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 R1
|
2169 |
63.0 |
3952800 |
76.2% |
3012033 |
62.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,019,201 |
G→A |
42.8% |
intergenic (+150/+76) |
ydgA → / ← uidC |
conserved hypothetical protein/predicted outer membrane porin protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,019,201 | 0 | G | A | 42.8%
| 20.4
/ 53.2
| 49 | intergenic (+150/+76) | ydgA/uidC | conserved hypothetical protein/predicted outer membrane porin protein |
| Reads supporting (aligned to +/- strand): ref base G (12/16); new base A (6/15); total (18/31) |
| Fisher's exact test for biased strand distribution p-value = 3.77e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CTTATCAGGCCTACCTTTTCCTGCAACACTTTGAATTTATGAGTTTTTGTAGGCTGGATAAGGCGTTTACGCCGCATCCGGCATAAAAA‑ACGCGCACTTTGTCAACAATCTGAAACGCCGGAGATTTTTCTCTCCGGCGT > minE/1019131‑1019270
|
cTTATCAGGCCTACCTTTTCCTGCAACACTTTGAATTTATGAGTTTTTGTAGGCTGGATAAGGCGTTTAcg < 1:1993423/71‑1 (MQ=255)
ttATCAGGCCTACCTTTTCCTGCAACACTTTGAATTTATGAGTTTTTGTAGGCTGGATAAGGCGTTTAcgc > 1:779747/1‑71 (MQ=255)
ttATCAGGCCTACCTTTTCCTGCAACACTTTGAATTTATGAGTTTTTGTAGGCTGGATAAGGCGTTTAcgc > 1:3282869/1‑71 (MQ=255)
aGGCCTACCTTTTCCTGCAACACTTTGAATTTATGAGTTTTTGTAGGCTGGATAAGGCGTTTACGCCGCa < 1:2404620/70‑1 (MQ=255)
ggCCTACCTTTTCCTGCAACACTTTGAATTTATGAGTTTTTGTAGGCTGGATAAGGCGTTTACGCCGCATc > 1:2137630/1‑71 (MQ=255)
ggCCTACCTTTTCCTGCAACACTTTGAATTTATGAGTTTTTGTAGGCTGGATAAGGCGTTTACGCCGCATc > 1:26500/1‑71 (MQ=255)
ggCCTACCTTTTCCTGCAACACTTTGAATTTATGAGTTTTTGTAGGCTGGATAAGGCGTTTACGCCGCATc < 1:3546599/71‑1 (MQ=255)
ggCCTACCTTTTCCTGCAACACTTTGAATTTATGAGTTTTTGTAGGCTGGATAAGGCGTTTACGCCGCATc < 1:1245248/71‑1 (MQ=255)
ctatgcctgatgcgacgctgaagcgtcttatcatgcctacatagcactgccacgtatGTTTACACCGCATc < 1:2371030‑M2/14‑1 (MQ=255)
ctatgcctgatgcgacgctgaagcgtcttatcatgcctacatagcactgccacgtatGTTTACACCGCATc < 1:2375456‑M2/14‑1 (MQ=255)
ctatgcctgatgcgacgctgaagcgtcttatcatgcctacatagcactgccacgtatGTTTACACCGCATc < 1:3491278‑M2/14‑1 (MQ=255)
tatgcctgatgcgacgctgaagcgtcttatcatgcctacatagcactgccacgtatGTTTACACCGCATcc > 1:790998‑M2/57‑71 (MQ=255)
atgcctgatgcgacgctgaagcgtcttatcatgcctacatagcactgccacgtatGTTTACACCGCATCCg > 1:243104‑M2/56‑71 (MQ=255)
tACCTTTTCCTGCAACACTTTGAATTTATGAGTTTTTGTAGGCTGGATAAGGCGTTTAcgcc > 1:2541036/1‑62 (MQ=255)
ctgatgcgacgctgaagcgtcttatcatgcctacatagcactgccacgtatGTTTACACCGCATCCGGCa > 1:1676041‑M2/52‑70 (MQ=255)
ctgatgcgacgctgaagcgtcttatcatgcctacatagcactgccacgtatGTTTACACCGCATCCGGCAt < 1:3283024‑M2/20‑1 (MQ=255)
ttttCCTGCAACACTTTGAATTTATGAGTTTTTGTAGGCTGGATAAGGCGTTTACGCCGCATCCGGc < 1:3815115/67‑1 (MQ=255)
atgcgacgctgaagcgtcttatcatgcctacatagcactgccacgtatGTTTACACCGCATCCGGCATaaa < 1:2519465‑M2/23‑1 (MQ=255)
atgcgacgctgaagcgtcttatcatgcctacatagcactgccacgtatGTTTACACCGCATCCGGCATaaa < 1:1079391‑M2/23‑1 (MQ=255)
atgcgacgctgaagcgtcttatcatgcctacatagcactgccacgtatGTTTACACCGCATCCGGCATaaa < 1:1089040‑M2/23‑1 (MQ=255)
atgcgacgctgaagcgtcttatcatgcctacatagcactgccacgtatGTTTACACCGCATCCGGCATaa < 1:2603307‑M2/22‑1 (MQ=255)
ttCCTGCAACACTTTGAATTTATGAGTTTTTGTAGGCTGGATAAGGCGTTTAcgcc > 1:564298/1‑56 (MQ=255)
ttCCTGCAACACTTTGAATTTATGAGTTTTTGTAGGCTGGATAAGGCGTTTAcgcc > 1:1302756/1‑56 (MQ=255)
tCCTGCAACACTTTGAATTTATGAGTTTTTGTAGGCTGGATAAGGCGTTTACGCCGCATCCGGCATaaaa < 1:986075/70‑1 (MQ=255)
gacgctgaaccgtcttatcatgcctacatagcactgccacgtatGTTTACACCGCATCCGGCataaaaaca < 1:2384417‑M2/27‑3 (MQ=255)
cTGCAACACTTTGAATTTATGAGTTTTTGTAGGCTGGATAAGGCGTTTACGCCGCATCCGGCATAAAAA‑Ac < 1:3191438/71‑1 (MQ=255)
cTGCAACACTTTGAATTTATGAGTTTTTGTAGGCTGGATAAGGCGTTTACGCCGCATCCGGCATAAAAA‑Ac < 1:979563/71‑1 (MQ=255)
acgctgaagcgtcttatcatgcctacatagcactgccacgtatGTTTACACCGCATCCGGcataaaaacac < 1:1965463‑M2/28‑4 (MQ=255)
acgctgaagcgtcttatcatgcctacatagcactgccacgtatGTTTACACCGCATCCGGCATa < 1:297767‑M2/21‑1 (MQ=255)
acgctgaagcgtcttatcatgcctacatagcactgccacgtatGTTTACACCGCATCAGGCATa < 1:697423‑M2/21‑1 (MQ=255)
cgctgaagcgtcttatcatgcctacatagcactgccacgtatGTTTACACCGCATCCg > 1:1409815‑M2/43‑58 (MQ=255)
cAACACTTTGAATTTATGAGTTTTTGTAGGCTGGATAAGGCGTTTACGCCGCATCCGGCATAAAAA‑Acgcg > 1:2160539/1‑71 (MQ=255)
tgaagcgtcttatcatgcctacatagcactgccacgtatGTTTACACCGCATCCGGCATAAAAACAcgcg > 1:3902961‑M2/40‑70 (MQ=255)
acTTTGAATTTATGAGTTTTTGTAGGCTGGATAAGGCGTTTACGCCGCATCCGGCATaa > 1:639830/1‑59 (MQ=255)
aagcgtcttatcatgcctacatagcactgccacgtatGTTTACACCGCATCCGGCATAAAAACACGCGCa < 1:526000‑M2/33‑1 (MQ=255)
aagcgtcttatcatgcctacatagcactgccacgtatGTTTACACCGCATCCGGCATAAAAACACGCGCAc > 1:1828998‑M2/38‑71 (MQ=255)
cTTTGAATTTATGAGTTTTTGTAGGCTGGATAAGGCGTTTACGCCGCATCCGGCATAAAAA‑ACGCGCACtt < 1:988757/71‑1 (MQ=255)
cTTTGAATTTATGAGTTTTTGTAGGCTGGATAAGGCGTTTACGCCGCATCCGGCATAAAAA‑ACGCGCACtt < 1:1905708/71‑1 (MQ=255)
tttGAATTTATGAGTTTTTGTAGGCTGGATAAGGCGTTTACGCCGCATCCGGCATAAAAA‑ACGCGCACttt > 1:414176/1‑71 (MQ=255)
gtcttatcatgcctacatagcactgccacgtatGTTTACACCGCATCCGGCATAAAAACACGCGCACTTTg < 1:2519438‑M2/38‑1 (MQ=255)
gAATTTATGAGTTTTTGTAGGCTGGATAAGGCGTTTACGCCGCATCCGGCATAAAAA‑ACGCGCACTTTGt < 1:1289499/70‑1 (MQ=255)
aaTTTATGAGTTTTTGTAGGCTGGATAAGGCGTTTACGCCGCATCCGGCATAAAAA‑ACGCGCACTTTGTc < 1:3356061/70‑1 (MQ=255)
gTTTTTGTAGGCTGGATAAGGCGTTTACGCCGCATCCGGCATAAAAA‑ACGCGCACTTTGTCAACAATCTGa < 1:2413387/71‑1 (MQ=255)
tttttGTAGGCTGGATAAGGCGTTTACGCCGCATCCGGCATAAAAA‑ACGCGCACTTTGTca < 1:1616320/61‑1 (MQ=255)
ctacatagcactgccacgtatGTTTACACCGCATCCGGCATAAAAACACGCGCACtt < 1:2384928‑M2/36‑1 (MQ=255)
tttGTAGGCTGGATAAGGCGTTTATGCCGGATGCGGCGTaa > 1:1969139/1‑41 (MQ=14)
tttGTAGGCTGGATAAGGCGTTTACGCCGCATCCGGCATAAAAA‑ACGCGCACTTTGTc > 1:1779547/1‑58 (MQ=255)
tGTAGGCTGGATAAGGCGTTTACGCCGCATCCGGCATAAAAA‑ACGCGCACTTTGTCAACAATCTGAAAc < 1:2370010/69‑1 (MQ=255)
tGTAGGCTGGATAAGGCGTTTACGCCGCATCCGGCATAAAAA‑ACGCGCACTTTGTCAACAATCTGAAACg < 1:2009320/70‑1 (MQ=255)
tGGATAAGGCGTTTACGCCGCATCCGGCATAAAAA‑ACGCGCACt > 1:604085/1‑44 (MQ=255)
aaGGCGTTTACGCCGCATCCGGCATAAAAA‑ACGCGCACTTTGTCAACAATCTGAAACGCCGGAGATTTTtc > 1:2418765/1‑71 (MQ=255)
gTTTACGCCGCATCCGGCATAAACA‑ACGCGCACTTTGTCAGCAATCTGa > 1:3026504/1‑49 (MQ=11)
ttACGCCGCATCCGGCATAAAAA‑ACGCGCACTTTGTCAACAATCTTAAACGCCGGAGATTTTTCTCTCCg > 1:3518056/1‑70 (MQ=255)
tACGCCGCATCCGGCATAAAAA‑ACGCGCACTTTGTCAACAATCTGAAACGCCGGAGATTTTTCTCTCCgg < 1:3416868/70‑1 (MQ=255)
tACGCCGCATCCGGCATAAAAA‑ACGCGCACTTTGTCAACAATCTGAAACGCCGGAGATTTTTCTCTCCGGc > 1:1989146/1‑71 (MQ=255)
cgccgcATCCGGCATAAAAA‑ACGCGCACTTTGTCAACAATc > 1:1567664/1‑41 (MQ=255)
gccgcATCCGGCATAAAAA‑ACGCGCACTTTGTCAACAATCTGAAACGCCGGAGATTTTTCTCTCCGGCGt > 1:2931215/1‑70 (MQ=255)
|
CTTATCAGGCCTACCTTTTCCTGCAACACTTTGAATTTATGAGTTTTTGTAGGCTGGATAAGGCGTTTACGCCGCATCCGGCATAAAAA‑ACGCGCACTTTGTCAACAATCTGAAACGCCGGAGATTTTTCTCTCCGGCGT > minE/1019131‑1019270
|
| 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
