Run ID: SRR5152936
Sample name:
Date: 04-04-2023 09:12:13
Number of reads: 8854307
Percentage reads mapped: 82.11
Strain: lineage2.2.1
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage2 | East-Asian | Beijing | RD105 | 1.0 |
lineage2.2 | East-Asian (Beijing) | Beijing-RD207 | RD105;RD207 | 1.0 |
lineage2.2.1 | East-Asian (Beijing) | Beijing-RD181 | RD105;RD207;RD181 | 0.99 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin |
rrs | 1472733 | n.888G>A | non_coding_transcript_exon_variant | 0.21 | streptomycin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2288703 | p.Val180Ala | missense_variant | 1.0 | pyrazinamide |
embB | 4247431 | p.Met306Ile | missense_variant | 0.99 | ethambutol |
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 | 575907 | p.Ala187Val | missense_variant | 1.0 |
ccsA | 620625 | p.Ile245Met | missense_variant | 1.0 |
rpoB | 761998 | p.Leu731Pro | missense_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 |
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 | 1472537 | n.692C>T | non_coding_transcript_exon_variant | 0.14 |
rrs | 1472544 | n.699C>T | non_coding_transcript_exon_variant | 0.13 |
rrs | 1472545 | n.700A>T | non_coding_transcript_exon_variant | 0.13 |
rrs | 1472557 | n.712G>A | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472570 | n.725G>A | non_coding_transcript_exon_variant | 0.13 |
rrs | 1472571 | n.726G>T | non_coding_transcript_exon_variant | 0.13 |
rrs | 1472573 | n.728C>T | non_coding_transcript_exon_variant | 0.13 |
rrs | 1472579 | n.734G>T | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472586 | n.741_742insAT | non_coding_transcript_exon_variant | 0.14 |
rrs | 1472598 | n.753A>C | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472599 | n.754G>T | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472728 | n.883G>T | non_coding_transcript_exon_variant | 0.21 |
rrs | 1472742 | n.897C>T | non_coding_transcript_exon_variant | 0.21 |
rrs | 1472744 | n.899A>G | non_coding_transcript_exon_variant | 0.2 |
rrs | 1472754 | n.909G>A | non_coding_transcript_exon_variant | 0.2 |
rrs | 1472767 | n.922G>A | non_coding_transcript_exon_variant | 0.2 |
rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.19 |
rrs | 1472793 | n.948A>T | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472803 | n.958T>A | non_coding_transcript_exon_variant | 0.16 |
rrl | 1475783 | n.2126T>G | non_coding_transcript_exon_variant | 0.12 |
rrl | 1475803 | n.2146T>C | non_coding_transcript_exon_variant | 0.11 |
rrl | 1475804 | n.2147G>C | non_coding_transcript_exon_variant | 0.11 |
rrl | 1475816 | n.2159C>G | non_coding_transcript_exon_variant | 0.11 |
rrl | 1475817 | n.2160A>G | non_coding_transcript_exon_variant | 0.11 |
rrl | 1475858 | n.2201T>C | non_coding_transcript_exon_variant | 0.11 |
rrl | 1475866 | n.2209T>A | non_coding_transcript_exon_variant | 0.11 |
rrl | 1475869 | n.2212C>T | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476332 | n.2675G>C | non_coding_transcript_exon_variant | 0.15 |
rrl | 1476338 | n.2681C>T | non_coding_transcript_exon_variant | 0.2 |
rrl | 1476353 | n.2696G>T | non_coding_transcript_exon_variant | 0.34 |
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.34 |
rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.37 |
rrl | 1476372 | n.2715T>C | non_coding_transcript_exon_variant | 0.37 |
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.41 |
rrl | 1476383 | n.2726T>A | non_coding_transcript_exon_variant | 0.41 |
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.48 |
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.51 |
rrl | 1476429 | n.2772A>T | non_coding_transcript_exon_variant | 0.51 |
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.39 |
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.4 |
rrl | 1476514 | n.2857C>T | non_coding_transcript_exon_variant | 0.27 |
rrl | 1476519 | n.2862C>G | non_coding_transcript_exon_variant | 0.25 |
rrl | 1476524 | n.2867C>T | non_coding_transcript_exon_variant | 0.21 |
rrl | 1476525 | n.2868A>G | non_coding_transcript_exon_variant | 0.19 |
rrl | 1476530 | n.2873C>T | non_coding_transcript_exon_variant | 0.2 |
rrl | 1476535 | n.2878G>A | non_coding_transcript_exon_variant | 0.21 |
rrl | 1476538 | n.2881A>G | non_coding_transcript_exon_variant | 0.2 |
rrl | 1476540 | n.2883C>G | non_coding_transcript_exon_variant | 0.2 |
rrl | 1476542 | n.2885T>C | non_coding_transcript_exon_variant | 0.2 |
rrl | 1476543 | n.2886G>A | non_coding_transcript_exon_variant | 0.2 |
rrl | 1476547 | n.2890C>T | non_coding_transcript_exon_variant | 0.18 |
rrl | 1476567 | n.2910C>T | non_coding_transcript_exon_variant | 0.17 |
rrl | 1476573 | n.2916A>C | non_coding_transcript_exon_variant | 0.14 |
rrl | 1476577 | n.2920T>G | non_coding_transcript_exon_variant | 0.11 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 1.0 |
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 |
ald | 3086731 | c.-89A>G | upstream_gene_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.99 |
fbiA | 3640390 | c.-153A>G | upstream_gene_variant | 0.14 |
embA | 4242490 | c.-743G>A | upstream_gene_variant | 0.66 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243346 | c.114A>G | synonymous_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 |
whiB6 | 4338371 | p.Thr51Pro | missense_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 0.99 |
gid | 4407927 | p.Glu92Asp | missense_variant | 1.0 |