Run ID: SRR6896565
Sample name:
Date: 04-04-2023 18:10:02
Number of reads: 478019
Percentage reads mapped: 99.43
Strain: lineage3.1.1
Drug-resistance: HR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage3 | East-African-Indian | CAS | RD750 | 1.0 |
lineage3.1 | East-African-Indian | Non-CAS1-Delhi | RD750 | 1.0 |
lineage3.1.1 | East-African-Indian | CAS1-Kili | RD750 | 0.99 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
katG | 2154733 | c.1378dupA | frameshift_variant | 0.11 | isoniazid |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
rpoB | 759697 | c.-110A>T | upstream_gene_variant | 0.15 |
rpoB | 759746 | c.-61C>T | upstream_gene_variant | 1.0 |
rpoC | 762434 | c.-936T>G | upstream_gene_variant | 1.0 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 766983 | p.Pro1205Gln | missense_variant | 0.11 |
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 | 1305310 | p.Arg794Trp | missense_variant | 0.11 |
fbiC | 1305494 | c.2565_*55delGGCCTAGCCCCGGCGACGATGCCGGGTCGCGGGATGCGGCCCGTTGAGGAGCGGGGCAATCT | frameshift_variant&stop_lost&splice_region_variant | 0.57 |
Rv1258c | 1406956 | p.Pro129Ala | missense_variant | 0.12 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472946 | n.1101A>T | non_coding_transcript_exon_variant | 0.11 |
rrl | 1473488 | n.-170A>G | upstream_gene_variant | 0.11 |
rrl | 1473608 | n.-50G>C | upstream_gene_variant | 0.13 |
rrl | 1473736 | n.83dupG | non_coding_transcript_exon_variant | 0.18 |
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 | 2168644 | p.Phe657Leu | missense_variant | 1.0 |
PPE35 | 2169850 | p.Asn255Asp | missense_variant | 0.15 |
PPE35 | 2170461 | p.Gly51Glu | missense_variant | 1.0 |
Rv1979c | 2222360 | c.804delG | frameshift_variant | 0.1 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289047 | c.195C>T | synonymous_variant | 1.0 |
pncA | 2289365 | c.-125delC | upstream_gene_variant | 1.0 |
pncA | 2289396 | c.-155T>G | upstream_gene_variant | 0.22 |
kasA | 2519315 | p.Ser401Pro | missense_variant | 0.13 |
ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 1.0 |
ahpC | 2726352 | p.Pro54Ser | missense_variant | 0.1 |
pepQ | 2859539 | c.880C>T | synonymous_variant | 0.12 |
Rv2752c | 3064781 | c.1408_1410delTCG | conservative_inframe_deletion | 0.12 |
Rv2752c | 3064866 | c.1326G>T | synonymous_variant | 0.12 |
thyA | 3074026 | p.Phe149Ser | missense_variant | 0.12 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.94 |
Rv3083 | 3448846 | p.Arg115Ser | missense_variant | 0.12 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474224 | p.Asp73Val | missense_variant | 0.1 |
fbiB | 3642483 | p.Trp317Arg | missense_variant | 0.22 |
rpoA | 3878471 | p.Val13Ile | missense_variant | 0.13 |
ddn | 3987034 | p.Leu64His | missense_variant | 0.15 |
clpC1 | 4038713 | c.1992T>C | synonymous_variant | 0.1 |
clpC1 | 4040506 | p.Ile67Leu | missense_variant | 0.11 |
embC | 4240172 | p.Val104Met | missense_variant | 1.0 |
embC | 4241562 | p.Arg567His | missense_variant | 0.91 |
embC | 4242075 | p.Arg738Gln | missense_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4245862 | p.Ile877Asn | missense_variant | 0.14 |
embB | 4246082 | c.-432T>G | upstream_gene_variant | 0.15 |
embB | 4246801 | c.288G>A | synonymous_variant | 0.12 |
ubiA | 4269128 | p.Trp236Arg | missense_variant | 0.14 |
ubiA | 4269820 | p.Val5Glu | missense_variant | 0.1 |
ubiA | 4269848 | c.-15A>G | upstream_gene_variant | 0.12 |
ethA | 4327220 | p.Val85Asp | missense_variant | 0.12 |
ethA | 4327411 | p.Trp21Cys | missense_variant | 0.12 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
fbiC | 1305494 | c.2565_*56delCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | frameshift_variant&stop_lost&splice_region_variant | 1.0 |