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 |
|
A4 F21 I0 R1
|
1009 |
73.8 |
4146436 |
87.4% |
3623985 |
60.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,954,083 |
A→G |
43.6% |
F9S (TTT→TCT) |
pepP ← |
proline aminopeptidase P II |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,954,083 | 0 | A | G | 43.6%
| 17.0
/ 70.7
| 55 | F9S (TTT→TCT) | pepP | proline aminopeptidase P II |
| Reads supporting (aligned to +/- strand): ref base A (15/16); new base G (10/14); total (25/30) |
| Fisher's exact test for biased strand distribution p-value = 7.85e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TGCAGCAAAAATCAGCGCGGCGCTGCCGGGTTGCATTTGCTCCACCAGGGCCTGACGGCGACGCTGAAACTCTTGCCGGGATATCTCACTCATAACACTCTCCTTACGTTTTTTGTTTTTAGTGTAGAGTCGGTTT > minE/1954016‑1954151
|
tGCAGCAAAAATCAGCGCGGCGCTGCCGGGTTGCATTTGCTCCACCAGGGCCTGACGGCGACGCTGAGAct < 1:2012872/71‑1 (MQ=255)
cagcaAAAATCAGCGCGGCGCTGCCGGGTTGCATTTGCTCCACCAGGGCCTGACGGCGACGCTGAAActct > 1:1644889/1‑71 (MQ=255)
aaaaTCAGCGCGGCGCTGCCGGGTTGCATTTGCTCCACCAGGGCCTGACGGCGACGCTGAGACTCTTGCCg > 1:3899598/1‑71 (MQ=255)
aTCAGCGCGGCGCTGCCGGGTTGCATTTGCTCCACCAGGGCCTGACGGCGACGCTGAAACTCTTGCCggg > 1:2554265/1‑70 (MQ=255)
aGCGCGGCGCTGCCGGGTTGCATTTGCTCCACCAGGGCCTGACGGCGACGCTGAAACTCTTGCCGGGatat < 1:2400673/71‑1 (MQ=255)
aGCGCGGCGCTGCCGGGTTGCATTTGCTCCACCAGGGCCTGACGGCGACGCTGAAACTCTTGCCGGGatat < 1:393335/71‑1 (MQ=255)
aGCGAGGCGCTGCCGGGTTGCATTTGCTCCACCAGGGCCTGACGGCGACGCTGAAACTCTTGCCGGGata > 1:1534522/1‑70 (MQ=255)
gcgcGGCGCTGCCGGGTTGCATTTGCTCCACCAGGGCCTGACGGCGACGCTGAAACTCTTGCCGGGat < 1:2765023/68‑1 (MQ=255)
gcggcgCTGCCGGGTTGCATTTGCTCCACCAGGGCCTGACGGCGACGCTGAAACTCTTGCCGGGATAtct < 1:3025126/70‑1 (MQ=255)
cTGCCGGGTTGCATTTGCTCCACCAGGGCCTGACGGCGACGCTGAGACTCTTGCCGGGATATCTCACTCAt < 1:891858/71‑1 (MQ=255)
cTGCCGGGTTGCATTTGCTCCACCAGGGCCTGACGGCGACGCTGAAACTCTTGCCGGGATATCTCACTCAt < 1:2312674/71‑1 (MQ=255)
gCCGGGTTGCATTTGCTCCACCAGGGCCTGACGGCGACGCTGAAACTCTTGCCGGGATATCTCACTCATaa > 1:1578672/1‑71 (MQ=255)
ccGGGTTGCATTTGCTCCACCAGGGCCTGACGGCGACGCTGAGACTCTTGCCGGGATATCTCACTCATaa < 1:2233814/70‑1 (MQ=255)
