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 |
1,402,439 |
A→T |
45.2% |
R94R (CGA→CGT) |
rtn → |
conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,402,439 | 0 | A | T | 45.2%
| 18.8
/ 93.2
| 84 | R94R (CGA→CGT) | rtn | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base A (16/30); new base T (9/29); total (25/59) |
| Fisher's exact test for biased strand distribution p-value = 3.40e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.58e-01 |
CAAGCTAACCCCGAACTGACCGCCCGCGCAGCGTTTAGCATGAATGTCCGAACGTTTGTGCTGGTGAAAGATAAAAAAACATTCTGTTCATCTGCGACCGGTGAGATGGACATTCC > minE/1402389‑1402504
|
cAAGCTAACCCCGAACTGACCGCCCGCGCAGCGTTTAGCATGAATGTCCGAACGTTTGTGCTGGt > 1:3354490/1‑65 (MQ=255)
gCTAACCCCGAACTGACCGCCCGCGCGGCGTTTAGCATTAATGTTCGTACGTTTGTGCTGGTAAAAGAt < 1:1710428/69‑1 (MQ=255)
gCTAACCCCGAACTGACCGCCCGCGCGGCGTTTAGCATGAATGTTCGTACGTTTGTGCTGGTAAAAGAt < 1:500187/69‑1 (MQ=255)
gCTAACCCCGAACTGACCGCCCGCGCGGCGTTTAGCATGAATGTTCGTACGTTTGTGCTGGTAAAAGAt < 1:1859630/69‑1 (MQ=255)
gCTAACCCCGAACTGACCGCCCGCGCGGCGTTTAGCATGAATGTTCGTACGTTTGTGCTGGTAAAAGAt < 1:2891160/69‑1 (MQ=255)
gCTAACCCCGAACTGACCGCCCGCGCGGCGTTTAGCATGAATGTTCGTACGTTTGTGCTGGTAAAAGAt < 1:2409450/69‑1 (MQ=255)
gCTAACCCCGAACTGACCGCCCGCGCGGCGTTTAGCATGAATGTTCGTACGTTTGTGCTGGTAAAAGAt < 1:3284109/69‑1 (MQ=255)
gCTAACCCCGAACTGACCGCCCGCGCGGCGTTTAGCATGAATGTTCGTACGTTTGTGCTGGTAAAAGAt < 1:1890875/69‑1 (MQ=255)
gCTAACCCCGAACTGACCGCCCGCGCGGCGTTTAGCATGAATGTTCGTACGTTTGTGCTGGTAAAAGAt < 1:1385246/69‑1 (MQ=255)
gCTAACCCCGAACTGACCGCCCGCGCGGCGTTTAGCATGAATGTTCGTACGTTTGTGCTGGTAAAAGAt < 1:495064/69‑1 (MQ=255)
gCTAACCCCGAACTGACCGCCCGCGCGGCGTTTAGCATGAATGTTCGTACGTTTGTGCTGGTAAAAGAt < 1:2332472/69‑1 (MQ=255)
gCTAACCCCGAACTGACCGCCCGCGCGGCGTTTAGCATGAATGTTCGTACGTTTGTGCTGGTAAAAGAt < 1:1199642/69‑1 (MQ=255)
gCTAACCCCGAACTGACCGCCCGCGCGGCGTTTAGCATGAATGTTCGTACGTTTGTGCTGGTAAAAGAt < 1:2019109/69‑1 (MQ=255)
gCTAACCCCGAACTGACCGCCCGCGCGGCGTTTAGCATGAATGTTCGTACGTTTGTGCTGGTAAAAGAt < 1:893066/69‑1 (MQ=255)
gCTAACCCCGAACTGACCGCCCGCGCGGCGTTTAGCATGAATGTTCGTACGTTTGTGCTGGTAAAAGAt < 1:1054084/69‑1 (MQ=255)
gCTAACCCCGAACTGACCGCCCGCGCGGCGTTTAGCATGAATGTTCGTACGTTTGTGCTGGTAAAAGAt < 1:975863/69‑1 (MQ=255)
gCTAACCCCGAACTGACCGCCCGCGCGGCGTTTAGCATGAATGTTCGTACGTTTGTGCTGGTAAAAGAt < 1:1994782/69‑1 (MQ=255)
