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 |
2,317,510 |
C→T |
59.7% |
A26A (GCC→GCT) |
fpr → |
ferredoxin‑NADP reductase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,317,510 | 0 | C | T | 59.7%
| 22.5
/ 42.0
| 62 | A26A (GCC→GCT) | fpr | ferredoxin‑NADP reductase |
| Reads supporting (aligned to +/- strand): ref base C (13/12); new base T (2/35); total (15/47) |
| Fisher's exact test for biased strand distribution p-value = 3.90e-05 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.48e-01 |
TAACAGGCAAAGTCACTAAAGTGCAGAACTGGACCGACGCCCTGTTTAGTCTCACCGTTCACGCCCCCGTGCTTCCGTTTACCGCCGGGCAATTTACCAAGCTTGGCCTTGAA > minE/2317446‑2317558
|
tAACAGGCAAAGTCACTAAAGTGCAGAACTGGACCGACGCCCTGTTTAGTCTCACCGTTCACGCCCCCg > 1:1564679/1‑69 (MQ=255)
aCAGGCAAAGTCACTAAAGTGCAGAACTGGACCGACGCCCTGTTTAGTCTCACCGTTCACGCTCCCGTg > 1:2849256/1‑69 (MQ=255)
aCAGGCAAAGTCACTAAAGTGCAGAACTGGACCGACGCCCTGTTTAGTCTCACCGTTCACGCTCCCGTg > 1:632091/1‑69 (MQ=255)
aGGCAAAGTCACTAAAGTGCAGAACTGGACCGACGCCCTGTTTAGTCTCACCGTTCACGCCCCCGTGCt > 1:3095646/1‑69 (MQ=255)
gTCACTAAAGTGCAGAACTGGACCGACGCCCTGTTTAGTCTCACCGTTCACGCCCCCGTGCTTCCGttt < 1:3094158/69‑1 (MQ=255)
gTCACTAAAGTGCAGAACTGGACCGACGCCCTGTTTAGTCTCACCGTTCACGCCCCCGTGCTTCCGttt < 1:3090079/69‑1 (MQ=255)
gTCACTAAAGTGCAGAACTGGACCGACGCCCTGTTTAGTCTCACCGTTCACGCCCCCGTGCTTCCGttt < 1:26667/69‑1 (MQ=255)
gTCACTAAAGTGCAGAACTGGACCGACGCCCTGTTTAGTCTCACCGTTCACGCCCCCGTGCTTCCGttt < 1:2028880/69‑1 (MQ=255)
gTCACTAAAGTGCAGAACTGGACCGACGCCCTGTTTAGTCTCACCGTTCACGCCCCCGTGCTTCCGttt < 1:2772765/69‑1 (MQ=255)
gTCACTAAAGTGCAGAACTGGACCGACGCCCTGTTTAGTCTCACCGTTCACGCCCCCGTGCTTCCGttt < 1:627979/69‑1 (MQ=255)
tCACTAAAGTGCAGAACTGGACCGACGCCCTGTTTAGTCTCACCGTTCACGCCCCCGTGCTTCCGttt > 1:740885/1‑68 (MQ=255)
tCACTAAAGTGCAGAACTGGACCGACGCCCTGTTTAGTCTCACCGTTCACGCCCCCGTGCTTCCGTTTa > 1:1885732/1‑69 (MQ=255)
tCACTAAAGTGCAGAACTGGACCGACGCCCTGTTTAGTCTCACCGTTCACGCCCCCGTGCTTCCGTTTa > 1:65870/1‑69 (MQ=255)
aCTAAAGTGCAGAACTGGACCGACGCCCTGTTTAGTCTCACCGTTCACGCCCCCGTGCTTCCGTTTAcc > 1:791588/1‑69 (MQ=255)
aCTAAAGTGCAGAACTGGACCGACGCCCTGTTTAGTCTCACCGTTCACGCCCCCGTGCTTCCGTTTAcc > 1:3391106/1‑69 (MQ=255)
