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 |
2,525,308 |
G→T |
65.1% |
pseudogene (384/688 nt) |
rph → |
Mutation in protein compared to W3110: p.Val138Ala; p.Val172Ile; p.Ile216Thr; p.Glu224_Glyfs*16 ECK3633:JW3618:b3643; ribonuclease PH |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,525,308 | 0 | G | T | 65.1%
| 25.5
/ 33.0
| 43 | pseudogene (384/688 nt) | rph | Mutation in protein compared to W3110: p.Val138Ala; p.Val172Ile; p.Ile216Thr; p.Glu224_Glyfs*16 ECK3633:JW3618:b3643; ribonuclease PH |
| Reads supporting (aligned to +/- strand): ref base G (6/9); new base T (13/15); total (19/24) |
| Fisher's exact test for biased strand distribution p-value = 7.55e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.93e-01 |
GGGTGAGTTCACCATTACGCTGGACTGCGACGTGCTTCAGGCTGATGGTGGCACGCGTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAA > minE/2525245‑2525376
|
gggTGAGTTCACCATTACGCTGGACTGCGACGTGCTTCAGGCTGATGGTGGCACGCGTACCGCGTCGAt < 1:3291702/69‑1 (MQ=255)
gggTGAGTTCACCATTACGCTGGACTGCGACGTGCTTCAGGCTGATGGTGGCACGCGTACCGCGTCGAt < 1:2350418/69‑1 (MQ=255)
gggTGAGTTCACCATTACGCTGGACTGCGACGTGCTTCAGGCTGATGGTGGCACGCGTACCGCGTCGAt < 1:3338159/69‑1 (MQ=255)
gggTGAGTTCACCATTACGCTGGACTGCGACGTGCTTCAGGCTGATGGTGGCACGCGTACCGCGTCGAt < 1:423115/69‑1 (MQ=255)
gAGTTCACCATTACGCTGGACTGCGACGTGCTTCAGGCTGATGGTGGCACGCGTACCGCGTCGATTACg < 1:119789/69‑1 (MQ=255)
gAGTTCACCATTACGCTGGACTGCGACGTGCTTCAGGCTGATGGTGGCACGCGTACCGCGTCGATTACg < 1:2758238/69‑1 (MQ=255)
gAGTTCACCATTACGCTGGACTGCGACGTGCTTCAGGCTGATGGTGGCACGCGTACCGCGTCGATTACg < 1:2623855/69‑1 (MQ=255)
cACCATTACGCTGGACTTCGACGTGCTTCAGGCTGATGGTGGCACGCGTACCGCGTCGATTACGGGTGc > 1:3057205/1‑69 (MQ=255)
aCGCTGGACTGCGACGTGCTTCAGGCTGATGGTGGCACGCGTACCGCGTCGATTACGGGTGCCTGc > 1:2340363/1‑66 (MQ=255)
aCGCTGGACTGCGACGTGCTTCAGGCTGATGGTGGCACGCGTACCGCGTCGATTACGGGTGCCTGCGTg > 1:2248467/1‑69 (MQ=255)
cTGGACTGCGACGTGCTTCAGGCTGATGGTGGCACGGGTACCGCGTCGATTACGGGTGCCTGCGTGgcg > 1:1390557/1‑69 (MQ=255)
cTGGACTGCGACGTGCTTCAGGCTGATGGTGGCACGCGTACCGCGTCGATTACGGGTGCCTGCGTGgcg > 1:1040854/1‑69 (MQ=255)
cTGGACTGCGACGTGCTTCAGGCTGATGGTGGCACGCGTACCGCGTCGATTACGGGTGCCTGCGTGgcg > 1:2603904/1‑69 (MQ=255)
aCGTGCTTCAGGCTGATGGTGGCACGCGTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATg < 1:1790602/69‑1 (MQ=255)
gCTTCAGGCTGATGGTGGCACGCGTACCGCTTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATgc < 1:1758193/66‑1 (MQ=255)
gCTTCAGGCTGATGGTGGCACGCGTACCGCTTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATgc < 1:1683234/66‑1 (MQ=255)
gCTTCAGGCTGATGGTGGCACGCGTACCGCTTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATgc < 1:3382018/66‑1 (MQ=255)
gCTTCAGGCTGATGGTGGCACGCGTACCGCTTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATgc < 1:1947322/66‑1 (MQ=255)
gCTTCAGGCTGATGGTGGCACGCGTACCGCTTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATgc < 1:550364/66‑1 (MQ=255)
gCTTCAGGCTGATGGTGGCACGCGTACCGCTTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATgc < 1:649553/66‑1 (MQ=255)
gCTTCAGGCTGATGGTGGCACGCGTACCGCTTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATgc < 1:701991/66‑1 (MQ=255)
gCTTCAGGCTGATGGTGGCACGCGTACCGCTTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATgc < 1:2358425/66‑1 (MQ=255)
gCTTCAGGCTGATGGTGGCACGCGTACCGCTTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATgc < 1:702411/66‑1 (MQ=255)
gCTTCAGGCTGATGGTGGCACGCGTACCGCTTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATgc < 1:131572/66‑1 (MQ=255)
gCTTCAGGCTGATGGTGGCACGCGTACCGCTTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATgc < 1:1299268/66‑1 (MQ=255)
gCTTCAGGCTGATGGTGGCACGCGTACCGCTTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATgc < 1:2759776/66‑1 (MQ=255)
gCTTCAGGCTGATGGTGGCACGCGTACCGCTTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATgc < 1:3099526/66‑1 (MQ=255)
gCTTCAGGCTGATGGTGGCACGCGTACCGCTTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATgc < 1:3130183/66‑1 (MQ=255)
gCTGATGGTGGCACGCGTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGa < 1:1472757/67‑1 (MQ=255)
tGATGGTGCCACGCGTACCGCTTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATgc < 1:1871160/57‑1 (MQ=39)
aCCGCTTCGATTACTGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAg > 1:1231746/1‑69 (MQ=255)
aCCGCTTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAg > 1:816584/1‑69 (MQ=255)
aCCGCTTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAg > 1:3120050/1‑69 (MQ=255)
aCCGCTTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAg > 1:2830982/1‑69 (MQ=255)
aCCGCTTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAg > 1:2800018/1‑69 (MQ=255)
aCCGCTTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAg > 1:2149473/1‑69 (MQ=255)
aCCGCTTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAg > 1:1898809/1‑69 (MQ=255)
aCCGCTTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAg > 1:1567426/1‑69 (MQ=255)
aCCGCTTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAg > 1:1548219/1‑69 (MQ=255)
aCCGCTTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAg > 1:1473425/1‑69 (MQ=255)
aCCGCTTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAg > 1:1471507/1‑69 (MQ=255)
aCCGCTTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAg > 1:1410266/1‑69 (MQ=255)
aCCGCTTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAg > 1:1112817/1‑69 (MQ=255)
gTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGaa < 1:3104589/69‑1 (MQ=255)
|
GGGTGAGTTCACCATTACGCTGGACTGCGACGTGCTTCAGGCTGATGGTGGCACGCGTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAA > minE/2525245‑2525376
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
