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 |
|
A6 F21 I0 R2
|
370 |
72.1 |
3738297 |
91.5% |
3420541 |
62.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
2,546,001 |
C→T |
51.6% |
M182I (ATG→ATA) |
rfaF ← |
ADP‑heptose:LPS heptosyltransferase II |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,546,001 | 0 | C | T | 51.6%
| 2.1
/ 88.3
| 62 | M182I (ATG→ATA) | rfaF | ADP‑heptose:LPS heptosyltransferase II |
| Reads supporting (aligned to +/- strand): ref base C (15/15); new base T (19/13); total (34/28) |
| Fisher's exact test for biased strand distribution p-value = 6.10e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CAGCTCCGCATAGTGGTAGTGTGGCCAGCGTTTTGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATCATCGGACGTTCTGATGAAAGCGAAAATTGATTACAGGTATATGATTTTTCACCTTCGCTCACCTGCAACT > minE/2545932‑2546071
|
cAGCTCCGCATAGTGGTAGTGTGGCCAGCGTTTTGCCGGACCAAACTCCGCACCCGGGCAAAAACCAatca < 1:3727724/71‑1 (MQ=255)
gCTCCGCATAGTGGTAGTGTGGCCAGCGTTTTGCCGGACCAAACTCCGCACCCGGGCAAAAACCAatcatc < 1:2405497/71‑1 (MQ=255)
gCTCCGCATAGTGGTAGTGTGGCCAGCGTTTTGCCGGACCAAACTCCGCACCCGGGCAAAAACCAatcatc > 1:1228174/1‑71 (MQ=255)
gCTCCGCATAGTGGTAGTGTGGCCAGCGTTTTGCCGGACCAAACTCCGCACCCGGGCAAAAACCAatcatc < 1:2618343/71‑1 (MQ=255)
cTCCGCATAGTGGTAGTGTGGCCAGCGTTTTGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATTATCg > 1:2379149/1‑71 (MQ=255)
cTCCGCATAGTGGTAGTGTGGCCAGCGTTTTGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATTATCg > 1:3677500/1‑71 (MQ=255)
ccGCATAGTGGTAGTGTGGCCAGCGTTTTGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATCATCg > 1:1458157/1‑69 (MQ=255)
gCATAGTGGTAGTGTGGCCAGCGTTTTGCCGGACCAAACTCCGCACCCGGGCAAAAACCAattatc > 1:3243920/1‑66 (MQ=255)
gCATAGTGGTAGTGTGGCCAGCGTTTTGCCGGACCAAACTCCGCACCCGGGCAAAAACCAattatc > 1:1691740/1‑66 (MQ=255)
gCATAGTGGTAGTGTGGCCAGCGTTTTGCCGGACCAAACTCCGCACCCGGGCAAAAACCAattatc > 1:1302510/1‑66 (MQ=255)
gCATAGTGGTAGTGTGGCCAGCGTTTTGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATTATCGGACg > 1:119903/1‑71 (MQ=255)
gCATAGTGGTAGTGTGGCCAGCGTTTTGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATTATCGGACg > 1:543173/1‑71 (MQ=255)
tAGTGTGGCCAGCGTTTTGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATTATCg < 1:1336456/58‑1 (MQ=255)
tAGTGTGGCCAGCGTTTTGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATTATCg < 1:1754213/58‑1 (MQ=255)
tAGTGTGGCCAGCGTTTTGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATCATCGGACGTTCtgatg > 1:1812829/1‑70 (MQ=255)
aGTGTGGCCAGCGTTTTGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATCATCGGACGTTCtgatga > 1:1567002/1‑70 (MQ=255)
gtgtGGCCAGCGTTTTGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATCATCGGACGTTCtgatga > 1:2437705/1‑69 (MQ=255)
gCCAGCGTTTTGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATCATCGGACGTTCTGATGAAAGCg < 1:1341541/69‑1 (MQ=255)
cAGCGTTTTGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATCATCGGACGTTCTGATGaa < 1:1715245/63‑1 (MQ=255)
cAGCGTTTTGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATCATCGGACGTTCTGATGAAAGCGaaaa > 1:1454600/1‑71 (MQ=255)
gCGTTTTGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATTATCGGACGTTCTGATGAAAGCGAAAAtt < 1:325238/71‑1 (MQ=255)
ttttGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATTATCGGACg < 1:3448072/48‑1 (MQ=255)
ttttGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATTATCGGACg < 1:2152974/48‑1 (MQ=255)
tttGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATTATCGGACg < 1:721953/47‑1 (MQ=255)
tttGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATTATCGGACGTTCTGATGAAAGCGAAAATTGAt > 1:559022/1‑70 (MQ=255)
tttGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATCATCGGACGTTCTGATGAAAGCGAAAATTGAt > 1:609926/1‑70 (MQ=255)
ttGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATTATCGGACGTTCTGATGAAAGCGAAAATTGAtt < 1:2778650/70‑1 (MQ=255)
ttGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATTATCGGACGTTCTGATGAAAGCGAAAATTGATTa > 1:2103461/1‑71 (MQ=255)
ttGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATTATCGGACGTTCTGATGAAAGCGAAAATTGATTa > 1:1680317/1‑71 (MQ=255)
tGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATTATCgg < 1:3199684/42‑1 (MQ=255)
tGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATTATCGGACGTTCtga > 1:3205979/1‑51 (MQ=255)
tGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATTATCGGACGTTCtga > 1:313233/1‑51 (MQ=255)
tGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATCATCGGACGTTCTGATGAAAGCGAAAATTGATTa < 1:2096905/70‑1 (MQ=255)
gCCGGACCAAACTCCGCACCCGGGCAAAAACCAATTATCGTACGTTCTGATGAAAGCTAAAATTGATTAc < 1:562090/70‑1 (MQ=255)
gCCGGACCAAACTCCGCACCCGGGCAAAAACCAATCATCGGACGTTCTGATGAAAGCGAAAATTGATTa > 1:2690928/1‑69 (MQ=255)
cGGACCAAACTCCGCACCCGGGCAAAAACCAATTATCGGACGTTCTGATGAAAGCGAAAATTGa > 1:1980364/1‑64 (MQ=255)
ggACCAAACTCCGCACCCGGGCAAAAACCAATCATCGGACGTTCTGATGaaa > 1:1766941/1‑52 (MQ=255)
gACCAAACTCCGCACCCGGGCAAAAACCAATTATCGGACGTTCTGATGaaa > 1:1378598/1‑51 (MQ=255)
aCCAAACTCCGCACCCGGGCAAAAACCAATCATCGGACGTTCTGATGAAAGCGAAAATTGATTACAGGtat < 1:942223/71‑1 (MQ=255)
aaCTCCGCACCCGGGCAAAAACCAATCATCGGACGTTCTGATGAAAGCGAAAATTGATTACAGGTATATGa < 1:1229687/71‑1 (MQ=255)
aaCTCCGCACCCGGGCAAAAACCAATCATCGGACGTTCTGATGAAAGCGAAAATTGATTACAGGTATATGa < 1:1488498/71‑1 (MQ=255)
aCTCCGCACCCGGGCAAAAACCAATTATCGGACGTTCTGATGAAAGCGAAAATTGATTACAGGTATATGAt > 1:1300823/1‑71 (MQ=255)
