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 |
|
A2 F1 I0 R1
|
4577 |
57.4 |
3436498 |
77.7% |
2670158 |
63.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
2,778,392 |
T→A |
100% |
R145R (CGA→CGT) |
iclR ← |
DNA‑binding transcriptional repressor |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,778,392 | 0 | T | A | 87.0%
| 142.8
/ 12.7
| 69 | R145R (CGA→CGT) | iclR | DNA‑binding transcriptional repressor |
| Reads supporting (aligned to +/- strand): ref base T (0/9); new base A (33/27); total (33/36) |
| Fisher's exact test for biased strand distribution p-value = 2.34e-03 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.57e-01 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
AAAAAGGCTTTACCCGCACCGGAAGCGTGCATCGGCAATTTACCGCCGATAGGCGCGGACATTCGCATCAGATGCGTACACTGTACCTGGTCGATAATAATCGCTTCGTGATCGCTTTGATCAAGCAC > minE/2778330‑2778457
|
aaaacGGCTTTACCCGCACCGGAAGCGTGCATCGGCAATTTACCGCCGATAGGCGCGGACATTCGCATc < 1:3072135/69‑1 (MQ=255)
aaGGCTTTACCCGCACCGGAAGCGTGCATCGGCAATTTACCGCCGATAGGCGCGGACATTCGCATCa < 1:936388/67‑1 (MQ=255)
aaGGCTTTACCCGCACCGGAAGCGTGCATCGGCAATTTACCGCCGATAGGCGCGGACATTCGCATCa < 1:839964/67‑1 (MQ=255)
aaGGCTTTACCCGCACCGGAAGCGTGCATCGGCAATTTACCGCCGATAGGCGCGGACATTCGCATCa < 1:3431130/67‑1 (MQ=255)
gCACCGGAAGCGTGCATCGGCAATTTACCGCCGATAGGCGCGGACATTCGCATCAGATGCGTACACTGt < 1:3266981/69‑1 (MQ=255)
gCACCGGAAGCGTGCATCGGCAATTTACCGCCGATAGGCGCGGACATACGCATCAGGTGAGTACACt > 1:496512/1‑67 (MQ=255)
gCACCGGAAGCGTGCATCGGCAATTTACCGCCGATAGGCGCGGACATACGCATCAGGTGAGTACACTg > 1:1500035/1‑68 (MQ=255)
gCACCGGAAGCGTGCATCGGCAATTTACCGCCGATAGGCGCGGACATACGCATCAGGTGAGTACACTg > 1:734567/1‑68 (MQ=255)
gCACCGGAAGCGTGCATCGGCAATTTACCGCCGATAGGCGCGGACATACGCATCAGGTGAGTACACTGt > 1:53962/1‑69 (MQ=255)
gCACCGGAAGCGTGCATCGGCAATTTACCGCCGATAGGCGCGGACATACGCATCAGGTGAGTACACTGt > 1:2599589/1‑69 (MQ=255)
gCACCGGAAGCGTGCATCGGCAATTTACCGCCGATAGGCGCGGACATACGCATCAGGTGAGTACACTGt > 1:543750/1‑69 (MQ=255)
gCACCGGAAGCGTGCATCGGCAATTTACCGCCGATAGGCGCGGACATACGCATCAGGTGAGTACACTGt > 1:76228/1‑69 (MQ=255)
gCACCGGAAGCGTGCATCGGCAATTTACCGCCGATAGGCGCGGACATACGCATCAGGTGAGTACACTGt > 1:292829/1‑69 (MQ=255)
gCACCGGAAGCGTGCATCGGCAATTTACCGCCGATAGGCGCGGACATACGCATCAGGTGAGTACACTGt > 1:2612643/1‑69 (MQ=255)
gCACCGGAAGCGTGCATCGGCAATTTACCGCCGATAGGCGCGGACATACGCATCAGGTGAGTACACTGt > 1:2433540/1‑69 (MQ=255)
gCACCGGAAGCGTGCATCGGCAATTTACCGCCGATAGGCGCGGACATACGCATCAGGTGAGTACACTGt > 1:2236871/1‑69 (MQ=255)
gCACCGGAAGCGTGCATCGGCAATTTACCGCCGATAGGCGCGGACATACGCATCAGGTGAGTACACTGt > 1:2230447/1‑69 (MQ=255)
gCACCGGAAGCGTGCATCGGCAATTTACCGCCGATAGGCGCGGACATACGCATCAGGTGAGTACACTGt > 1:1159596/1‑69 (MQ=255)
gCACCGGAAGCGTGCATCGGCAATTTACCGCCGATAGGCGCGGACATACGCATCAGGTGAGTACACTGt > 1:1502798/1‑69 (MQ=255)
gCACCGGAAGCGTGCATCGGCAATTTACCGCCGATAGGCGCGGACATACGCATCAGGTGAGTACACTGt > 1:182025/1‑69 (MQ=255)
gCATCGGCAATTTACCGCCGATAGGCGCGGACATACGCATCAGGTGAGTACACTGTACCTGGTCGata > 1:555548/1‑68 (MQ=255)
gCATCGGCAATTTACCGCCGATAGGCGCGGACATACGCATCAGGTGAGTACACTGTACCTGGTCGata > 1:3395805/1‑68 (MQ=255)
gCATCGGCAATTTACCGCCGATAGGCGCGGACATACGCATCAGGTGAGTACACTGTACCTGGTCGata > 1:15738/1‑68 (MQ=255)
gCATCGGCAATTTACCGCCGATAGGCGCGGACATACGCATCAGGTGAGTACACTGTACCTGGTCGata > 1:451871/1‑68 (MQ=255)
gCATCGGCAATTTACCGCCGATAGGCGCGGACATACGCATCAGGTGAGTACACTGTACCTGGTCGata > 1:47676/1‑68 (MQ=255)
gCATCGGCAATTTACCGCCGATAGGCGCGGACATACGCATCAGGTGAGTACACTGTACCTGGTCGata > 1:2660445/1‑68 (MQ=255)
gCATCGGCAATTTACCGCCGATAGGCGCGGACATACGCATCAGGTGAGTACACTGTACCTGGTCGata > 1:1664838/1‑68 (MQ=255)
gCATCGGCAATTTACCGCCGATAGGCGCGGACATACGCATCAGGTGAGTACACTGTACCTGGTCGata > 1:2612625/1‑68 (MQ=255)
gCATCGGCAATTTACCGCCGATAGGCGCGGACATACGCATCAGGTGAGTACACTGTACCTGGTCGata > 1:259482/1‑68 (MQ=255)
gCATCGGCAATTTACCGCCGATAGGCGCGGACATACGCATCAGGTGAGTACACTGTACCTGGTCGata > 1:1309327/1‑68 (MQ=255)
gCATCGGCAATTTACCGCCGATAGGCGCGGACATACGCATCAGGTGAGTACACTGTACCTGGTCGata > 1:2402742/1‑68 (MQ=255)
gCATCGGCAATTTACCGCCGATAGGCGCGGACATACGCATCAGGTGAGTACACTGTACCTGGTCGata > 1:6095/1‑68 (MQ=255)
gCATCGGCAATTTACCGCCGATAGGCGCGGACATACGCATCAGGTGAGTACACTGTACCTGGTCGata > 1:2376336/1‑68 (MQ=255)
gCATCGGCAATTTACCGCCGATAGGCGCGGACATACGCATCAGGTGAGTACACTGTACCTGGTCGata > 1:804213/1‑68 (MQ=255)
gCATCGGCAATTTACCGCCGATAGGCGCGGACATACGCATCAGGTGAGTACACTGTACCTGGTCGata > 1:2001757/1‑68 (MQ=255)
gCATCGGCAATTTACCGCCGATAGGCGCGGACATACGCATCAGGTGAGTACACTGTACCTGGTCGata > 1:1967608/1‑68 (MQ=255)
gCATCGGCAATTTACCGCCGATAGGCGCGGACATACGCATCAGGTGAGTACACTGTACCTGGTCGat > 1:195780/1‑67 (MQ=255)
gCATCGGCAATTTACCGCCGATAGGCGCGGACATACGCATCAGGTAAGTACACTGTACCTGGTCGata > 1:2654018/1‑68 (MQ=255)
ggCAATTTACCGCCGATAGGCGCGGACATTCGCATc < 1:2337729/36‑1 (MQ=255)
gccgATAGGCGCGGACATACGCATCAGGTGAGTACACTGTACCTGGTCGATAATAATCGCTTCTTGAtt < 1:1191529/69‑2 (MQ=255)
gccgATAGGCGCGGACATACGCATCAGGTGAGTACACTGTACCTGGTCGATAATAATCGCTTCGTGAtt < 1:1086197/69‑2 (MQ=255)
gccgATAGGCGCGGACATACGCATCAGGTGAGTACACTGTACCTGGTCGATAATAATCGCTTCGTGAtt < 1:1499242/69‑2 (MQ=255)
gccgATAGGCGCGGACATACGCATCAGGTGAGTACACTGTACCTGGTCGATAATAATCGCTTCGTGAtt < 1:663116/69‑2 (MQ=255)
gccgATAGGCGCGGACATACGCATCAGGTGAGTACACTGTACCTGGTCGATAATAATCGCTTCGTGAtt < 1:474219/69‑2 (MQ=255)
gccgATAGGCGCGGACATACGCATCAGGTGAGTACACTGTACCTGGTCGATAATAATCGCTTCGTGAtt < 1:1885457/69‑2 (MQ=255)