ccGGGTTGCATTTGCTCCACCAGGGCCTGACGGCGACGCTGAAACTCTTGCCGGGATATCTCACTCATaa < 1:725472/70‑1 (MQ=255)
gTTGCATTTGCTCCACCAGGGCCTGACGGCGACGCTGAAACTCTTGCCGGGATATCTCACTCATAACActc < 1:1691777/71‑1 (MQ=255)
tttGCTCCACCAGGGCCTGACGGCGACGCTGAAACTCTTGCCGGGATATctcac > 1:862656/1‑54 (MQ=255)
tttGCTCCACCAGGGCCTGACGGCGACGCTGAAACTCTTGCCGGGATATCTCACTCATAACACTCTCCTTa < 1:3830780/71‑1 (MQ=255)
caccaGGGCCTGACGGCGACGCTGAGACTCTTGCCGGGATATCTCACTCATAACACTCTCCTTACGtttt < 1:3831840/70‑1 (MQ=255)
caccaGGGCCTGACGGCGACGCTGAAACTCTTGCCGGGATATCTCACTCATAACACTCTCCTTACGtttt < 1:3177619/70‑1 (MQ=255)
ccaGTGCCTGACGGCGACGCTGAGACTCTTGCCGGGATAtc < 1:3510232/41‑1 (MQ=38)
ccaGGGCCTGACTGCGACGCTGAGACTCTTGCCGGGATATCTCACTCAt < 1:1159283/49‑1 (MQ=39)
ccaGGGCCTGACGGCGACGCTGAGACTCTTGCCggg < 1:3475501/36‑1 (MQ=255)
ccaGGGCCTGACGGCGACGCTGAGACTCTTGCCgg < 1:2969154/35‑1 (MQ=255)
ccaGGGCCTGACGGCGACGCTGAGACTCTTGCCGGGATATCTCACTCATaa > 1:56499/1‑51 (MQ=255)
ccaGGGCCTGACGGCGACGCTGAGACTCTTGCCGGGATATCTCACTCATAACACTCTCCTTACGtttttt < 1:1326586/70‑1 (MQ=255)
ccaGGGCCTGACGGCGACGCTGAGACTCTTGCCGGGATATCTCACTCATAACACTCTCCTTACGTTTTTTg > 1:1466774/1‑71 (MQ=255)
ccaGGGCCTGACGGCGACGCTGAGACTCTTGCCGGGATATCTCACTAATAACACTCTCCTTACGTTTTTTg > 1:4123331/1‑71 (MQ=255)
acaGGGCCTGACGGCGACGCTGAGACTCTTGCCGGGATATCTCACTCATAACACTCTCCTTACGTTTTTTg > 1:2936488/2‑71 (MQ=255)
aGGGCCTGACGGCGACGCTGAGACTCTTGCCGGGATATctca > 1:3812198/1‑42 (MQ=255)
aGGGCCTGACGGCGACGCTGAGACTCTTGCCGGGATATCTCACTCATAACACTCTCCTTACGTTTTTTg > 1:2302245/1‑69 (MQ=255)
aGGGCCTGACGGCGACGCTGAGACTCTTGCCGGGATATCTCACTCATAACACTCTCCTTACGTTTTTTg > 1:2297490/1‑69 (MQ=255)
aGGGCCTGACGGCGACGCTGAAACTCTTGCCGGGATATCTCACTCAt < 1:2046454/47‑1 (MQ=255)
aGGGCCTGACGGCGACGCTGAAACTCTTGCCGGGATATCTCACTCAt < 1:496386/47‑1 (MQ=255)
gggCCTGACGGCGACGCTGAAACTCTTGCCGGGATAtct > 1:3183065/1‑39 (MQ=255)
ggCCTGACGGCGACGCTGAGACTCTTGCCGGGATATCTCACTCATAACACTCTCCTTACGTTTTTTGtttt > 1:3840016/1‑71 (MQ=255)
ggCCTGACGGCGACGCTGAGACTCTTGCCGGGATATCTCACTCATAACACTCTCCTTACGTTTTTTGtttt < 1:649804/71‑1 (MQ=255)