cGCACCCGGGCAAAAACCAATTATCGGACGTTCtgatga < 1:1824593/39‑1 (MQ=255)
cGCACCCGGGCAAAAACCAATTATCGGACGTTCTGATGAAAGCGAAAATTGAt > 1:3017481/1‑53 (MQ=255)
cGCACCCGGGCAAAAACCAATTATCGGACGTTCTGATGAAAGCGAAAATTGAt > 1:3377111/1‑53 (MQ=255)
cGCACCCGGGCAAAAACCAATCATCGGACGTTCTGATGAAAGCGAAAATTGATTACAGGTATATGAttttt < 1:1597963/71‑1 (MQ=255)
cACCCGGGAAAAAACCAATTATCGGACGTTCTGATGAAAGCGaaa > 1:118626/1‑45 (MQ=255)
aCCCGGGCAAAAACCAATCATCGGACGTTCTGATGAAAGCGAAAATTGATTACAGGTATATGATTTTTCa > 1:3502979/1‑70 (MQ=255)
cccGGGCAAAAACCAATCATCGGACGTTCTGATGAAAGCGAAAATTGATTACAGGTATATGATTTTTCAcc < 1:479825/71‑1 (MQ=255)
ccGGGCAAAAACCAATTATCGGACGTTCTGATGAAAGCGAAAATTGATTACAGGTATATGATTTTTCACCt > 1:68524/1‑71 (MQ=255)
cGGGCAAAAACCAATCATCGGACGTTCTGATGAAAGCGAAAATTGATTACAGGTATATGATTTTTCACCtt < 1:2764852/71‑1 (MQ=255)
gggCAAAAACCAATCATCGGACGTTCTGATGAAAGGGAAAATTGATTa > 1:3582537/1‑48 (MQ=255)
ggCAAAAACCAATCATCGGACGTTCTGATGAAAGCGAAAATTGATTACAGGTATATGATTTTTCACCTTCg > 1:1240442/1‑71 (MQ=255)
aaaaaCCAATTATCGGACGTTCTGATGAAAGCGAAAATTGATTACAGGTATATGATTTTTCACCTTCGCTc < 1:3324193/71‑1 (MQ=255)
aaaaaCCAATCATCGGACGTTCTGATGAAAGCGaa < 1:1646994/35‑1 (MQ=255)
aaaCCAATTATCGGACGTTCTGATGAAAGCGAAAAtt < 1:303495/37‑1 (MQ=255)
aaaCCAATTATCGGACGTTCTGATGAAAGCGAAAATTGATTACAGGTATATGATTTTTCACCTTCGCTCAc > 1:1952523/1‑71 (MQ=255)
aaaCCAATCATCGGACGTTCTGATGAAAGCGAAAATTGAt > 1:3308546/1‑40 (MQ=255)
aaaCCAATCATCGGACGTTCTGATGAAAGCGAAAATTGATTa > 1:2200642/1‑42 (MQ=255)
aaaCCAATCATCGGACGTTCTGATGAAAGCGAAAATTGATTACAGGTATATGATTTTTCACCTTCGCTCAc < 1:3168199/71‑1 (MQ=255)
aaCCAATTATCGGACGTTCTGATGAAAGCGAAAATTGATTa < 1:2391705/41‑1 (MQ=255)
ccAATTATCGGACGTTCTGATGAAAGCGAAAATTGATTACa > 1:562778/1‑41 (MQ=255)
ccAATTATCGGACGTTCTGATGAAAGCGAAAATTGATTACAGGTATATGATTTTTCACCTTCGCTCACCTg > 1:3235689/1‑71 (MQ=255)
ccAATCATCGGACGTTCTGATGAAAGCGAAAATTGATTa < 1:1945129/39‑1 (MQ=255)
ccAATCATCGGACGTTCTGATGAAAGCGAAAATTGATTa < 1:1905310/39‑1 (MQ=255)
cAATCATCGGACGTTCTGATGAAAGCGAAAATTGATTa < 1:2828444/38‑1 (MQ=255)
cAATCATCGGACGTTCTGATGAAAGCGAAAATTGATTACAGGTATATGATTTTTCACCTTCGCTCACCt > 1:1803228/1‑69 (MQ=255)
cAATCATCGGACGTTCTGATGAAAGCGAAAATTGATTACAGGTATATGATTTTTCACCTTCGCTCACCt > 1:1291959/1‑69 (MQ=255)
aaTCATCGGACGTTCTGATGAAAGCGAAAATTGATTa < 1:2338951/37‑1 (MQ=255)
catcGGACGTTCTGATGAAAGCGAAAATTGATTACAGGTATATGAtttt > 1:2041530/1‑49 (MQ=255)
catcGGACGTTCTGATGAAAGCGAAAATTGATTACAGGTATATGATTTTTCACCTTCGCTCACCTGCAACt > 1:18823/1‑71 (MQ=255)
|
CAGCTCCGCATAGTGGTAGTGTGGCCAGCGTTTTGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATCATCGGACGTTCTGATGAAAGCGAAAATTGATTACAGGTATATGATTTTTCACCTTCGCTCACCTGCAACT > minE/2545932‑2546071
|
| 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
