Run ID: SRR13423553
Sample name:
Date: 03-04-2023 08:52:06
Number of reads: 2849331
Percentage reads mapped: 68.72
Strain: lineage2.2.1
Drug-resistance: Pre-XDR-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 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7582 | p.Asp94Gly | missense_variant | 0.96 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761095 | p.Leu430Pro | missense_variant | 0.97 | rifampicin |
rpoB | 761097 | p.Ser431Gly | missense_variant | 1.0 | rifampicin |
rpoB | 761110 | p.Asp435Gly | missense_variant | 0.97 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 1.0 | kanamycin, capreomycin, aminoglycosides, amikacin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2288719 | p.Met175Val | missense_variant | 1.0 | pyrazinamide |
embA | 4243221 | c.-12C>T | upstream_gene_variant | 0.95 | ethambutol |
embB | 4249518 | p.His1002Arg | missense_variant | 1.0 | ethambutol |
ethA | 4327347 | p.Gly43Ser | missense_variant | 1.0 | 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 |
ccsA | 620625 | p.Ile245Met | missense_variant | 1.0 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 766318 | p.Met983Ile | missense_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 1.0 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472975 | n.1130T>G | non_coding_transcript_exon_variant | 0.1 |
rrs | 1472977 | n.1132G>C | non_coding_transcript_exon_variant | 0.1 |
rrs | 1472982 | n.1137G>C | non_coding_transcript_exon_variant | 0.1 |
rrs | 1472991 | n.1146G>A | non_coding_transcript_exon_variant | 0.11 |
rrs | 1473004 | n.1159T>A | non_coding_transcript_exon_variant | 0.12 |
rrs | 1473008 | n.1163C>A | non_coding_transcript_exon_variant | 0.12 |
rrs | 1473009 | n.1164T>C | non_coding_transcript_exon_variant | 0.12 |
rrs | 1473020 | n.1175T>C | non_coding_transcript_exon_variant | 0.12 |
rrs | 1473035 | n.1190G>A | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476251 | n.2594T>C | non_coding_transcript_exon_variant | 0.1 |
rrl | 1476260 | n.2603A>G | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476280 | n.2623A>C | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476293 | n.2636C>T | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476294 | n.2637A>G | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476295 | n.2638C>G | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476296 | n.2639C>T | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476297 | n.2640C>A | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476301 | n.2644A>C | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476302 | n.2645G>A | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476311 | n.2654G>C | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476312 | n.2655T>C | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476313 | n.2656G>A | non_coding_transcript_exon_variant | 0.15 |
rrl | 1476332 | n.2675G>C | non_coding_transcript_exon_variant | 0.18 |
rrl | 1476338 | n.2681C>T | non_coding_transcript_exon_variant | 0.21 |
rrl | 1476353 | n.2696G>T | non_coding_transcript_exon_variant | 0.3 |
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.36 |
rrl | 1476372 | n.2715T>C | non_coding_transcript_exon_variant | 0.46 |
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.42 |
rrl | 1476383 | n.2726T>A | non_coding_transcript_exon_variant | 0.42 |
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.37 |
rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.42 |
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.42 |
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.52 |
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.54 |
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.45 |
rrl | 1476512 | n.2855C>T | non_coding_transcript_exon_variant | 0.31 |
rrl | 1476514 | n.2857C>T | non_coding_transcript_exon_variant | 0.31 |
rrl | 1476517 | n.2860C>T | non_coding_transcript_exon_variant | 0.31 |
rrl | 1476519 | n.2862C>G | non_coding_transcript_exon_variant | 0.31 |
rrl | 1476524 | n.2867C>A | non_coding_transcript_exon_variant | 0.29 |
rrl | 1476525 | n.2868A>G | non_coding_transcript_exon_variant | 0.29 |
rrl | 1476530 | n.2873C>T | non_coding_transcript_exon_variant | 0.28 |
rrl | 1476536 | n.2879G>A | non_coding_transcript_exon_variant | 0.28 |
rrl | 1476537 | n.2880A>G | non_coding_transcript_exon_variant | 0.28 |
rrl | 1476538 | n.2881A>G | non_coding_transcript_exon_variant | 0.28 |
rrl | 1476540 | n.2883C>G | non_coding_transcript_exon_variant | 0.26 |
rrl | 1476547 | n.2890C>T | non_coding_transcript_exon_variant | 0.26 |
rrl | 1476567 | n.2910C>T | non_coding_transcript_exon_variant | 0.35 |
rrl | 1476573 | n.2916A>T | non_coding_transcript_exon_variant | 0.25 |
rrl | 1476577 | n.2920T>G | non_coding_transcript_exon_variant | 0.21 |
rrl | 1476594 | n.2937C>T | non_coding_transcript_exon_variant | 0.14 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
ndh | 2103157 | c.-115G>T | upstream_gene_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
Rv1979c | 2221889 | p.Val426Ile | missense_variant | 0.99 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
ald | 3087160 | p.Ser114Leu | missense_variant | 0.33 |
ald | 3087351 | p.Thr178Gly | missense_variant | 0.28 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 |
fbiA | 3641104 | p.Val188Ile | missense_variant | 0.95 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
embA | 4246085 | p.Glu951Asp | missense_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 | 0.98 |
mshA | 573653 | c.-1694_874del | frameshift_variant&start_lost | 1.0 |