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 |
|
A5 F1 I2 R1
|
77 |
34.8 |
1608548 |
95.0% |
1528120 |
114.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
1,428,875 |
T→C |
pseudogene (80/189 nt) |
lomR → |
pseudogene, Rac prophage lom homolog,Phage or Prophage Related, interrupted by IS5 and N‑ter deletion |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 1,428,875 | 0 | T | C | 92.9%
| 80.0
/ ‑1.4
| 28 | pseudogene (80/189 nt) | lomR | pseudogene, Rac prophage lom homolog,Phage or Prophage Related, interrupted by IS5 and N‑ter deletion |
| Reads supporting (aligned to +/- strand): ref base T (1/1); new base C (13/13); total (14/14) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.41e-01 |
GGATGCGCTCCGGATGAATATGATGATCTCATATCAGGAACTTGTTCGCACCTTCCCAAGGGGAAAACGCACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGTGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACTGACGGTTTCATCGTGGGTGTCGGTTATAAGTTCTGATTAGCCAGGTAACAC > NC_000913/1428739‑1428999
|
ggATGCGCTCCGGATGAATATGATGATCTCATATCAGGAACTTGTTCGCACCTTCCCAAGGGGAAAACGCACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGgcgcgc > 2:549666/1‑139 (MQ=255)
tgatCTCATATCAGGAACTTGTTCGCACCTTCCCAAGGGGAAAACGCACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTg < 2:788976/139‑1 (MQ=255)
tgatCTCATATCAGGAACTTGTTCGCACCTTCCCAAGGGGAAAACGCACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTg < 1:549666/139‑1 (MQ=255)
tctcATATCAGGAACTTGTTCGCACCTTCCCAAGGGGAAAACGCACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTg > 1:333560/1‑136 (MQ=255)
tctcATATCAGGAACTTGTTCGCACCTTCCCAAGGGGAAAACGCACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTg < 2:333560/136‑1 (MQ=255)
ctcATATCAGGAACTTGTTCGCACCTTCCCAAGGGGAAAACGCACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCa > 2:637480/1‑139 (MQ=255)
gAACTTGTTCGCACCTTCCCAAGGGGAAAACGCACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGc > 2:469895/1‑139 (MQ=255)
cTTGTTCGCACCTTCCCAAGGGGAAAACGCACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTa > 2:649848/1‑139 (MQ=255)
tGTTCGCACCTTCCCAAGGGGAAAACGCACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATg > 2:583261/1‑139 (MQ=255)
cccAAGGGGAAAACGCACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCa > 1:547699/1‑112 (MQ=255)
cccAAGGGGAAAACGCACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCa < 2:547699/112‑1 (MQ=255)
gAAAACGCACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAGGCCCCGGCAGTGGCGAc < 1:60420/139‑1 (MQ=255)
aaaaCGCACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAGGCCCCGGCAGTGGCGACt > 1:228734/1‑139 (MQ=255)
acgTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCATTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACTGa < 2:228734/139‑1 (MQ=255)
aaGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGTGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTg > 2:420068/1‑89 (MQ=255)
aaGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGTGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTg < 1:420068/89‑1 (MQ=255)
atgaCGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACTGACGGTTTCATCGTGGgtgt < 1:208739/139‑1 (MQ=255)
gaCGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACTGACGGTTTCATCGTGGGTGTCg < 1:649848/139‑1 (MQ=255)
aaCACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACTGACGGTTTCATCGTGGGTGTCGGTTATAAGTTCTGAt > 1:162482/1‑139 (MQ=255)
acGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACTGACGGTTTCATCGTGGGTGTCGGTTATAAGTTCTGATTAg < 2:277970/139‑1 (MQ=255)
acGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACTGACGGTTTCATCGTGGGTGTCGGTTATAAGTTCTGATTAg > 2:143164/1‑139 (MQ=255)
cGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACTGACGGTTTCATCGTGGGTGTCGGTTATAAGTTCTGATTAGc > 2:47335/1‑139 (MQ=255)
tctGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACTGACGGTTTCATCGTGGGTGTCGGTTATAAGTTCTTATTAGCCAgg < 1:539345/139‑1 (MQ=255)
gCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACTGACGGTTTCATCGTGGGTGTCGGTTATAAGTTCTGATTAGCCAGGTAac > 1:606807/1‑139 (MQ=255)
gTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACTGACGGTTTCATCGTGGGTGTCGGTTATAAGTTCTGATTAGCCAGGTAacac < 2:606807/139‑1 (MQ=255)
tGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACTGa < 2:272163/89‑1 (MQ=255)
tGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACTGa > 1:272163/1‑89 (MQ=255)
gggAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTg < 2:308971/37‑1 (MQ=255)
gggAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTg > 1:308971/1‑37 (MQ=255)
|
GGATGCGCTCCGGATGAATATGATGATCTCATATCAGGAACTTGTTCGCACCTTCCCAAGGGGAAAACGCACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGTGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACTGACGGTTTCATCGTGGGTGTCGGTTATAAGTTCTGATTAGCCAGGTAACAC > NC_000913/1428739‑1428999
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
