Run ID: SRR1180179
Sample name:
Date: 03-04-2023 03:53:18
Number of reads: 2846039
Percentage reads mapped: 87.01
Strain: lineage3
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage3 | East-African-Indian | CAS | RD750 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrB | 6741 | p.Glu501Val | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Trp | missense_variant | 1.0 | rifampicin |
rrs | 1472359 | n.514A>C | non_coding_transcript_exon_variant | 0.95 | streptomycin |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 0.87 | kanamycin, capreomycin, aminoglycosides, amikacin |
rrs | 1473247 | n.1402C>A | non_coding_transcript_exon_variant | 0.11 | kanamycin, capreomycin, aminoglycosides, amikacin |
katG | 2156093 | c.18dupA | frameshift_variant | 1.0 | isoniazid |
pncA | 2288790 | c.450_451dupCT | frameshift_variant | 0.97 | pyrazinamide |
ald | 3087252 | c.436_437dupGC | frameshift_variant | 0.28 | cycloserine |
embB | 4247431 | p.Met306Ile | missense_variant | 1.0 | ethambutol |
ethA | 4326980 | p.Gln165Pro | missense_variant | 0.99 | ethionamide |
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 |
mshA | 576161 | p.Gly272Arg | missense_variant | 0.27 |
mshA | 576217 | c.873dupC | frameshift_variant | 0.13 |
rpoB | 759746 | c.-61C>T | upstream_gene_variant | 1.0 |
rpoB | 761963 | c.2157G>C | synonymous_variant | 0.11 |
rpoB | 761974 | p.His723Leu | missense_variant | 0.11 |
rpoB | 762003 | p.Asn733Gln | missense_variant | 0.12 |
rpoB | 762009 | p.Leu735Met | missense_variant | 0.11 |
rpoB | 762015 | p.Glu737Ser | missense_variant | 0.12 |
rpoB | 762026 | c.2220G>C | synonymous_variant | 0.15 |
rpoB | 762053 | c.2247T>C | synonymous_variant | 0.15 |
rpoB | 762057 | p.Ile751Val | missense_variant | 0.12 |
rpoC | 762434 | c.-936T>G | upstream_gene_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 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472150 | n.305T>A | non_coding_transcript_exon_variant | 0.2 |
rrs | 1472160 | n.315C>T | non_coding_transcript_exon_variant | 0.11 |
rrs | 1472172 | n.327T>C | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472581 | n.736A>T | non_coding_transcript_exon_variant | 0.13 |
rrs | 1472990 | n.1145A>G | non_coding_transcript_exon_variant | 0.1 |
rrs | 1473145 | n.1300C>T | non_coding_transcript_exon_variant | 0.12 |
rrs | 1473166 | n.1321G>A | non_coding_transcript_exon_variant | 0.12 |
rrs | 1473252 | n.1407T>C | non_coding_transcript_exon_variant | 0.11 |
rrl | 1474498 | n.841G>T | non_coding_transcript_exon_variant | 0.12 |
rrl | 1474505 | n.848C>G | non_coding_transcript_exon_variant | 0.12 |
rrl | 1474516 | n.859C>A | non_coding_transcript_exon_variant | 0.16 |
rrl | 1474529 | n.872A>C | non_coding_transcript_exon_variant | 0.15 |
rrl | 1474530 | n.873G>A | non_coding_transcript_exon_variant | 0.15 |
rrl | 1474537 | n.880G>A | non_coding_transcript_exon_variant | 0.18 |
rrl | 1474539 | n.882C>T | non_coding_transcript_exon_variant | 0.14 |
rrl | 1474540 | n.883T>G | non_coding_transcript_exon_variant | 0.15 |
rrl | 1474626 | n.969T>C | non_coding_transcript_exon_variant | 0.13 |
rrl | 1474627 | n.970G>A | non_coding_transcript_exon_variant | 0.15 |
rrl | 1474632 | n.975G>T | non_coding_transcript_exon_variant | 0.15 |
rrl | 1474636 | n.979A>T | non_coding_transcript_exon_variant | 0.14 |
rrl | 1474637 | n.980C>T | non_coding_transcript_exon_variant | 0.16 |
rrl | 1474639 | n.982G>C | non_coding_transcript_exon_variant | 0.15 |
rrl | 1474784 | n.1127C>T | non_coding_transcript_exon_variant | 0.14 |
rrl | 1474794 | n.1137C>T | non_coding_transcript_exon_variant | 0.2 |
rrl | 1474823 | n.1166C>G | non_coding_transcript_exon_variant | 0.2 |
rrl | 1474827 | n.1170C>T | non_coding_transcript_exon_variant | 0.13 |
rrl | 1474830 | n.1173A>T | non_coding_transcript_exon_variant | 0.13 |
rrl | 1474831 | n.1174A>G | non_coding_transcript_exon_variant | 0.14 |
rrl | 1474904 | n.1247G>C | non_coding_transcript_exon_variant | 0.15 |
rrl | 1474905 | n.1248T>C | non_coding_transcript_exon_variant | 0.12 |
rrl | 1474913 | n.1256T>C | non_coding_transcript_exon_variant | 0.14 |
rrl | 1475626 | n.1969T>G | non_coding_transcript_exon_variant | 0.41 |
rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.16 |
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.12 |
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 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289047 | c.195C>T | synonymous_variant | 0.98 |
pncA | 2289365 | c.-125delC | upstream_gene_variant | 1.0 |
ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 0.99 |
ahpC | 2726116 | c.-77T>G | upstream_gene_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
ald | 3087794 | c.976_977dupGA | frameshift_variant | 0.17 |
ald | 3087892 | c.1074_1077dupCCTG | frameshift_variant | 0.37 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
alr | 3841473 | c.-53G>A | upstream_gene_variant | 1.0 |
clpC1 | 4038845 | c.1860G>C | synonymous_variant | 0.11 |
clpC1 | 4038854 | p.Lys617Arg | missense_variant | 0.12 |
clpC1 | 4038860 | c.1845G>C | synonymous_variant | 0.25 |
clpC1 | 4038863 | c.1842G>C | synonymous_variant | 0.22 |
clpC1 | 4038878 | c.1827A>G | synonymous_variant | 0.25 |
clpC1 | 4038899 | c.1806C>G | synonymous_variant | 0.2 |
clpC1 | 4038905 | c.1800A>C | synonymous_variant | 0.17 |
clpC1 | 4038911 | c.1794G>T | synonymous_variant | 0.12 |
embC | 4240221 | c.368_370dupTGC | disruptive_inframe_insertion | 0.16 |
embC | 4242075 | p.Arg738Gln | missense_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
ubiA | 4269718 | p.Ala39Glu | missense_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |