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 |
2,170,169 |
G→A |
61.2% |
L120L (TTG→TTA) |
rpoN → |
RNA polymerase, sigma 54 (sigma N) factor |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,170,169 | 0 | G | A | 61.2%
| 33.2
/ 47.2
| 72 | L120L (TTG→TTA) | rpoN | RNA polymerase, sigma 54 (sigma N) factor |
| Reads supporting (aligned to +/- strand): ref base G (21/7); new base A (24/20); total (45/27) |
| Fisher's exact test for biased strand distribution p-value = 1.33e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.54e-01 |
GCACCAGCGGTGACTACATTGACGACGAGCTGCCGGTCTACCAGGGCGAAACGACGCAGACCTTGCAGGATTACCTGATGTGGCAGGTTGAGCTGACACCGTTTTCCGACACTGACCGCGCTAT > minE/2170105‑2170228
|
gCACCAGCGGTGACTACATTGACGACGAGCTGCCGGTCTACCAGGGCGAAACGACGCAGACCTTGCAgg < 1:2823446/69‑1 (MQ=255)
gCGGTGACTACATTGACGACGAGCTGCCGGTCTACCAGGGCGAAACGACGCAGACCTTGCAGGATTAc > 1:1031241/1‑68 (MQ=255)
gCGGTGACTACATTGACGACGAGCTGCCGGTCTACCAGGGCGAAACGACGCAGACCTTGCAGGATTAc > 1:2316578/1‑68 (MQ=255)
gCGGTGACTACATTGACGACGAGCTGCCGGTCTACCAGGGCGAAACGACGCAGACCTTGCAGGATTAc > 1:2992855/1‑68 (MQ=255)
gCGGTGACTACATTGACGAAGAGCTGCCGGTCTACCAGGGCGAAACGAGGCAGACCTTGCAGGATTAc > 1:240208/1‑68 (MQ=255)
cGGTGACTACATTGACGACGAGCTGCCGGTCTACCAGGGCGAAACGACGCAGACCTTGCAGTATTACCt < 1:950257/69‑1 (MQ=255)
cGGTGACTACATTGACGACGAGCTGCCGGTCTACCAGGGCGAAACGACGCAGACCTTGCAGGATTACCt < 1:1013449/69‑1 (MQ=255)
gaGCTGCCGGTCTACCAGGGCGAAACGACTCAGACCTTGCAGGATTACCTGATGTGGCAGGTTGAGCt > 1:1870233/1‑68 (MQ=255)
gaGCTGCCGGTCTACCAGGGCGAAACGACGCAGACCTTGCAGGATTACCTGATGTGGc > 1:3038703/1‑58 (MQ=255)
gaGCTGCCGGTCTACCAGGGCGAAACGACGCAGACCTTGCAGGATTACCTGATGTGGCAGGTTGAGc > 1:128575/1‑67 (MQ=255)
gaGCTGCCGGTCTACCAGGGCGAAACGACGCAGACCTTGCAGGATTACCTGATGTGGCAGGTTGAGCt > 1:2946221/1‑68 (MQ=255)
gaGCTGCCGGTCTACCAGGGCGAAACGACGCAGACCTTGCAGGATTACCTGATGTGGCAGGTTGAGCt > 1:2554424/1‑68 (MQ=255)
gaGCTGCCGGTCTACCAGGGCGAAACGACGCAGACCTTGCAGGATTACCTGATGTGGCAGGTTGAGCt > 1:189552/1‑68 (MQ=255)
gaGCTGCCGGTCTACCAGGGCGAAACGACGCAGACCTTGCAGGATTACCTGATGTGGCAGGTTGAGCt > 1:2038506/1‑68 (MQ=255)
gaGCTGCCGGTCTACCAGGGCGAAACGACGCAGACCTTGCAGGATTACCTGATGTGGCAGGTTGAGCt > 1:2552217/1‑68 (MQ=255)
gaGCTGCCGGTCTACCAGGGCGAAACGACGCAGACCTTGCAGGATTACCTGATGTGGCAGGTTGAGCt > 1:2626912/1‑68 (MQ=255)
gaGCTGCCGGTCTACCAGGGCGAAACGACGCAGACCTTGCAGGATTACCTGATGTGGCAGGTTGAGCt > 1:2707383/1‑68 (MQ=255)
gaGCTGCCGGTCTACCAGGGCGAAACGACGCAGACCTTGCAGGATTACCTGATGTGGCAGGTTGAGCt > 1:788854/1‑68 (MQ=255)
gaGCTGCCGGTCTACCAGGGCGAAACGACGCAGACCTTGCAGGATTACCTGATGTGGCAGGTTGAGCt > 1:3174769/1‑68 (MQ=255)
gaGCTGCCGGTCTACCAGGGCGAAACGACGCAGACCTTGCAGGATTACCTGATGTGGCAGGTTGAGCt > 1:3262953/1‑68 (MQ=255)
gaGCTGCCGGTCTACCAGGGCGAAACGACGCAGACCTTGCAGGATTACCTGATGTGGCAGGTTGAGCt > 1:645742/1‑68 (MQ=255)
gTCTATCAGGGCGAAACGACACAGACCTTACAGGATTACCTGATGTGGCAGGtcg < 1:2515537/55‑3 (MQ=255)
gTCTATCAGGGCGAAACGACACAGACCTTACAGGATTACCTGATGTGGCAGGtcg < 1:2524915/55‑3 (MQ=255)
gTCTATCAGGGCGAAACGACACAGACCTTACAGGATTACCTGATGTGGCAGGtcg < 1:99365/55‑3 (MQ=255)
gTCTATCAGGGCGAAACGACACAGACCTTACAGGATTACCTGATGTGGCAGGtcg < 1:2601295/55‑3 (MQ=255)
gTCTATCAGGGCGAAACGACACAGACCTTACAGGATTACCTGATGTGGCAGGtcg < 1:2606633/55‑3 (MQ=255)
gTCTATCAGGGCGAAACGACACAGACCTTACAGGATTACCTGATGTGGCAGGtcg < 1:2885260/55‑3 (MQ=255)
gTCTATCAGGGCGAAACGACACAGACCTTACAGGATTACCTGATGTGGCAGGtcg < 1:2966309/55‑3 (MQ=255)
gTCTATCAGGGCGAAACGACACAGACCTTACAGGATTACCTGATGTGGCAGGtcg < 1:3149437/55‑3 (MQ=255)
gTCTATCAGGGCGAAACGACACAGACCTTACAGGATTACCTGATGTGGCAGGtcg < 1:376331/55‑3 (MQ=255)
gTCTATCAGGGCGAAACGACACAGACCTTACAGGATTACCTGATGTGGCAGGtcg < 1:1456565/55‑3 (MQ=255)
gTCTATCAGGGCGAAACGACACAGACCTTACAGGATTACCTGATGTGGCAGGtcg < 1:1062548/55‑3 (MQ=255)
gTCTATCAGGGCGAAACGACACAGACCTTACAGGATTACCTGATGTGGCAGGtcg < 1:1130132/55‑3 (MQ=255)
gTCTATCAGGGCGAAACGACACAGACCTTACAGGATTACCTGATGTGGCAGGtcg < 1:118784/55‑3 (MQ=255)
gTCTATCAGGGCGAAACGACACAGACCTTACAGGATTACCTGATGTGGCAGGtcg < 1:1558297/55‑3 (MQ=255)
gTCTATCAGGGCGAAACGACACAGACCTTACAGGATTACCTGATGTGGCAGGtcg < 1:1593726/55‑3 (MQ=255)
gTCTATCAGGGCGAAACGACACAGACCTTACAGGATTACCTGATGTGGCAGGtcg < 1:1680454/55‑3 (MQ=255)
gTCTATCAGGGCGAAACGACACAGACCTTACAGGATTACCTGATGTGGCAGGtcg < 1:177496/55‑3 (MQ=255)
gTCTATCAGGGCGAAACGACACAGACCTTACAGGATTACCTGATGTGGCAGGtcg < 1:1823184/55‑3 (MQ=255)
gTCTATCAGGGCGAAACGACAAAGACCTTACAGGATTACCTGATGTGGCAGGtcg < 1:1106012/55‑3 (MQ=255)
tCTATCAGGGCGAAACGACACAGACCTTACAGGATTACCTGATGTGGCAGGtcg < 1:63588/54‑3 (MQ=38)
tACCAGGGCGAAACGACGCAGACCTTGCAGGATTACCTGATGTGGCAGGTTGAGCTGACACCGTTTTcc < 1:3413817/69‑1 (MQ=255)
aGGGCGAAACGACGCAGACCTTGCAGGATTACCTGATGTGGCAGGTTGAGCTGACACCGTTTTCCGac < 1:2447740/68‑1 (MQ=255)
aGGGCGAAACGACGCAGACCTTGCAGGATTACCTGATGTGGCAGGTTGAGCTGACACCGTTTTCCGac < 1:428264/68‑1 (MQ=255)
aGGGCGAAACGACGCAGACCTTGCAGGATTACCTGATGTGGCAGGTTGAGCTGACACCGTTTTCCGac < 1:2509165/68‑1 (MQ=255)
cGAAACGACGCAGACCTTGCAGGATTACCTGATGTGGCAGGTTGAGCTGACACCGTTTTCCGCCACTg > 1:277192/1‑68 (MQ=255)
cGAAACGACGCAGACCTTGCAGGATTACCTGATGTGGAAGGTTGAGCTGACACCGTTTTCCGACACTg > 1:1215658/1‑68 (MQ=255)
cGAAACGACGCAGACCTTGCAGGATCACCTGATGTGGCAGGTTGAGCTGACACCGTTTTCCGACACTGa > 1:3080812/1‑69 (MQ=255)
acAGACCTTACAGGATTACCTGATGTGGCAGGTCTAGTTGACACCGTTTTCCGACACTGACCGCGCTa > 1:3144662/2‑68 (MQ=255)
acAGACCTTACAGGATTACCTGATGTGGCAGGTCGAGTTGACACCGTTTTCCGACACTGACCGCGCTa > 1:1751984/2‑68 (MQ=255)
acAGACCTTACAGGATTACCTGATGTGGCAGGTCGAGTTGACACCGTTTTCCGACACTGACCGCGCTa > 1:2288085/2‑68 (MQ=255)
acAGACCTTACAGGATTACCTGATGTGGCAGGTCGAGTTGACACCGTTTTCCGACACTGACCGCGCTa > 1:476018/2‑68 (MQ=255)
acAGACCTTACAGGATTACCTGATGTGGCAGGTCGAGTTGACACCGTTTTCCGACACTGACCGCGCTAt > 1:2900202/2‑69 (MQ=255)
acAGACCTTACAGGATTACCTGATGTGGCAGGTCGAGTTGACACCGTTTTCCGACACTGACCGCGCTAt > 1:1691039/2‑69 (MQ=255)
acAGACCTTACAGGATTACCTGATGTGGCAGGTCGAGTTGACACCGTTTTCCGACACTGACCGCGCTAt > 1:2604925/2‑69 (MQ=255)
acAGACCTTACAGGATTACCTGATGTGGCAGGTCGAGTTGACACCGTTTTCCGACACTGACCGCGCTAt > 1:826760/2‑69 (MQ=255)
acAGACCTTACAGGATTACCTGATGTGGCAGGTCGAGTTGACACCGTTTTCCGACACTGACCGCGCTAt > 1:2849884/2‑69 (MQ=255)
acAGACCTTACAGGATTACCTGATGTGGCAGGTCGAGTTGACACCGTTTTCCGACACTGACCGCGCTAt > 1:762550/2‑69 (MQ=255)
acAGACCTTACAGGATTACCTGATGTGGCAGGTCGAGTTGACACCGTTTTCCGACACTGACCGCGCTAt > 1:1181898/2‑69 (MQ=255)
acAGACCTTACAGGATTACCTGATGTGGCAGGTCGAGTTGACACCGTTTTCCGACACTGACCGCGCTAt > 1:1603449/2‑69 (MQ=255)
acAGACCTTACAGGATTACCTGATGTGGCAGGTCGAGTTGACACCGTTTTCCGACACTGACCGCGCTAt > 1:562277/2‑69 (MQ=255)
acAGACCTTACAGGATTACCTGATGTGGCAGGTCGAGTTGACACCGTTTTCCGACACTGACCGCGCTAt > 1:552226/2‑69 (MQ=255)
acAGACCTTACAGGATTACCTGATGTGGCAGGTCGAGTTGACACCGTTTTCCGACACTGACCGCGCTAt > 1:1282176/2‑69 (MQ=255)
acAGACCTTACAGGATTACCTGATGTGGCAGGTCGAGTTGACACCGTTTTCCGACACTGACCGCGCTAt > 1:159824/2‑69 (MQ=255)
acAGACCTTACAGGATTACCTGATGTGGCAGGTCGAGTTGACACCGTTTTCCGACACTGACCGCGCTAt > 1:37647/2‑69 (MQ=255)
acAGACCTTACAGGATTACCTGATGTGGCAGGTCGAGTTGACACCGTTTTCCGACACTGACCGCGCTAt > 1:2111439/2‑69 (MQ=255)
acAGACCTTACAGGATTACCTGATGTGGCAGGTCGAGTTGACACCGTTTTCCGACACTGACCGCGCTAt > 1:1995597/2‑69 (MQ=255)
acAGACCTTACAGGATTACCTGATGTGGCAGGTCGAGTTGACACCGTTTTCCGACACTGACCGCGCTAt > 1:3328409/2‑69 (MQ=255)
acAGACCTTACAGGATTACCTGATGTGGCAGGTCGAGTTGACACCGTTTTCCGACACTGACCGCGCTAt > 1:3291146/2‑69 (MQ=255)
acAGACCTTACAGGATTACCTGATGTGGCAGGTCGAGTTGACACCGTTTTCCGACACTGACCGCGCTAt > 1:1529799/2‑69 (MQ=255)
acAGACCTTACAGGATTACCTGATGTGGCAGGTCGAGTTGACACCGTTTTCCGACACTGACCGCGCTAt > 1:3223610/2‑69 (MQ=255)
acAGACCTTACAGGATTACCTGATGTGGCAGGTCGAGTTGACACCGTTTTCCGACACTGACCGCGCTAt > 1:3195855/2‑69 (MQ=255)
|
GCACCAGCGGTGACTACATTGACGACGAGCTGCCGGTCTACCAGGGCGAAACGACGCAGACCTTGCAGGATTACCTGATGTGGCAGGTTGAGCTGACACCGTTTTCCGACACTGACCGCGCTAT > minE/2170105‑2170228
|
| 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
