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 |
2,389,219 |
A→G |
32.8% |
Y75Y (TAT→TAC) |
pldB ← |
lysophospholipase L(2) |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,389,219 | 0 | A | G | 32.8%
| 50.8
/ 34.1
| 67 | Y75Y (TAT→TAC) | pldB | lysophospholipase L(2) |
| Reads supporting (aligned to +/- strand): ref base A (33/12); new base G (10/12); total (43/24) |
| Fisher's exact test for biased strand distribution p-value = 3.26e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.48e-01 |
AGGCGACCGGAACGTCCCTGCCCGCGATGGTCGATGATTAAGACATCAAACCCCAAATGGAACAGGTCATAGGCCAGTTCCGCATATTTTACGTAGCTCTCAATACGCCCCGGGCAGATGACTAC > minE/2389151‑2389275
|
aGGCGACCGGAACGTCCCTGCCCGCGATGGTCGATGATTAAGACATCAAACCCCAAATGGAACAGGTCa < 1:714609/69‑1 (MQ=255)
aGGCGACCGGAACGTCCCTGCCCGCGATGGTCGATGATTAAGACATCAAACCCCAAATGGAACAGGTCa < 1:3319339/69‑1 (MQ=255)
aGGCGACCGGAACGTCCCTGCCCGCGATGGTCGATGATTAAGACATCAAACCCCAAATGGAACAGGTCa < 1:2915471/69‑1 (MQ=255)
cGGAACGTCCCTGCCCGCGATGGTCGATGATTAAGACATCAAACCCCAAATGGAACAGGTCATAGGCCa > 1:3310621/1‑69 (MQ=255)
cGGAACGTCCCTGCCCGCGATGGTCGATGATTAAGACATCAAACCCCAAATGGAACAGGTCATAGGCCa > 1:2537325/1‑69 (MQ=255)
ccTGCCCGCGATGGTCGATGATTAAGACATCAAACCCCAAATGGAACAGGTCa < 1:1245390/53‑1 (MQ=255)
tGCCCGCGATGGTCGATGATTAAGACATCAAACCCCAAATGGAACAGGTCATAGGCCAg > 1:2492086/1‑59 (MQ=255)
tGCCCGCGATGGTCGATGATTAAGACATCAAACCCCAAATGGAACAGGTCATAGGCCAGTTCCGCatat > 1:982997/1‑69 (MQ=255)
tGCCCGCGATGGTCGATGATTAAGACATCAAACCCCAAATGGAACAGGTCATAGGCCAGTTCCGCatat > 1:779816/1‑69 (MQ=255)
tGCCCGCGATGGTCGATGATTAAGACATCAAACCCCAAATGGAACAGGTCATAGGCCAGTTCCGCatat > 1:2740841/1‑69 (MQ=255)
tGCCCGCGATGGTCGATGATTAAGACATCAAACCCCAAATGGAACAGGTCATAGGCCAGTTCCGCatat > 1:201231/1‑69 (MQ=255)
tGCCCGCGATGGTCGATGATTAAGACATCAAACCCCAAATGGAACAGGTCATAGGCCAGTTCCGCatat > 1:192447/1‑69 (MQ=255)
tGCCCGCGATGGTCGATGATTAAGACATCAAACCCCAAATGGAACAGGTCATAGGCCAGTTCCGCatat > 1:1613976/1‑69 (MQ=255)
tGCCCGCGATGGTCGATGATTAAGACATCAAACCCCAAATGGAACAGGTCATAGGCCAGTTCCGCata > 1:94741/1‑68 (MQ=255)
tGCCCGCGATGGTCGATGATTAAGACATCAAACCCCAAATGGAACAGGTCATAGGCCAGTTCCGCata > 1:2011625/1‑68 (MQ=255)
tGCCCGCGATGGTCGATGATTAAGACATCAAACCCCAAATGGAACAGGTCATAGGCCAGTTCCGCata > 1:927111/1‑68 (MQ=255)
tGCCCGCGATGGTCGATGATTAAGACATCAAACCCCAAATGGAACAGGTCATAGGCCAGTTCCGCata > 1:2100982/1‑68 (MQ=255)
tGCCCGCGATGGTCGATGATTAAGACATCAAACCCCAAATGGAACAGGTCATAGGCCAGTTCCGCata > 1:2594967/1‑68 (MQ=255)
aTGGTCGATGATTAAGACATCAAACCCCAAATGGAACAGGTCATAGGCCAGTTCCGCATATTTTACGt > 1:2023099/1‑68 (MQ=255)