cTAACCCCGAACTGACCGCCCGCGCGGCGTTTAGCATGAATGTTCGTACGTTTGTGCTGGTAAAAGAt < 1:828341/68‑1 (MQ=255)
cTAACCCCGAACTGACCGCCCGCGCAGCGTTTAGCATGAATGTCCGAACGTTTGTGCTGGTGAAAGAt > 1:3326619/1‑68 (MQ=255)
cTAACCCCGAACTGACCGCCCGCGCAGCGTTTAGCATGAATGTCCGAACGTTTGTGCTGGTGAAAGAt > 1:287666/1‑68 (MQ=255)
cTAACCCCGAACTGACCGCCCGCGCAGCGTTTAGCATGAATGTCCGAACGTTTGTGCTGGTGAAAGAt > 1:2924645/1‑68 (MQ=255)
cTAACCCCGAACTGACCGCCCGCGCAGCGTTTAGCATGAATGTCCGAACGTTTGTGCTGGTGAAAGAt > 1:691099/1‑68 (MQ=255)
cTAACCCCGAACTGACCGCCCGCGCAGCGTTTAGCATGAATGTCCGAACATTTGTGCTGGTGAAAGAt > 1:240433/1‑68 (MQ=255)
ccccGAACTGACCGCCCGCGCAGCGTTTAGCATGAATGTCCGAACGTTTGTGCTGGTGAAAGATaaaaa > 1:892000/1‑69 (MQ=255)
ccccGAACTGACCGCCCGCGCAGCGTTTAGCATGAATGTCCGAACGTTTGTGCTGGTGAAAGATaaaaa > 1:993020/1‑69 (MQ=255)
ccccGAACTGACCGCCCGCGCAGCGTTTAGCATGAATGTCAGAACGTTTGTGCTGGTGaaa > 1:1037802/1‑61 (MQ=255)
ccccGAACTGACCGCCCGCGCAGCGTTTAGCATCAATGTCAGa > 1:2019425/1‑43 (MQ=38)
ccccGAACTGACCGCCCGCGCAGCGTTTAGAATGAATGTCCGAACGTTTGTGCTGGTGAAAGATaaaa > 1:1202317/1‑68 (MQ=255)
ccGAACTGACCGCCCGCGCAGCGTTTAGCATGAATGTCCGAACGTTTGTGCTGGTGAAAGATaaaaaaa < 1:2298991/69‑1 (MQ=255)
cGAACTGACCGCCCGCGCAGCGTTTAGCATGAATGTCCGAACGTTTGTGCTGGTGAAAGATaaaaaaa < 1:3196101/68‑1 (MQ=255)
gAACTGACCGCCCGCGCAGCGTTTAGCATGAATGTCCGAACGTTTGTGCTGGTGAAAGATAAAAAAACa < 1:2700279/69‑1 (MQ=255)
gAACTGACCGCCCGCGCAGCGTTTAGCATGAATGTCCGAACGTTTGTGCTGGTGAAAGATAAAAAAACa < 1:2618239/69‑1 (MQ=255)
gAACTGACCGCCCGCGCAGCGTTTAGCATGAATGTCCGAACGTTTGTGCTGGTGAAAGATAAAAAAACa < 1:682522/69‑1 (MQ=255)
gcccgcGCGGCGTTTAGCATGAATGTTCGTACGTTTGTGCTGGTAAAAGATAAAAAAACATTCTGTTCa > 1:1893460/1‑69 (MQ=255)
gcccgcGCGGCGTTTAGCATGAATGTTCGTACGTTTGTGCTGGTAAAAGATAAAAAAACATTCTGTTCa > 1:1589031/1‑69 (MQ=255)
gcccgcGCGGCGTTTAGCATGAATGTTCGTACGTTTGTGCTGGTAAAAGATAAAAAAACATTCTGTTCa > 1:2792898/1‑69 (MQ=255)
gcccgcGCGGCGTTTAGCATGAATGTTCGTACGTTTGTGCTGGTAAAAGATAAAAAAACATTCTGTTCa > 1:325034/1‑69 (MQ=255)
gcccgcGCGGCGTTTAGCATGAATGTTCGTACGTTTGTGCTGGTAAAAGATAAAAAAACATTCTGTTCa > 1:462052/1‑69 (MQ=255)
gcccgcGCGGCGTTTAGCATGAATGTTCGTACGTTTGTGCTGGTAAAAGATAAAAAAACATTCTGTTCa > 1:2370547/1‑69 (MQ=255)
gcccgcGCGGCGTTTAGCATGAATGTTCGTACGTTTGTGCTGGTAAAAGATAAAAAAACATTCTGTTCa > 1:1933019/1‑69 (MQ=255)
