Run ID: SRR1048852
Sample name:
Date: 02-04-2023 17:48:16
Number of reads: 162676
Percentage reads mapped: 5.74
Strain: lineage4.9
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage4.9 | Euro-American (H37Rv-like) | T1 | None | 0.77 |
lineage2.2.2 | East-Asian (Beijing) | Beijing-RD105/RD207 | RD105;RD207 | 0.32 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrB | 6579 | p.Ser447Phe | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.5 | rifampicin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
katG | 2155693 | p.Ser140Asn | missense_variant | 0.9 | isoniazid |
pncA | 2288839 | p.Thr135Pro | missense_variant | 1.0 | pyrazinamide |
thyX | 3067961 | c.-16C>T | upstream_gene_variant | 1.0 | para-aminosalicylic_acid |
embB | 4248003 | p.Gln497Arg | missense_variant | 1.0 | ethambutol |
ethA | 4326643 | c.820_830delGAGGGGTACGA | frameshift_variant | 1.0 | ethionamide |
gid | 4408100 | c.102delG | frameshift_variant | 1.0 | streptomycin |
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 |
rpoB | 762699 | p.Ile965Val | missense_variant | 0.22 |
rpoB | 762881 | p.Met1025Ile | missense_variant | 0.43 |
rpoC | 762893 | c.-477C>T | upstream_gene_variant | 0.5 |
rpoC | 762896 | c.-474G>C | upstream_gene_variant | 0.5 |
rpoC | 762917 | c.-453C>G | upstream_gene_variant | 0.62 |
rpoC | 762920 | c.-450C>T | upstream_gene_variant | 0.62 |
rpoC | 762923 | c.-447C>G | upstream_gene_variant | 0.62 |
rpoB | 762925 | p.Thr1040Ile | missense_variant | 0.62 |
rpoC | 762929 | c.-441G>T | upstream_gene_variant | 0.59 |
rpoB | 762939 | p.Met1045Leu | missense_variant | 0.59 |
rpoB | 762942 | p.Ile1046Val | missense_variant | 0.59 |
rpoC | 762965 | c.-405T>C | upstream_gene_variant | 0.64 |
rpoC | 762980 | c.-390T>C | upstream_gene_variant | 0.54 |
rpoC | 762989 | c.-381G>C | upstream_gene_variant | 0.5 |
rpoC | 762995 | c.-375G>C | upstream_gene_variant | 0.43 |
rpoC | 762998 | c.-372G>A | upstream_gene_variant | 0.43 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 764329 | c.960C>T | synonymous_variant | 0.43 |
rpoC | 764338 | p.Glu323Asp | missense_variant | 0.56 |
rpoC | 764344 | c.975C>T | synonymous_variant | 0.62 |
rpoC | 764348 | p.Met327Leu | missense_variant | 0.62 |
rpoC | 764355 | p.Gln329Pro | missense_variant | 0.67 |
rpoC | 764377 | c.1008C>G | synonymous_variant | 0.75 |
rpoC | 764380 | c.1011G>C | synonymous_variant | 0.75 |
rpoC | 764383 | c.1014C>G | synonymous_variant | 0.75 |
rpoC | 764387 | c.1018_1020delTTGinsCTC | synonymous_variant | 0.75 |
rpoC | 764398 | c.1029G>C | synonymous_variant | 0.67 |
rpoC | 764405 | c.1036_1038delAGGinsCGC | synonymous_variant | 0.75 |
rpoC | 764410 | c.1041G>T | synonymous_variant | 0.75 |
rpoC | 764428 | c.1059G>T | synonymous_variant | 0.57 |
rpoC | 764723 | p.Phe452Leu | missense_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 779254 | c.-774G>T | upstream_gene_variant | 0.33 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 1.0 |
rrs | 1472160 | n.315C>T | non_coding_transcript_exon_variant | 1.0 |
rrs | 1472172 | n.327T>C | non_coding_transcript_exon_variant | 1.0 |
rrs | 1472181 | n.336G>A | non_coding_transcript_exon_variant | 0.85 |
rrs | 1472214 | n.369C>G | non_coding_transcript_exon_variant | 0.72 |