aTGGTCGATGATTAAGACATCAAACCCCAAATGGAACAGGTCATAGGCCAGTTCCGCATATTTTACGTa > 1:2778001/1‑69 (MQ=255)
aTGGTCGATGATTAAGACATCAAACCCCAAATGGAACAGGTCATAGGCCAGTTCCGCATATTTTACGTa > 1:1234326/1‑69 (MQ=255)
aTGGTCGATGATTAAGACATCAAACCCCAAATGGAACAGGTCATAGGCCAGTTCCGCATATTTTACGTa > 1:574708/1‑69 (MQ=255)
aTGGTCGATGATTAAGACATCAAACCCCAAATGGAACAGGTCATAGGCCAGTTCCGCATATTTTACGTa < 1:2313772/69‑1 (MQ=255)
aTGGTCGATGATTAAGACATCAAACCCCAAATGGAACAGGTCATAGGCCAGTTCCGCATATTTTACGTa > 1:3016612/1‑69 (MQ=255)
aTGGTCGATGATTAAGACATCAAACCCCAAATGGAACAGGTCATAGGCCAGTTCCGCATATTTTACGTa > 1:2772047/1‑69 (MQ=255)
aTGGTCGATGATTAAGACATCAAACCCCAAATGGAACAGGTCATAGGCCAGTTCCGCATATTTTACGTa > 1:1593991/1‑69 (MQ=255)
aTGGTCGATGATTAAGACATCAAACCCCAAATGGAACAGGTCATAGGCCAGTTCCGCATATTTTACGTa > 1:1951467/1‑69 (MQ=255)
gatgatTAAGACATCAAACCCCAAATGGAACAGGTCATAGGCCAGTTCCGCATATTTTACGTAGCtctc < 1:919493/69‑1 (MQ=255)
gatgatTAAGACATCAAACCCCAAATGGAACAGGTCATAGGCCAGTTCCGCATATTTTACGTAGCtctc < 1:622435/69‑1 (MQ=255)
tgatTAAGACATCAAACCCCAAATGGAACAGGTCATAGGCCAGTTCCGCATATTTTACGTAGCTCTCaa < 1:2703816/69‑1 (MQ=255)
tgatTAAGACATCAAACCCCAAATGGAACAGGTCATAGGCCAGTTCCGCATATTTTACGTAGCTCTCaa < 1:959043/69‑1 (MQ=255)
tgatTAAGACATCAAACCCCAAATGGAACAGGTCATAGGCCAGTTCCGCATATTTTACGTAGCTCTCaa < 1:845911/69‑1 (MQ=255)
tgatTAAGACATCAAACCCCAAATGGAACAGGTCATAGGCCAGTTCCGCATATTTTACGTAGCTCTCaa < 1:3152141/69‑1 (MQ=255)
tgatTAAGACATCAAACCCCAAATGGAACAGGTCATAGGCCAGTTCCGCATATTTTACGTAGCTCTCaa < 1:2011371/69‑1 (MQ=255)
aCATCAAACCCCAAATGGAACAGGTCGTAGGCCAGTTCCGCATATTTTACGTAGCTCTCAATACGccc < 1:54794/68‑1 (MQ=255)
aCATCAAACCCCAAATGGAACAGGTCGTAGGCCAGTTCCGCATATTTTACGTAGCTCTCAATACGccc < 1:26426/68‑1 (MQ=255)
aCATCAAACCCCAAATGGAACAGGTCGTAGGCCAGTTCCGCATATTTTACGTAGCTCTCAATACGccc < 1:2655611/68‑1 (MQ=255)
aCATCAAACCCCAAATGGAACAGGTCGTAGGCCAGTTCCGCATATTTTACGTAGCTCTCAATACGccc < 1:2160865/68‑1 (MQ=255)
aCATCAAACCCCAAATGGAACAGGTCGTAGGCCAGTTCCGCATATTTTACGTAGCTCTCAATACGccc < 1:2263768/68‑1 (MQ=255)
aTCAAACCCCAAATGGAACAGGTCATAGGCCAGTTCCGCATATTTTACGTAGCTCTCAAAACGCCCCg > 1:3039940/1‑68 (MQ=255)
aaaCCCCAAATGGAACAGGTCATAGGCCAGTTCCGCATATTTTACGTAGCTCTCAATACGCCCCGGGCa < 1:2063381/69‑1 (MQ=255)
aaaCCCCAAATGGAACAGGTCATAGGCCAGTTCCGCATATTTTACGTAGCTCTCAATACGCCCCGGGCa < 1:1737861/69‑1 (MQ=255)
aaCCCCAAATGGAACAGGTCATAGGCCAGTTCCGCATATTTTACGTAGCTCTCAATACGCCCCGGGCa < 1:2370526/68‑1 (MQ=255)
aCCCCAAATGGAACAGGTCGTAGGCCAGTTCCGCATATTTTACGTAGCTCTCAATACGCCCCGGACAg < 1:3000155/68‑1 (MQ=255)
aCCCCAAATGGAACAGGTCGTAGGCCAGTTCCGCATATTTTACGTAGCTCTCAATACGCCCCGGACAg < 1:3207411/68‑1 (MQ=255)