gcccgcGCGGCGTTTAGCATGAATGTTCGTACGTTTGTGCTGGTAAAAGATAAAAAAACATTCTGTTCa > 1:954643/1‑69 (MQ=255)
gcccgcGCGGCGTTTAGCATGAAGGTTCGTACGTTTGTGCTGGTAAAAGATAAAAAAACATTCTGt > 1:1118514/1‑66 (MQ=255)
cATGAATGTTCGTACGTTTGTGCTGGTAAAAGATAAAAAAACATTCTGTTCATCTGCGACCGGTgaga < 1:1998273/68‑1 (MQ=255)
cATGAATGTTCGTACGTTTGTGCTGGTAAAAGATAAAAAAACATTCTGTTCATCTGCGACCGGTgaga < 1:1351875/68‑1 (MQ=255)
cATGAATGTTCGTACGTTTGTGCTGGTAAAAGATAAAAAAACATTCTGTTCATCTGCGACCGGTgaga < 1:1580699/68‑1 (MQ=255)
cATGAATGTTCGTACGTTTGTGCTGGTAAAAGATAAAAAAACATTCTGTTCATCTGCGACCGGTgaga < 1:495180/68‑1 (MQ=255)
cATGAATGTTCGTACGTTTGTGCTGGTAAAAGATAAAAAAACATTCTGTTCATCTGCGACCGGTgaga < 1:3158319/68‑1 (MQ=255)
cATGAATGTTCGTACGTTTGTGCTGGTAAAAGATAAAAAAACATTCTGTTCATCTGCGACCGGTgaga < 1:849138/68‑1 (MQ=255)
cATGAATGTTCGTACGTTTGTGCTGGTAAAAGATAAAAAAACATTCTGTTCATCTGCGACCGGTgaga < 1:2577835/68‑1 (MQ=255)
cATGAATGTTCGTACGTTTGTGCTGGTAAAAGATAAAAAAACATTCTGTTCATCTGCGACCGGTgaga < 1:225046/68‑1 (MQ=255)
cATGAATGTTCGTACGTTTGTGCTGGTAAAAGATAAAAAAACATTCTGTTCATCTGCGACCGGTgaga < 1:2305788/68‑1 (MQ=255)
cATGAATGTTCGTACGTTTGTGCTGGTAAAAGATAAAAAAACATTCTGTTCATCTGCGACCGGTgaga < 1:1913613/68‑1 (MQ=255)
cATGAATGTTCGTACGTTTGTGCTGGTAAAAGATAAAAAAACATTCTGTTCATCTGCGACCGGTgaga < 1:1883677/68‑1 (MQ=255)
cATGAATGTCCGAACGTTTGTGCTGGTGAAAGATAAAAAAACATTCTGTTCATCTGCGACCGGTgaga < 1:1021748/68‑1 (MQ=255)
cATGAATGTCCGAACGTTTGTGCTGGTGAAAGATAAAAAAACATTCTGTTCATCTGCGACCGGTgaga < 1:1039396/68‑1 (MQ=255)
cATGAATGTCCGAACGTTTGTGCTGGTGAAAGATAAAAAAACATTCTGTTCATCTGCGACCGGTgaga < 1:730440/68‑1 (MQ=255)
cATGAATGTCCGAACGTTTGTGCTGGTGAAAGATAAAAAAACATTCTGTTCATCTGCGACCGGTgaga < 1:576454/68‑1 (MQ=255)
cATGAATGTCCGAACGTTTGTGCTGGTGAAAGATAAAAAAACATTCTGTTCATCTGCGACCGGTgaga < 1:2432136/68‑1 (MQ=255)
cATGAATGTCCGAACGTTTGTGCTGGTGAAAGATAAAAAAACATTCTGTTCATCTGCGACCGGTgaga < 1:37445/68‑1 (MQ=255)
aTGAATGTTCGTACGTTTGTGCTGGTAAAAGATAAAAAAACATTCTGTTCATCTGCGACCGGTgaga < 1:1070986/67‑1 (MQ=255)
aTGAATGTCCGAACGTTTGTGCTGGTGAAAGATAAAAAAACATTCTGTTCATCTGCGACCGGTgaga < 1:1937277/67‑1 (MQ=255)
aTGAATGTCCGAACGTTTGTGCTGGTGAAAGATAAAAAAACATTCTGTTCATCTGCGACCGGTGAGATg < 1:1147478/69‑1 (MQ=255)
aTGAATGTCCGAACGTTTGTGCTGGTGAAAGATAAAAAAACATTCTGTTCATCTGCGACCGGTGAGATg < 1:4584/69‑1 (MQ=255)