gccgATAGGCGCGGACATACGCATCAGGTGAGTACACTGTACCTGGTCGATAATAATCGCTTCGTGAtt < 1:380870/69‑2 (MQ=255)
gccgATAGGCGCGGACATACGCATCAGGTGAGTACACTGTACCTGGTCGATAATAATCGCTTCGTGAtt < 1:3214842/69‑2 (MQ=255)
gccgATAGGCGCGGACATACGCATCAGGTGAGTACACTGTACCTGGTCGATAATAATCGCTTCGTGAtt < 1:2086414/69‑2 (MQ=255)
gccgATAGGCGCGGACATACGCATCAGGTGAGTACACTGTACCTGGTCGATAATAATCGCTTCGTGAtt < 1:2176025/69‑2 (MQ=255)
gccgATAGGCGCGGACATACGCATCAGGTGAGTACACTGTACCTGGTCGATAATAATCGCTTCGTGAtt < 1:170551/69‑2 (MQ=255)
gccgATAGGCGCGGACATACGCATCAGGTGAGTACACTGTACCTGGTCGATAATAATCGCTTCGTGAtt < 1:2613155/69‑2 (MQ=255)
gccgATAGGCGCGGACATACGCATCAGGTGAGTACACTGTACCTGGTCGATAATAATCGCTTCGTGAtt < 1:2396155/69‑2 (MQ=255)
gccgATAGGCGCGGACATACGCATCAGGTGAGTACACTGTACCTGGTCGATAATAATCGCTTCGTGAtt < 1:1581740/69‑2 (MQ=255)
gccgATAGGCGCGGACATACGCATCAGGTGAGTACACTGTACCTGGTCGATAATAATCGCTTCGTGAtt < 1:2414330/69‑2 (MQ=255)
ccgATAGGCGCGGACATACGCATCAGGTGAGTACACTGTACCTGGTCGATAATAATCGCTTCGTGAtt < 1:2712785/68‑2 (MQ=255)
aGGCGCGGACATACGCATCAGGTGAGTACACTGTACCTGGTCGATAATAATCGCTTCGTGAtt < 1:578631/63‑2 (MQ=255)
aCATACGCATCAGGTGAGTACACTGTACCTGGTCGATAATAATCGCTTCGTGATTGCTTTGATCAAGCa < 1:1697486/69‑1 (MQ=255)
aCATACGCATCAGGTGAGTACACTGTACCTGGTCGATAATAATCGCTTCGTGATTGCTTTGATCAAGCa < 1:49699/69‑1 (MQ=255)
aCATACGCATCAGGTGAGTACACTGTACCTGGTCGATAATAATCGCTTCGTGATTGCTTTGATCAAGCa < 1:658393/69‑1 (MQ=255)
aCATACGCATCAGGTGAGTACACTGTACCTGGTCGATAATAATCGCTTCGTGATTGCTTTGATCAAGCa < 1:1200686/69‑1 (MQ=255)
aCATACGCATCAGGTGAGTACACTGTACCTGGTCGATAATAATCGCTTCGTGATTGCTTTGATCAAGCa < 1:750490/69‑1 (MQ=255)
aCATACGCATCAGGTGAGTACACTGTACCTGGTCGATAATAATCGCTTCGTGATTGCTTTGATCAAGCa < 1:1592801/69‑1 (MQ=255)
aCATACGCATCAGGTGAGTACACTGTACCTGGTCGATAATAATCGCTTCGTGATTGCTTTGATCAAGCa < 1:2000150/69‑1 (MQ=255)
cATTCGCATCAGATGCGTACACTGTACCTGGTCGATAATAATCGCTTCGTGATCGCTTTGATCAAGCAc < 1:2752115/69‑1 (MQ=255)
cATTCGCATCAGATGCGTACACTGTACCTGGTCGATAATAATCGCTTCGTGATCGCTTTGATCAAGCAc < 1:1590111/69‑1 (MQ=255)
cATTCGCATCAGATGCGTACACTGTACCTGGGCGATAATAATCGCTTCGTGATCGCTTTGATCAAGCAc < 1:678819/69‑1 (MQ=255)
cATACGCATCAGGTGAGTACACTGTACCTGGTCGATAATAATCGCTTCGTGATTGCTTTGATCAAGCa < 1:1040615/68‑1 (MQ=255)
cATACGCATCAGGTGAGTACACTGTACCTGGTCGATAATAATCGCTTCGTGATTGCTTTGATCAAGCa < 1:2220756/68‑1 (MQ=255)
cATACGCATCAGGTGAGTACACTGTACCTGGTCGATAATAATCGCTTCGTGATTGCTTTGATCAAGCa < 1:8643/68‑1 (MQ=255)
|
AAAAAGGCTTTACCCGCACCGGAAGCGTGCATCGGCAATTTACCGCCGATAGGCGCGGACATTCGCATCAGATGCGTACACTGTACCTGGTCGATAATAATCGCTTCGTGATCGCTTTGATCAAGCAC > minE/2778330‑2778457
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
