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 |
|
A14 F34 I0 R1
|
25 |
22.0 |
717516 |
96.1% |
689532 |
148.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
CP009273 |
3,208,019 |
A→G |
27.7% |
E538E (GAA→GAG) |
rpoD → |
RNA polymerase, sigma 70 (sigma D) factor |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | CP009273 | 3,208,019 | 0 | A | G | 27.7%
| 38.1
/ 12.1
| 32 | E538E (GAA→GAG) | rpoD | RNA polymerase, sigma 70 (sigma D) factor |
| Reads supporting (aligned to +/- strand): ref base A (10/11); new base G (2/7); total (12/20) |
| Fisher's exact test for biased strand distribution p-value = 2.49e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
AAGACAAGATCCGCAAAGTGCTGAAGATCGCCAAAGAGCCAATCTCCATGGAAACGCCGATCGGTGATGATGAAGATTCGCATCTGGGGGATTTCATCGAGGATACCACCCTCGAGCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACG > CP009273/3207877‑3208162
|
aaGACAAGATCCGCAAAGTGCTGAAGATCGCCAAAGAGCCAATCTCCATGGAAACGCCGATCGGTGATGATGAAGATTCGCATCTGGGGGATTTCATCGAGGATACCACCCTCGAGCTGCCGCTGGATTCTGCGACCACCGAGAGCCtg > 2:234426/1‑149 (MQ=255)
gACAAGATCCGCAAAGTGCTGAAGATCGCCAAAGAGCCAATCTCCATGGAAACGCCGATCGGTGATGATGAAGATTCGCATCTGGGGGATTTCATCGAGGATACCACCCTCGAGCTGCCGCTGGATTCTGCGACCACCGAAAGCCtgcg > 1:336006/1‑149 (MQ=255)
aaGTGCTGAAGATCGCCAAAGAGCCAATCTCCATGGAAACGCCGATCGGTGATGATGAAGATTCGCATCTGGGGGATTTCATCGAGGATACCACCCTCGAGCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCac < 2:296871/149‑1 (MQ=255)
tGCTGAAGATCGCCAAAGAGCCAATCTCCATGGACACGCCGATCGGTGCTGATGACGCTTCGCGCCGCGTTGATGTCATCGCGGAGCCAATGCCCTAATCCCCTCTGCACCCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCacgac > 1:76422/1‑149 (MQ=255)
cTGAAGATCGCCAAAGAGCCAATCTCCATGGAAACGCCGATCGGTGATGATGAAGATTCGCATCTGGGGGATTTCATCGAGGATACCACCCTCGAGCTGCCGCTGGATTCTGCGACCACCGAGAGCCTGCGTGCGGCGAGGCacgcagt > 1:240455/1‑145 (MQ=255)
cTGAAGATCGCCAAAGAGCCAATCTCCATGGAAACGCCGATCGGTGATGATGAAGATTCGCATCTGGGGGATTTCATCGAGGATACCACCCTCGAGCTGCCGCTGGATTCTGCGACCACCGAAAGCCtgcgtgcgttgccgcacgcagg < 2:347225/149‑15 (MQ=255)
gAAGATCGCCAAAGAGCCAATGTCCCTGGAAACGCCGCTCGGGGCTGATGTAGATTCGCATCTGGGGGCTTTCATCGAGGATATCACCCTTGTTTTTTTTAATGATACGGCGACCACCGAGAGCCTGCGTGCGGCAACGCACGACGTgc < 1:278048/149‑1 (MQ=255)
aTCGCCAAAGAGCCAATCTCCATGGAAACGCCGATCGGTGATGATGAAGATTCGCATCTGGGGGATTTCATCGAGGATACCACCCTCGAGCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGCCGTgctggc > 2:207547/1‑149 (MQ=255)
aTCGCCAAAGAGCCAATCTCCATGGAAACGCCGATCGGTGATGATGAAGATTCGCATCTGGGGGATTTCATCGAGGATACCACCCTCGAGCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTgctggc > 2:37623/1‑149 (MQ=255)
ccAAAGAGCCAATCTCCATGGAAACGCCGATCGGTGATGATGAAGATTCGCATCTGGGGGATTTCATCGAGGATACCACCCTCGAGCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCtggctggc < 2:336006/149‑1 (MQ=255)
cAAAGAGCCAATCTCCATGGAAACGCCGATCGGTGATGATGAAGATTCGCATCTGGGGGATTTCATCGAGGATACCACCCTCGAGCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGcc > 1:294490/1‑149 (MQ=255)