aTGAATGTCCGAACGTTTGTGCCGGTGAAAGATAAAAAAACATTCTGTTCATCTGCGACCGGTGAGATg < 1:1810472/69‑1 (MQ=255)
tGAATGTCCGAACGTTTGTGCTGGTGAAAGATAAAAAAACATTCTGTTCATCTGCGACCGGTGAGATg > 1:875938/1‑68 (MQ=255)
gAATGTCCGAACGTTTGTGCTGGTGAAAGATAAAAAAACATTCTGTTCATCTGCGACCGGTGAGATGGa < 1:3404751/69‑1 (MQ=255)
gAATGTCCGAACGTTTGTGCTGGTGAAAGATAAAAAAACATTCTGTTCATCTGCGACCGGTGAGATGGa < 1:2506770/69‑1 (MQ=255)
aaTGTCCGAACGTTTGTGCTGGTGAAATATAAAAAAACATTCTGTTCATCTGCGACCGGTga < 1:403367/62‑1 (MQ=255)
aaTGTCCGAACGTTTGTGCTGGTGAAAGATAAAAAAACATTCTGTTCATCTGCGACCGGTga < 1:2554983/62‑1 (MQ=255)
aaTGTCCGAACGTTTGTGCTGGTGAAAGATAAAAAAACATTCTGTTCATCTGCGACCGGTga < 1:1591984/62‑1 (MQ=255)
aaTGTCCGAACGTTTGTGCTGGTGAAAGATAAAAAAACATTCTGTTCATCTGCGACCGGTga < 1:2958388/62‑1 (MQ=255)
aaTGTCCGAACGTTTGTGCTGGTGAAAGATAAAAAAACATTCTGTTCATCTGCGACCGGTga > 1:2154108/1‑62 (MQ=255)
aaTGTCCGAACGTTTGTGCTGGTGAAAGATAAAAAAACATTCTGTTCATCTGCGACCGGTga > 1:2165478/1‑62 (MQ=255)
aaTGTCCGAACGTTTGTGCTGGTGAAAGATAAAAAAACATTCTGTTCATCTGCGACCGGTga > 1:467215/1‑62 (MQ=255)
aaTGTCCGAACGTTTGTGCTGGTGAAAGATAAAAAAACATTCTGTTCATCTGCGACCGGTga > 1:332086/1‑62 (MQ=255)
aaTGTCCGAACGTTTGTGCTGGTGAAAGATAAAAAAACATTCTGTTCATCTGCGACCGGTga < 1:1499896/62‑1 (MQ=255)
aaTGTCCGAACGTTTGTGCTGGTGAAAGATAAAAAAACATTCTGTTCATCTGCGACCGGTga > 1:552252/1‑62 (MQ=255)
ccGAACGTTTGTGCTGGTGAAAGATAAAAAAACATTCTGTTCATCTGCGACCGGTGAGATg < 1:2572001/61‑1 (MQ=255)
cGAACGTTTGTGCTGGTGAAAGATAAAAAAACATTCTGTTCATCTGCGACCGGTGAGATGGACATTcc < 1:725226/68‑1 (MQ=255)
cGAACGTTTGTGCTGGTGAAAGATAAAAAAACATTCTGTTCATCTGCGACCGGTGAGATGGACATTcc < 1:469507/68‑1 (MQ=255)
cGAACGTTTGTGCTGGTGAAAGATAAAAAAACATTCTGTTCATCTGCGACCGGTGAGATGGACATTcc < 1:1207252/68‑1 (MQ=255)
cGAACGTTTGTGCTGGTGAAAGATAAAAAAACATTCTGTTCATCTGCGACCGGTGAGATGGACATTcc < 1:3144950/68‑1 (MQ=255)
cGAACGTTTGTGCTGGTGAAAGATAAAAAAACATTCTGTTCATCTGCGACCGGTGAGATGGACATTcc < 1:2974132/68‑1 (MQ=255)
cGAACGTTTGTGCTGGTGAAAGATAAAAAAACATTCTGTTCATCTGCGACCGGTGAGATGGACATTcc < 1:3349451/68‑1 (MQ=255)
cGAACGTTTGTGCTGGTGAAAGATAAAAAAACATTCTGTTCATCTGCGACCGGTGAGATGGACATTcc < 1:1233350/68‑1 (MQ=255)
|
CAAGCTAACCCCGAACTGACCGCCCGCGCAGCGTTTAGCATGAATGTCCGAACGTTTGTGCTGGTGAAAGATAAAAAAACATTCTGTTCATCTGCGACCGGTGAGATGGACATTCC > minE/1402389‑1402504
|
| 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
