Run ID: SRR125288
Sample name:
Date: 03-04-2023 06:50:05
Number of reads: 4145607
Percentage reads mapped: 98.63
Strain: lineage2.2.1;lineage1.1.1.1
Drug-resistance: Sensitive
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage2 | East-Asian | Beijing | RD105 | 0.08 |
lineage1 | Indo-Oceanic | EAI | RD239 | 0.87 |
lineage2.2 | East-Asian (Beijing) | Beijing-RD207 | RD105;RD207 | 0.11 |
lineage2.2.1 | East-Asian (Beijing) | Beijing-RD181 | RD105;RD207;RD181 | 0.15 |
lineage1.1.1 | Indo-Oceanic | EAI4;EAI5 | RD239 | 0.86 |
lineage1.1.1.1 | Indo-Oceanic | EAI4;ZERO | RD239 | 0.86 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6112 | p.Met291Ile | missense_variant | 0.93 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7504 | p.Arg68Pro | missense_variant | 0.14 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 8452 | p.Ala384Val | missense_variant | 0.92 |
gyrA | 9143 | c.1842T>C | synonymous_variant | 0.86 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 490972 | p.Arg64Ser | missense_variant | 0.86 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 763884 | p.Ala172Val | missense_variant | 0.83 |
rpoC | 763886 | c.517C>A | synonymous_variant | 0.84 |
rpoC | 765171 | p.Pro601Leu | missense_variant | 0.91 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.2 |
mmpL5 | 777581 | p.Tyr300* | stop_gained | 0.89 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.1 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
fbiC | 1303036 | p.Gly36Ser | missense_variant | 0.17 |
embR | 1417019 | p.Cys110Tyr | missense_variant | 0.88 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1474709 | n.1052G>T | non_coding_transcript_exon_variant | 0.87 |
fabG1 | 1673449 | p.Thr4Pro | missense_variant | 0.3 |
inhA | 1674892 | p.Asn231Asp | missense_variant | 0.23 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.14 |
rpsA | 1834319 | p.Val260Ile | missense_variant | 0.91 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
katG | 2156389 | c.-278G>C | upstream_gene_variant | 0.91 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2167983 | p.Gly877Asp | missense_variant | 0.91 |
PPE35 | 2169320 | p.Leu431Phe | missense_variant | 0.34 |
PPE35 | 2169866 | c.747G>C | synonymous_variant | 0.23 |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 0.75 |
Rv1979c | 2222357 | p.Thr270Ala | missense_variant | 0.19 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2518132 | c.18C>T | synonymous_variant | 0.77 |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 0.92 |
pepQ | 2859381 | c.1038C>G | synonymous_variant | 0.25 |
Rv2752c | 3064552 | p.Arg547Pro | missense_variant | 0.21 |
Rv2752c | 3064632 | c.1560C>T | synonymous_variant | 0.84 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
Rv3083 | 3448714 | p.Asp71His | missense_variant | 0.73 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474597 | c.591C>A | synonymous_variant | 0.94 |
fprA | 3475159 | p.Asn385Asp | missense_variant | 0.96 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.11 |
fbiA | 3640372 | c.-171A>G | upstream_gene_variant | 0.79 |
rpoA | 3878630 | c.-124delC | upstream_gene_variant | 0.88 |
clpC1 | 4039363 | p.Ala448Pro | missense_variant | 0.27 |
clpC1 | 4039932 | p.Gly258Val | missense_variant | 0.29 |
clpC1 | 4040517 | p.Val63Ala | missense_variant | 0.87 |
embC | 4240671 | p.Thr270Ile | missense_variant | 0.94 |
embC | 4241042 | p.Asn394Asp | missense_variant | 1.0 |
embC | 4242476 | p.Pro872Ala | missense_variant | 0.15 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embC | 4242822 | p.Val987Gly | missense_variant | 0.31 |
embA | 4243460 | c.228C>T | synonymous_variant | 0.12 |
embA | 4243848 | p.Val206Met | missense_variant | 0.95 |
embA | 4244096 | c.864C>T | synonymous_variant | 0.93 |
embA | 4245969 | p.Pro913Ser | missense_variant | 0.84 |
embB | 4247646 | p.Glu378Ala | missense_variant | 0.92 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.15 |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 0.82 |
ubiA | 4269529 | p.Ala102Gly | missense_variant | 0.16 |
aftB | 4269606 | c.-770T>C | upstream_gene_variant | 0.88 |
whiB6 | 4338575 | c.-54A>G | upstream_gene_variant | 0.14 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
whiB6 | 4338603 | c.-82C>T | upstream_gene_variant | 0.73 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407873 | c.330G>T | synonymous_variant | 0.86 |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.11 |