Run ID: SRR1172848
Sample name:
Date: 03-04-2023 03:11:39
Number of reads: 1315807
Percentage reads mapped: 70.47
Strain: lineage1.1.2
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage1 | Indo-Oceanic | EAI | RD239 | 1.0 |
lineage1.1 | Indo-Oceanic | EAI3;EAI4;EAI5;EAI6 | RD239 | 1.0 |
lineage1.1.2 | Indo-Oceanic | EAI3;EAI5 | RD239 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761161 | p.Leu452Pro | missense_variant | 1.0 | rifampicin |
rrs | 1472723 | n.878G>A | non_coding_transcript_exon_variant | 0.93 | streptomycin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2288844 | p.Ile133Thr | missense_variant | 0.1 | pyrazinamide |
pncA | 2289228 | p.Ile5Thr | missense_variant | 0.32 | pyrazinamide |
embB | 4247429 | p.Met306Val | missense_variant | 1.0 | ethambutol |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6112 | p.Met291Ile | missense_variant | 1.0 |
gyrB | 6124 | c.885C>T | synonymous_variant | 1.0 |
gyrA | 6736 | c.-566C>T | upstream_gene_variant | 1.0 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 8452 | p.Ala384Val | missense_variant | 1.0 |
gyrA | 9143 | c.1842T>C | synonymous_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 575278 | c.-70C>A | upstream_gene_variant | 1.0 |
mshA | 576707 | p.Arg454Ser | missense_variant | 0.18 |
ccsA | 620070 | c.180C>A | synonymous_variant | 0.11 |
rpoB | 762911 | p.Ile1035Met | missense_variant | 0.11 |
rpoC | 762923 | c.-447C>G | upstream_gene_variant | 0.1 |
rpoB | 762944 | p.Ile1046Met | missense_variant | 0.12 |
rpoC | 762965 | c.-405T>C | upstream_gene_variant | 0.15 |
rpoC | 762989 | c.-381G>T | upstream_gene_variant | 0.12 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 763884 | p.Ala172Val | missense_variant | 1.0 |
rpoC | 763886 | c.517C>A | synonymous_variant | 1.0 |
rpoC | 764650 | c.1281G>T | synonymous_variant | 0.16 |
rpoC | 764665 | c.1296C>G | synonymous_variant | 0.17 |
rpoC | 764668 | c.1299C>T | synonymous_variant | 0.17 |
rpoC | 764695 | c.1326T>C | synonymous_variant | 0.17 |
rpoC | 764713 | c.1344G>C | synonymous_variant | 0.11 |
rpoC | 764719 | c.1350G>A | synonymous_variant | 0.12 |
rpoC | 765171 | p.Pro601Leu | missense_variant | 1.0 |
rpoC | 766715 | c.3348delC | frameshift_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 |
rpsL | 781889 | c.330C>T | synonymous_variant | 1.0 |
Rv1258c | 1406503 | p.Val280Leu | missense_variant | 1.0 |
embR | 1417019 | p.Cys110Tyr | missense_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472741 | n.896G>A | non_coding_transcript_exon_variant | 0.1 |
rrs | 1472767 | n.922G>A | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.11 |
rrs | 1472785 | n.940G>T | non_coding_transcript_exon_variant | 0.11 |
rrs | 1472786 | n.941C>G | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476357 | n.2700T>C | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476383 | n.2726T>G | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.23 |
rrl | 1476411 | n.2754G>T | non_coding_transcript_exon_variant | 0.23 |
rrl | 1476425 | n.2768G>T | non_coding_transcript_exon_variant | 0.25 |
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.25 |
rrl | 1476442 | n.2785T>A | non_coding_transcript_exon_variant | 0.18 |
rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.18 |
rrl | 1476455 | n.2798C>A | non_coding_transcript_exon_variant | 0.18 |
rrl | 1476456 | n.2799A>T | non_coding_transcript_exon_variant | 0.18 |
rrl | 1476463 | n.2806C>A | non_coding_transcript_exon_variant | 0.16 |
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.17 |
rrl | 1476470 | n.2813C>T | non_coding_transcript_exon_variant | 0.17 |
rrl | 1476483 | n.2826G>A | non_coding_transcript_exon_variant | 0.17 |
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 | 2167983 | p.Gly877Asp | missense_variant | 1.0 |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2518132 | c.18C>T | synonymous_variant | 1.0 |
kasA | 2518218 | p.Gly35Asp | missense_variant | 1.0 |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 1.0 |
Rv2752c | 3064632 | c.1560C>T | synonymous_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
Rv3083 | 3448714 | p.Asp71His | missense_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474597 | c.591C>A | synonymous_variant | 1.0 |
fprA | 3475159 | p.Asn385Asp | missense_variant | 1.0 |
clpC1 | 4040517 | p.Val63Ala | missense_variant | 1.0 |
embC | 4240618 | c.756C>T | synonymous_variant | 1.0 |
embC | 4240671 | p.Thr270Ile | missense_variant | 1.0 |
embC | 4241042 | p.Asn394Asp | missense_variant | 1.0 |
embC | 4241201 | p.Gly447Cys | missense_variant | 0.12 |
embC | 4242564 | p.Ala901Asp | missense_variant | 0.11 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243848 | p.Val206Met | missense_variant | 1.0 |
embA | 4245969 | p.Pro913Ser | missense_variant | 1.0 |
embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 1.0 |
aftB | 4269606 | c.-770T>C | upstream_gene_variant | 1.0 |
whiB6 | 4338224 | c.297delC | frameshift_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
whiB6 | 4338603 | c.-82C>T | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407873 | c.330G>T | synonymous_variant | 0.97 |