aCTAAAGTGCAGAACTGGACCGACGCCCTGTTTAGTCTCACCGTTCACGCCCCCGTGCTTCCGTTTAcc > 1:2329163/1‑69 (MQ=255)
cAGAACTGGACCGACGCCCTGTTTAGTCTCACCGTTCACGCTCCCGTGCTTCCGTTTACCGCCGGGCaa < 1:2901426/69‑1 (MQ=255)
cAGAACTGGACCGACGCCCTGTTTAGTCTCACCGTTCACGCTCCCGTGCTTCCGTTTACCGCCGGGCaa < 1:3365146/69‑1 (MQ=255)
cAGAACTGGACCGACGCCCTGTTTAGTCTCACCGTTCACGCTCCCGTGCTTCCGTTTACCGCCGGGCaa < 1:2823934/69‑1 (MQ=255)
cAGAACTGGACCGACGCCCTGTTTAGTCTCACCGTTCACGCTCCCGTGCTTCCGTTTACCGCCGGGCaa < 1:2532658/69‑1 (MQ=255)
cAGAACTGGACCGACGCCCTGTTTAGTCTCACCGTTCACGCTCCCGTGCTTCCGTTTACCGCCGGGCaa < 1:2435481/69‑1 (MQ=255)
cAGAACTGGACCGACGCCCTGTTTAGTCTCACCGTTCACGCTCCCGTGCTTCCGTTTACCGCCGGGCaa < 1:3027821/69‑1 (MQ=255)
cAGAACTGGACCGACGCCCTGTTTAGTCTCACCGTTCACGCTCCCGTGCTTCCGTTTACCGCCGGGCaa < 1:3048499/69‑1 (MQ=255)
cAGAACTGGACCGACGCCCTGTTTAGTCTCACCGTTCACGCTCCCGTGCTTCCGTTTACCGCCGGGCaa < 1:2278935/69‑1 (MQ=255)
cAGAACTGGACCGACGCCCTGTTTAGTCTCACCGTTCACGCTCCCGTGCTTCCGTTTACCGCCGGGCaa < 1:223425/69‑1 (MQ=255)
cAGAACTGGACCGACGCCCTGTTTAGTCTCACCGTTCACGCTCCCGTGCTTCCGTTTACCGCCGGGCaa < 1:3185815/69‑1 (MQ=255)
cAGAACTGGACCGACGCCCTGTTTAGTCTCACCGTTCACGCTCCCGTGCTTCCGTTTACCGCCGGGCaa < 1:355303/69‑1 (MQ=255)
cAGAACTGGACCGACGCCCTGTTTAGTCTCACCGTTCACGCTCCCGTGCTTCCGTTTACCGCCGGGCaa < 1:1989680/69‑1 (MQ=255)
cAGAACTGGACCGACGCCCTGTTTAGTCTCACCGTTCACGCTCCCGTGCTTCCGTTTACCGCCGGGCaa < 1:1762370/69‑1 (MQ=255)
cAGAACTGGACCGACGCCCTGTTTAGTCTCACCGTTCACGCTCCCGTGCTTCCGTTTACCGCCGGGCaa < 1:1584722/69‑1 (MQ=255)
cAGAACTGGACCGACGCCCTGTTTAGTCTCACCGTTCACGCTCCCGTGCTTCCGTTTACCGCCGGGCaa < 1:1294368/69‑1 (MQ=255)
cTGGACCGACGCCCTGTTTAGTCTCACCGTTCACGCCCCCGTGCTTCCGTTTACCGCCGGGCAATTTa > 1:2913653/1‑68 (MQ=255)
cTGGACCGACGCCCTGTTTAGTCTCACCGTTCACGCCCCCGTGCTTCCGTTTACCGCCGGGCAATTTa > 1:2296795/1‑68 (MQ=255)
cTGGACCGACGCCCTGTTTAGTCTCACCGTTCACGCCCCCGTGCTTCCGTTTACCGCCGGGCAATTTa > 1:2341710/1‑68 (MQ=255)
cTGGACCGACGCCCTGTTTAGTCTCACCGTTCACGCCCCCGTGCTTCCGTTTACCGCCGGGCAATTTa > 1:1326274/1‑68 (MQ=255)
gCCCTGTTTAGTCTCACCGTTCACGCTCCCGTGCTTCCGTTTACCGCCGGGCaa < 1:3031698/54‑1 (MQ=255)
tAGTCTCACCGTTCACGCCCCCGTGCTTCCGTTTACCGCCGGGCAATTTACCAAGCTTGGCCTTGaa < 1:2597219/67‑1 (MQ=255)