gCCTGACGGCGACGCTGAAACTCTTGCCGGGATATCTCACTCATAACACTCTCCTTACGTTTTTTGttttt < 1:4026301/71‑1 (MQ=255)
gCCTGACGGCGACGCTGAAACTCTTGCCGGGATATCTCACTCATAACACTCTCCTTACGTTTTTTGttttt < 1:1878340/71‑1 (MQ=255)
ccTGACGGCGACGCTGAAACTCTTGCCGGGATATCTCACTCATAACACTCTCCTTACGTTTTTTGtttt > 1:510919/1‑69 (MQ=255)
cTGACGGCGACGCTGAAACTCTTGCCGGGATATCTCACTCATAACACTCTCCTTACGTTTTTTGtttt < 1:2226256/68‑1 (MQ=255)
tGACGGCGACGCTGAAACTCTTGCCGGGATATCTCACTCAt < 1:1238286/41‑1 (MQ=255)
aCGGCGACGCTGAGACTCTTGCCGGGATATCTCACTCATAACACTCTCCTTACGTTTTTTGttttt < 1:2000609/66‑1 (MQ=255)
aCGGCGACGCTGAGACTCTTGCCGGGATATCTCACTCATAACACTCTCCTTACGTTTTTTGTTTTTAgtgt < 1:1960533/71‑1 (MQ=255)
aCGGCGACGCTGAGACTCTTGCCGGGATATCTCACTCATAACACTCTCCTTACGTTTTTTGTTTTTAgtg > 1:1897046/1‑70 (MQ=255)
aCGGCGACGCTGAAACTCTTGCCGGGATATCTCACTCATAACACtctc > 1:2979792/1‑48 (MQ=255)
aCGGCGACGCTGAAACTCTTGCCGGGATATCTCACTCATAACACTCTCCt > 1:2602062/1‑50 (MQ=255)
aCGGCGACGCTGAAACTCTTGCCGGGATATCTCACTCATAACACTCTCCTTAc > 1:693183/1‑53 (MQ=255)
cGGCGACGCTGAGACTCTTGCCGGGATATCTCACTCATAACACTCTCCTTACGTTTTTTGTTTTTAGTGTa < 1:1064171/71‑1 (MQ=255)
cGGCGACGCTGAAACTCTTGCCGGGATATCTCACTCATAACACTCTCCTTACGTTTTTTGTTTTTAgtg > 1:784751/1‑69 (MQ=255)
cGACGCTGAAACTCTTGCCGGGATATCTCACTCATAACACTCTCCTTACGTTTTTTGtttt < 1:973827/61‑1 (MQ=255)
aCGCTGAAACTCTTGCCGGGATATCTCACTCATAACACTCTCCTTACGTTTTTTGttt > 1:3013725/1‑58 (MQ=255)
cTGAAACTCTTGCCGGGATATCTCACTCATAACACTCTCCTTACGt > 1:3339571/1‑46 (MQ=255)
cTGAAACTCTTGCCGGGATATCTCACTCATAACACTCTCCTTACGTTTTTTGTTTTTAgtg > 1:3601139/1‑61 (MQ=255)
tGAGACTCTTGCCGGGATATCTCACTCATAACActct < 1:3298121/37‑1 (MQ=255)
gAAACTCTTGCCGGGATATCTCACTCATAACACTCTCCTTACGTTTTTTGttt > 1:1370381/1‑53 (MQ=255)
aaaCTCTTGCCGGGATATCTCACTCATAACACTCTCCTTACGTTTTTTGTTTTTAgtg < 1:3723811/58‑1 (MQ=255)
aaaCTCTTGCCGGGATATCTCACTCATAACACTCTCCTTACGTTTTTTGTTTTTAGTGTAGAGTCGGttt < 1:2215894/70‑1 (MQ=255)
|
TGCAGCAAAAATCAGCGCGGCGCTGCCGGGTTGCATTTGCTCCACCAGGGCCTGACGGCGACGCTGAAACTCTTGCCGGGATATCTCACTCATAACACTCTCCTTACGTTTTTTGTTTTTAGTGTAGAGTCGGTTT > minE/1954016‑1954151
|
| 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