tcccctgggcaaCGCCGATGGGTGATGTTGGAGATTCGCATCTGGGGGATTTCATCGAGGATACCACCCTTTTGTTTTTGATGGATTCGGCGACCACCGAGAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGt < 1:304599/139‑1 (MQ=255)
gtcCGTGGAAACGCGGATCGGGTATGATGAAGAGTCGCTCCTGGGGGAGTTCATCGAGGCTCCCGCCCGTTTTTTTTTGAATGATACGGCGACCACCGAGAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTg < 1:60737/148‑1 (MQ=255)
gCCGACCGGTGATGATGAAGATTCGCATCTGGGGGAATTCAACGAGGACACCACCCTCGAGCTGCCGCTGGATACTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTc > 2:54608/1‑149 (MQ=255)
gatgaGGAGTCGCATCGGGGGGATTTCATCGAGTATCGCACCCTTGTGCTGCTGAAGGATACGGCGACCACCGAGAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGttt < 1:285657/149‑1 (MQ=255)
atgaAGATTCGCATCTGGGGGATTTCATCGAGGATACCACCCTCGAGCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTc > 2:2556/1‑149 (MQ=255)
aTTCGCATCTGGGGGATTTCATCGAGGATACCACCCTCGAGCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATc > 2:17658/1‑149 (MQ=255)
ttgcagttGGGGGCTTTCAGCGAGGATCCCACCCTCTTGTTTTTGCATGATTCGGCGACCACCGAGAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGa < 1:115154/142‑1 (MQ=255)
tacgtCATCCAGCAAACCACCCCCGAGCTGCCTAATGATACGGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGa < 1:89085/145‑1 (MQ=255)
gATTTCATCGAGGATACCCCCCTCGAGCTGCCGCTGGATTCTGTGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGa < 1:103450/149‑1 (MQ=255)
ttCATCGAGGATACCACCCTCGAGCTGCCGCTGGATTCTGCGACCACCGACAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACTa < 2:260232/149‑1 (MQ=255)
cATCGAGGATACCACCCTCGAGCTGCCGCTGGATTCTGCGACAAACGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACTaca < 2:294490/149‑1 (MQ=255)
aTACCACCCTCGAGCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACTACACGCTGgaa < 2:240455/149‑1 (MQ=255)
tACCCCCCGCGAGCTGCCGCTGGATTCGGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTCCTGCGTATGCGTTTCGGTATCGATATGAACACCGACTACACGCTGgaag < 2:287180/149‑1 (MQ=255)
cctggtgCTGCCGCTGGATTCTGCGACCACCGAGAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTgg < 1:207547/143‑1 (MQ=255)
cGAGCTTCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTa < 2:241447/149‑1 (MQ=255)
tgtttctgCTGGATTCGGCGACCACCGAGAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTaaa < 1:234426/142‑1 (MQ=255)
gccgggATTCGGCGACCACCGACGGCCTGCGGGCGGCAACGTACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTc < 1:85423/145‑1 (MQ=255)
cGCTGGATTCGGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTc < 1:37623/149‑1 (MQ=255)
tCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTAc > 2:230728/1‑149 (MQ=255)
gACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTCTGCGTTTCGGTATCGATATGAACACCGACTCCACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCcgcg < 2:76422/149‑1 (MQ=255)
accGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACg > 2:112685/1‑149 (MQ=255)
|
AAGACAAGATCCGCAAAGTGCTGAAGATCGCCAAAGAGCCAATCTCCATGGAAACGCCGATCGGTGATGATGAAGATTCGCATCTGGGGGATTTCATCGAGGATACCACCCTCGAGCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACG > CP009273/3207877‑3208162
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