tAGTCTCACCGTTCACGCCCCCGTGCTTCCGTTTACCGCCGGGCAATTTACCAAGCTTGGCCTTGaa < 1:2156255/67‑1 (MQ=255)
tAGTCTCACCGTTCACGCCCCCGTGCTTCCGTTTACCGCCGGGCAATTTACCAAGCTTGGCCTTGaa < 1:143865/67‑1 (MQ=255)
tAGTCTCACCGTTCACGCCCCCGTGCTTCCGTTTACCGCCGGGCAATTTACCAAGCTTGGCCTTGaa < 1:1043442/67‑1 (MQ=255)
tAGTCTCACCGTTCACGCCCCCGTGCTTCCGTTTACCGCCGGGCAATTTACCAAGCTTGGCCTTGa < 1:970639/66‑1 (MQ=255)
tAGTCTCACCGTTCACGCCCCCGTGCTTCCGTTTACCACCGGGCAATTTACCAAGCTTGGCCTTGa < 1:899101/66‑1 (MQ=255)
tcACCGTTCACGCCCCCGTGCTTCCGTTTACCGCCGGGCAATTTACCAAGCTTgg > 1:267459/1‑55 (MQ=255)
cGTTCACGCTCCCGTGCTTCCGTTTACCGCCGTGCAATTCACCaaa < 1:525294/46‑2 (MQ=37)
cGTTCACGCTCCCGTGCTTCCGTTTACCGCCGGGCAATTCACCaaa < 1:1218662/46‑2 (MQ=38)
cGTTCACGCTCCCGTGCTTCCGTTTACCGCCGGGCAATTCACCaaa < 1:947502/46‑2 (MQ=38)
cGTTCACGCTCCCGTGCTTCCGTTTACCGCCGGGCAATTCACCaaa < 1:828616/46‑2 (MQ=38)
cGTTCACGCTCCCGTGCTTCCGTTTACCGCCGGGCAATTCACCaaa < 1:1503073/46‑2 (MQ=38)
cGTTCACGCTCCCGTGCTTCCGTTTACCGCCGGGCAATTCACCaaa < 1:1667374/46‑2 (MQ=38)
cGTTCACGCTCCCGTGCTTCCGTTTACCGCCGGGCAATTCACCaaa < 1:1939657/46‑2 (MQ=38)
cGTTCACGCTCCCGTGCTTCCGTTTACCGCCGGGCAATTCACCaaa < 1:1947659/46‑2 (MQ=38)
cGTTCACGCTCCCGTGCTTCCGTTTACCGCCGGGCAATTCACCaaa < 1:466535/46‑2 (MQ=38)
cGTTCACGCTCCCGTGCTTCCGTTTACCGCCGGGCAATTCACCaaa < 1:2444518/46‑2 (MQ=38)
cGTTCACGCTCCCGTGCTTCCGTTTACCGCCGGGCAATTCACCaaa < 1:3372703/46‑2 (MQ=38)
cGTTCACGCTCCCGTGCTTCCGTTTACCGCCGGGCAATTCACCaaa < 1:3366819/46‑2 (MQ=38)
cGTTCACGCTCCCGTGCTTCCGTTTACCGCCGGGCAATTCACCaaa < 1:3211916/46‑2 (MQ=38)
cGTTCACGCTCCCGTGCTTCCGTTTACCGCCGGGCAATTCACCaaa < 1:3063995/46‑2 (MQ=38)
cGTTCACGCTCCCGTGCTTCCGTTTACAGCCGGGCAATTCACCaaa < 1:2083129/46‑2 (MQ=255)
gTTCACGCTCCCGTGCTTCCGTTTACCGCCGGGCAATTCACCaaa < 1:619692/45‑2 (MQ=38)
gTTCACGCTCCCGTGCTTCCGTTTACCGCCGGGCAATTCACCaaa < 1:1768504/45‑2 (MQ=38)
gTTCACGCTCCCGTGCTTCCGTTTACCGCCGGGCAATTCACCaaa < 1:336115/45‑2 (MQ=38)
cGCTCCCGTGCTTCCGTTTACCGCCGGGCAATTCACCaaa < 1:3160765/40‑2 (MQ=37)
|
TAACAGGCAAAGTCACTAAAGTGCAGAACTGGACCGACGCCCTGTTTAGTCTCACCGTTCACGCCCCCGTGCTTCCGTTTACCGCCGGGCAATTTACCAAGCTTGGCCTTGAA > minE/2317446‑2317558
|
| 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
