | 0.2 |
embB | 4246555 | c.42G>C | synonymous_variant | 0.17 |
embB | 4246556 | p.Ala15Pro | missense_variant | 0.17 |
embB | 4246563 | p.Leu17Trp | missense_variant | 0.12 |
embB | 4246567 | c.54G>T | synonymous_variant | 0.12 |
embB | 4247496 | c.984delT | frameshift_variant | 0.11 |
embB | 4247646 | p.Glu378Ala | missense_variant | 0.2 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.7 |
aftB | 4267960 | p.Val293Met | missense_variant | 0.15 |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 0.23 |
aftB | 4269606 | c.-770T>C | upstream_gene_variant | 0.13 |
ethA | 4326148 | c.1326G>T | synonymous_variant | 0.16 |
ethA | 4326439 | p.Asn345Lys | missense_variant | 0.2 |
ethR | 4327617 | p.Asp23Glu | missense_variant | 0.16 |
whiB6 | 4338203 | p.Arg107Cys | missense_variant | 0.25 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
whiB6 | 4338603 | c.-82C>T | upstream_gene_variant | 0.22 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407873 | c.330G>T | synonymous_variant | 0.12 |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.79 |