Run ID: SRR11972248
Sample name:
Date: 03-04-2023 05:33:27
Number of reads: 293848
Percentage reads mapped: 99.37
Strain: lineage2.2.1.1
Drug-resistance: HR-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 |
lineage2.2.1.1 | East-Asian (Beijing) | Beijing-RD150 | RD105;RD207;RD181;RD150 | 0.99 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7315 | p.Thr5Met | missense_variant | 0.17 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 8657 | c.1356C>A | synonymous_variant | 0.2 |
gyrA | 8699 | c.1398A>G | synonymous_variant | 0.25 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
gyrA | 9702 | p.Val801Ile | missense_variant | 0.22 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 575340 | c.-8C>T | upstream_gene_variant | 0.22 |
mshA | 575907 | p.Ala187Val | missense_variant | 1.0 |
mshA | 576359 | p.Thr338Ala | missense_variant | 0.18 |
ccsA | 620015 | p.Arg42His | missense_variant | 0.22 |
ccsA | 620439 | c.553delG | frameshift_variant | 0.17 |
ccsA | 620625 | p.Ile245Met | missense_variant | 1.0 |
rpoB | 760154 | c.348C>T | synonymous_variant | 0.4 |
rpoB | 760166 | c.360C>T | synonymous_variant | 0.17 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 764704 | c.1335G>A | synonymous_variant | 0.2 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 775834 | p.Ala883Thr | missense_variant | 0.17 |
mmpL5 | 775994 | c.2487C>A | synonymous_variant | 0.33 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 1.0 |
mmpL5 | 776621 | c.1860G>A | synonymous_variant | 0.14 |
mmpL5 | 777318 | p.Arg388His | missense_variant | 0.25 |
mmpL5 | 778831 | c.-351G>T | upstream_gene_variant | 0.18 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rplC | 801154 | p.Gly116Cys | missense_variant | 0.25 |
fbiC | 1303396 | p.Arg156Gly | missense_variant | 0.15 |
fbiC | 1304516 | p.Ala529Val | missense_variant | 0.17 |
Rv1258c | 1406565 | p.Gln259Arg | missense_variant | 0.13 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 1.0 |
embR | 1416745 | c.603C>T | synonymous_variant | 0.15 |
embR | 1417426 | c.-79T>C | upstream_gene_variant | 0.12 |
atpE | 1460935 | c.-110T>C | upstream_gene_variant | 0.1 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472784 | n.939A>G | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472882 | n.1037A>T | non_coding_transcript_exon_variant | 0.12 |
rrl | 1473619 | n.-39G>A | upstream_gene_variant | 0.13 |
rrl | 1473899 | n.242A>G | non_coding_transcript_exon_variant | 0.17 |
rrl | 1474553 | n.896T>C | non_coding_transcript_exon_variant | 1.0 |
rrl | 1475339 | n.1682T>A | non_coding_transcript_exon_variant | 0.14 |
fabG1 | 1673537 | p.Gln33Arg | missense_variant | 0.2 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
ndh | 2102594 | p.Arg150His | missense_variant | 0.2 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2168140 | p.Ala825Thr | missense_variant | 0.13 |
PPE35 | 2169503 | c.1109delG | frameshift_variant | 0.14 |
PPE35 | 2169652 | p.Leu321Ile | missense_variant | 0.22 |
PPE35 | 2169797 | c.816G>T | synonymous_variant | 0.17 |
Rv1979c | 2221961 | p.Val402Leu | missense_variant | 0.12 |
Rv1979c | 2222842 | c.322delG | frameshift_variant | 0.13 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289660 | c.-419G>A | upstream_gene_variant | 0.22 |
kasA | 2518088 | c.-27T>C | upstream_gene_variant | 0.29 |
kasA | 2518744 | c.630C>T | synonymous_variant | 0.15 |
kasA | 2518919 | p.Gly269Ser | missense_variant | 0.2 |
eis | 2714846 | p.Val163Ile | missense_variant | 1.0 |
ribD | 2986729 | c.-110G>A | upstream_gene_variant | 0.25 |
Rv2752c | 3065074 | p.Ser373Phe | missense_variant | 0.22 |
Rv2752c | 3066053 | p.Val47Met | missense_variant | 0.18 |
Rv2752c | 3066069 | p.Leu41Phe | missense_variant | 0.29 |
thyA | 3074438 | p.Leu12Phe | missense_variant | 0.17 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fbiD | 3339471 | c.354G>A | synonymous_variant | 0.25 |
Rv3083 | 3448622 | p.Arg40His | missense_variant | 0.2 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612360 | p.Gly253Arg | missense_variant | 0.25 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 |
alr | 3840824 | c.597C>T | synonymous_variant | 0.12 |
alr | 3841546 | c.-126C>A | upstream_gene_variant | 0.25 |
rpoA | 3877611 | p.Ile299Met | missense_variant | 0.13 |
rpoA | 3878039 | p.Ala157Ser | missense_variant | 0.18 |
clpC1 | 4039441 | p.Arg422Ser | missense_variant | 0.15 |
clpC1 | 4039473 | p.Arg411Pro | missense_variant | 0.2 |
embC | 4240242 | p.Asn127Ser | missense_variant | 0.11 |
embC | 4241125 | c.1263G>A | synonymous_variant | 0.18 |
embC | 4242492 | p.Arg877Gln | missense_variant | 0.2 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embC | 4242944 | p.Asn1028Asp | missense_variant | 0.1 |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
embB | 4248115 | c.1602C>T | synonymous_variant | 0.98 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 |
aftB | 4269270 | c.-434G>A | upstream_gene_variant | 0.33 |
ethA | 4327142 | p.Thr111Ile | missense_variant | 0.2 |
whiB6 | 4338278 | p.Pro82Ser | missense_variant | 0.14 |
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 |