aCCCCAAATGGAACAGGTCGTAGGCCAGTTCCGCATATTTTACGTAGCTCTCAATACGCCCCGGACAg < 1:783003/68‑1 (MQ=255)
aCCCCAAATGGAACAGGTCGTAGGCCAGTTCCGCATATTTTACGTAGCTCTCAATACGCCCCGGACAg < 1:1037009/68‑1 (MQ=255)
aCCCCAAATGGAACAGGTCGTAGGCCAGTTCCGCATATTTTACGTAGCTCTCAATACGCCCCGGACAg < 1:2981164/68‑1 (MQ=255)
aCCCCAAATGGAACAGGTCGTAGGCCAGTTCCGCATATTTTACGTAGCTCTCAATACGCCCCGGACAg < 1:2452780/68‑1 (MQ=255)
cccAAATGGAACAGGTCATAGGCCAGTTCCGCATATTTTACGTAGCTCTCAATACGCCCCGGGCAGATg < 1:2426297/69‑1 (MQ=255)
aaTGGAACAGGTCGTAGGCCAGATCCGCAGATTTTACGTAGCTCTCAATACGCCCCGGACAg < 1:1860805/62‑1 (MQ=255)
aTGGAACAGGTCGTAGGCCAGTTCCGCATATTTTACGTAGCTCTCAATACGCCCCGGACAGATGCCTa > 1:74414/1‑68 (MQ=255)
aTGGAACAGGTCGTAGGCCAGTTCCGCATATTTTACGTAGCTCTCAATACGCCCCGGACAGATGACTac > 1:183339/1‑69 (MQ=255)
aTGGAACAGGTCGTAGGCCAGTTCCGCATATTTTACGTAGCTCTCAATACGCCCCGGACAGATGACTac > 1:597334/1‑69 (MQ=255)
aTGGAACAGGTCGTAGGCCAGTTCCGCATATTTTACGTAGCTCTCAATACGCCCCGGACAGATGACTac > 1:3398616/1‑69 (MQ=255)
aTGGAACAGGTCGTAGGCCAGTTCCGCATATTTTACGTAGCTCTCAATACGCCCCGGACAGATGACTac > 1:2938147/1‑69 (MQ=255)
aTGGAACAGGTCGTAGGCCAGTTCCGCATATTTTACGTAGCTCTCAATACGCCCCGGACAGATGACTac > 1:2817784/1‑69 (MQ=255)
aTGGAACAGGTCGTAGGCCAGTTCCGCATATTTTACGTAGCTCTCAATACGCCCCGGACAGATGACTac > 1:2751830/1‑69 (MQ=255)
aTGGAACAGGTCGTAGGCCAGTTCCGCATATTTTACGTAGCTCTCAATACGCCCCGGACAGATGACTac > 1:1701147/1‑69 (MQ=255)
aTGGAACAGGTCGTAGGCCAGTTCCGCATATTTTACGTAGCTCTCAATACGCCCCGGACAGATGACTac > 1:2457459/1‑69 (MQ=255)
aTGGAACAGGTCGTAGGCCAGTTCCGCATATTTTACGTAGCTCTCAATACGCCCCGGACAGATGACTac > 1:931476/1‑69 (MQ=255)
gAACAGGTCATAGGCCAGTTCCGCATATTTTACGTAGCTCTCaa > 1:2683103/1‑44 (MQ=255)
gAACAGGTCATAGGCCAGTTCCGCATATTTTACGTAGCTCTCaa > 1:3095460/1‑44 (MQ=255)
gAACAGGTCATAGGCCAGTTCCGCATATTTTACGTAGCTCTCaa > 1:3071753/1‑44 (MQ=255)
gAACAGGTCATAGGCCAGTTCCGCATATTTTACGTAGCTCTCaa > 1:258785/1‑44 (MQ=255)
gAACAGGTCATAGGCCAGTTCCGCATATTTTACGTAGCTCTCaa > 1:2443465/1‑44 (MQ=255)
gAACAGGTCATAGGCCAGTTCCGCATATTTTACGTAGCTCTCaa > 1:1818242/1‑44 (MQ=255)
gAACAGGTCATAGGCCAGTTCCGCATATTTTACGTAGCTCTCaa > 1:1809903/1‑44 (MQ=255)
gAACAGGTCATAGGCCAGTTCCGCATATTTTACGTAGCTCTCaa > 1:1425395/1‑44 (MQ=255)
gAACAGGTCATAGGCCAGTTCCGCATATTTTACGTAGCTCTCaa > 1:1053224/1‑44 (MQ=255)
gAACAGGTCATAGGCCAGTTCCGCATATTTTACGTAGCTCCCaa > 1:960777/1‑44 (MQ=255)
|
AGGCGACCGGAACGTCCCTGCCCGCGATGGTCGATGATTAAGACATCAAACCCCAAATGGAACAGGTCATAGGCCAGTTCCGCATATTTTACGTAGCTCTCAATACGCCCCGGGCAGATGACTAC > minE/2389151‑2389275
|
| 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
