Sample Resequencing Stats
Note: The mutation counts shown below represent unfiltered mutation sets.
| ALE, Flask, Isolate |
Predicted Mutations |
Mean Coverage |
Total Reads |
Percent Mapped |
Mapped Reads |
Average Read Length |
|
A1 F4 I88 R1
|
217 |
30.5 |
1742422 |
95.9% |
1670982 |
87.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
737,899 |
A→G |
N38N (AAT→AAC) |
dtpD ← |
dipeptide permease DtpD |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 737,899 | 0 | A | G | 100.0%
| 110.1
/ NA
| 30 | N38N (AAT→AAC) | dtpD | dipeptide permease DtpD |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (10/20); total (10/20) |
GCCACCGAGGATTGGCGTGACATACACCAGCGAACAGTAGGCGCTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGATTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAGCGCAACGACA > NZ_CP009273/737815‑737974
|
gCCACCGAGGATTGGCGTGACATACACCAGCGAACAGTAGGCGCTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTg < 1:447961/91‑1 (MQ=255)
gCCACCGAGGATTGGCGTGACATACACCAGCGAACAGTAGGCGCTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTg < 2:145461/91‑1 (MQ=255)
gCCACCGAGGATTGGCGTGACATACACCAGCGAACAGTAGGCGCTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTg < 1:740438/91‑1 (MQ=255)
gAGGATTGGCGTGACATACACCAGCGAACAGTAGGCGCTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATag < 2:160243/91‑1 (MQ=255)
aGGATTGGCGTGACATACACCAGCGAACAGTAGGCGCTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATaga < 1:17688/91‑1 (MQ=255)
gACATACACCAGCGAACAGTAGGCGCTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAgg > 1:81751/1‑91 (MQ=255)
gCGAACAGTAGGCGCTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGcc > 2:458740/1‑91 (MQ=255)
gCGAACAGTAGGCGCTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGcc > 2:492906/1‑91 (MQ=255)
aCAGTAGGCGCTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTaa < 2:642314/91‑1 (MQ=255)
cAGTAGGCGCTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTaaa < 1:360631/91‑1 (MQ=255)
aaCTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTccc < 1:148187/91‑1 (MQ=255)
aCTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCa > 2:703749/1‑91 (MQ=255)
cGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATaga < 2:133463/45‑1 (MQ=255)
cGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATaga > 1:133463/1‑45 (MQ=255)
tAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGAttt > 1:362539/1‑91 (MQ=255)
ggCGTGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGc < 2:240482/91‑1 (MQ=255)
gTGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAgc > 1:858779/1‑91 (MQ=255)
gTGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAgc > 2:422346/1‑91 (MQ=255)
tGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAgcg > 1:238342/1‑91 (MQ=255)
tATCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAGCGCAAc < 2:748618/91‑1 (MQ=255)
tATCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAGCGCAAc < 2:238342/91‑1 (MQ=255)
tCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAGCGCAAc < 2:295965/89‑1 (MQ=255)
tCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAGCGCAAc > 1:295965/1‑89 (MQ=255)
tCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAGCGCAACGa < 2:858779/91‑1 (MQ=255)
tCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAGCGCAACGa < 2:362539/91‑1 (MQ=255)
tCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAGCGCAACGa < 1:482635/91‑1 (MQ=255)
gTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAGCGCAACGACa < 2:549818/91‑1 (MQ=255)
gTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAGCGCAACGACa < 2:308530/91‑1 (MQ=255)
gTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAGCGCAACGACa < 2:154086/91‑1 (MQ=255)
gTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAGCGCAACGACa < 1:615305/91‑1 (MQ=255)
|
GCCACCGAGGATTGGCGTGACATACACCAGCGAACAGTAGGCGCTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGATTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAGCGCAACGACA > NZ_CP009273/737815‑737974
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GCCAAAAAGCCACCGAGGATTGGCGTGACATACACCAGCGAACAGTAGGCGCTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGATTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAGCGCAACGACATAGTAAATAGCGCGCGGCTGTGATG > NZ_CP009273/737807‑737999
|
GCCAAAAAGCCACCGAGGATTGGCGTGACATACACCAGCGAACAGTAGGCGCTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTGAG < SRR3722118.319821/101‑1 (MQ=60)
GCCACCGAGGATTGGCGTGACATACACCAGCGAACAGTAGGCGCTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAA < SRR3722118.457404/101‑1 (MQ=60)
GCCACCGAGGATTGGCGTGACATACACCAGCGAACAGTAGGCGCTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAA < SRR3722118.756721/101‑1 (MQ=60)
AGGATTGGCGTGACATACACCAGCGAACAGTAGGCGCTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAG < SRR3722118.18033/101‑1 (MQ=60)
GGATTGGCGTGACATACACCAGCGAACAGTAGGCGCTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGG > SRR3722118.83274/1‑101 (MQ=60)
CAGTAGGCGCTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATA < SRR3722118.368137/101‑1 (MQ=60)
CTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTGCGATAGAGAATCAGCAGctgtctcttatacacatctccgagcccacgagacgg > SRR3722118.135992/1‑65 (MQ=60)
CTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGAT > SRR3722118.766322/1‑101 (MQ=60)
AAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTT > SRR3722118.370090/1‑101 (MQ=60)
AACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAG < SRR3722118.151037/101‑1 (MQ=60)
ACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAGC > SRR3722118.877856/1‑101 (MQ=60)
CTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAGCG > SRR3722118.243155/1‑101 (MQ=60)
GGCGTGAGTATCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAGCGCAACGA > SRR3722118.302029/1‑101 (MQ=60)
TCGTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAGCGCAACGACATAGTAAAT < SRR3722118.492849/101‑1 (MQ=60)
GTTGTATTTTAGTTGGTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAGCGCAACGACATAGTAAATAG < SRR3722118.628485/101‑1 (MQ=60)
GTTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAGCGCAACGACATAGTAAATAGCGCGCGGCTGTGATG > SRR3722118.717858/1‑101 (MQ=60)
|
GCCAAAAAGCCACCGAGGATTGGCGTGACATACACCAGCGAACAGTAGGCGCTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGATTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAGCGCAACGACATAGTAAATAGCGCGCGGCTGTGATG > NZ_CP009273/737807‑737999
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