rrs | 1472235 | n.390G>C | non_coding_transcript_exon_variant | 0.72 |
rrs | 1472240 | n.395G>C | non_coding_transcript_exon_variant | 0.78 |
rrs | 1472242 | n.397C>T | non_coding_transcript_exon_variant | 0.78 |
rrs | 1472251 | n.406G>A | non_coding_transcript_exon_variant | 0.69 |
rrs | 1472253 | n.408G>T | non_coding_transcript_exon_variant | 0.67 |
rrs | 1472259 | n.414C>A | non_coding_transcript_exon_variant | 0.64 |
rrs | 1472264 | n.419T>C | non_coding_transcript_exon_variant | 0.54 |
rrs | 1472266 | n.421C>A | non_coding_transcript_exon_variant | 0.54 |
rrs | 1472277 | n.432C>G | non_coding_transcript_exon_variant | 0.44 |
rrs | 1472557 | n.712G>A | non_coding_transcript_exon_variant | 0.33 |
rrs | 1472571 | n.726G>C | non_coding_transcript_exon_variant | 0.4 |
rrs | 1472574 | n.729T>A | non_coding_transcript_exon_variant | 0.4 |
rrs | 1472579 | n.734G>C | non_coding_transcript_exon_variant | 0.4 |
rrs | 1472581 | n.736A>C | non_coding_transcript_exon_variant | 0.5 |
rrs | 1472583 | n.738T>A | non_coding_transcript_exon_variant | 0.5 |
rrs | 1472584 | n.739A>T | non_coding_transcript_exon_variant | 0.5 |
rrs | 1472598 | n.753A>C | non_coding_transcript_exon_variant | 0.5 |
rrs | 1472599 | n.754G>A | non_coding_transcript_exon_variant | 0.5 |
rrs | 1472616 | n.771G>A | non_coding_transcript_exon_variant | 0.4 |
rrs | 1472734 | n.889C>T | non_coding_transcript_exon_variant | 0.43 |
rrs | 1472741 | n.896G>A | non_coding_transcript_exon_variant | 0.43 |
rrs | 1472742 | n.897C>T | non_coding_transcript_exon_variant | 0.43 |
rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.44 |
rrs | 1472793 | n.948A>T | non_coding_transcript_exon_variant | 0.4 |
rrs | 1472803 | n.958T>C | non_coding_transcript_exon_variant | 0.38 |
rrs | 1472812 | n.967A>C | non_coding_transcript_exon_variant | 0.6 |
rrs | 1473145 | n.1300C>T | non_coding_transcript_exon_variant | 0.57 |
rrs | 1473149 | n.1304G>C | non_coding_transcript_exon_variant | 0.57 |
rrs | 1473162 | n.1317C>G | non_coding_transcript_exon_variant | 0.62 |
rrs | 1473166 | n.1321G>A | non_coding_transcript_exon_variant | 0.62 |
rrs | 1473173 | n.1328C>T | non_coding_transcript_exon_variant | 0.62 |
rrs | 1473177 | n.1332G>A | non_coding_transcript_exon_variant | 0.62 |
rrs | 1473191 | n.1346C>T | non_coding_transcript_exon_variant | 0.56 |
rrs | 1473192 | n.1347A>G | non_coding_transcript_exon_variant | 0.56 |
rrs | 1473199 | n.1356delA | non_coding_transcript_exon_variant | 0.56 |
rrs | 1473205 | n.1360T>C | non_coding_transcript_exon_variant | 0.56 |
rrs | 1473206 | n.1361G>A | non_coding_transcript_exon_variant | 0.56 |
rrl | 1475791 | n.2134A>G | non_coding_transcript_exon_variant | 0.6 |
rrl | 1475803 | n.2146T>C | non_coding_transcript_exon_variant | 0.57 |
rrl | 1475804 | n.2147G>C | non_coding_transcript_exon_variant | 0.57 |
rrl | 1475816 | n.2159C>G | non_coding_transcript_exon_variant | 0.71 |
rrl | 1475817 | n.2160A>G | non_coding_transcript_exon_variant | 0.71 |
rrl | 1475874 | n.2217C>T | non_coding_transcript_exon_variant | 0.75 |
rrl | 1475881 | n.2224T>C | non_coding_transcript_exon_variant | 0.6 |
rrl | 1475883 | n.2226A>C | non_coding_transcript_exon_variant | 0.6 |
rrl | 1475884 | n.2227A>G | non_coding_transcript_exon_variant | 0.6 |
rrl | 1475892 | n.2235A>C | non_coding_transcript_exon_variant | 0.5 |
rrl | 1475894 | n.2237C>A | non_coding_transcript_exon_variant | 0.67 |
rrl | 1476336 | n.2679C>G | non_coding_transcript_exon_variant | 0.9 |
rrl | 1476356 | n.2699C>G | non_coding_transcript_exon_variant | 0.92 |
rrl | 1476357 | n.2700T>A | non_coding_transcript_exon_variant | 0.92 |
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.92 |
rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.92 |
rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.9 |
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.9 |
rrl | 1476384 | n.2727G>C | non_coding_transcript_exon_variant | 0.91 |
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.89 |
rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.89 |
rrl | 1476428 | n.2771C>A | non_coding_transcript_exon_variant | 0.83 |
rrl | 1476443 | n.2786G>C | non_coding_transcript_exon_variant | 0.81 |
rrl | 1476455 | n.2798C>G | non_coding_transcript_exon_variant | 0.76 |
rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.75 |
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.75 |
rrl | 1476470 | n.2813C>T | non_coding_transcript_exon_variant | 0.73 |
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.69 |
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.4 |
rpsA | 1833909 | p.Asp123Ala | missense_variant | 1.0 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 1.0 |
rpsA | 1834972 | c.1431C>T | synonymous_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
katG | 2155600 | p.Cys171Val | missense_variant | 0.67 |
katG | 2155613 | p.Phe167Leu | missense_variant | 0.71 |
katG | 2155614 | c.498T>C | synonymous_variant | 0.75 |
katG | 2155617 | p.Ile165Met | missense_variant | 0.75 |
katG | 2155626 | c.486G>C | synonymous_variant | 0.82 |
katG | 2155637 | p.Leu159Ile | missense_variant | 0.88 |
katG | 2155641 | p.Lys157Arg | missense_variant | 0.94 |
katG | 2155650 | c.462G>A | synonymous_variant | 0.94 |
katG | 2155655 | p.Lys153Gln | missense_variant | 0.94 |
katG | 2155661 | p.Val151Ile | missense_variant | 0.95 |
katG | 2155668 | c.444G>C | synonymous_variant | 0.95 |
katG | 2155689 | c.421_423delTTGinsCTC | synonymous_variant | 0.91 |
katG | 2155704 | c.408C>T | synonymous_variant | 0.9 |
katG | 2155716 | c.396T>C | synonymous_variant | 0.82 |
katG | 2155722 | c.390G>C | synonymous_variant | 0.78 |
katG | 2155728 | c.384G>C | synonymous_variant | 0.78 |
katG | 2155735 | p.Met126Gln | missense_variant | 0.67 |
katG | 2155737 | c.375C>T | synonymous_variant | 0.67 |
katG | 2155741 | p.Gly124Ala | missense_variant | 0.67 |
katG | 2155743 | c.369G>T | synonymous_variant | 0.67 |
katG | 2155765 | p.His116Thr | missense_variant | 0.38 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2518736 | p.Ala208Thr | missense_variant | 1.0 |
thyA | 3073979 | p.Gln165* | stop_gained | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474569 | p.Pro188Gln | missense_variant | 0.5 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 |
embC | 4241465 | p.Phe535Leu | missense_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
aftB | 4267647 | p.Asp397Gly | 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 |