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 |
|
A1 F8 I0 R2
|
422 |
46.8 |
3726540 |
94.7% |
3529033 |
61.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
2,777,419:1 |
+A |
100% |
coding (3964/4581 nt) |
ypjA ← |
adhesin‑like autotransporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 2,777,419 | 1 | . | A | 88.1%
| 107.3
/ 11.9
| 42 | coding (3964/4581 nt) | ypjA | adhesin‑like autotransporter |
| Reads supporting (aligned to +/- strand): ref base . (2/3); new base A (14/23); total (16/26) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.02e-01 |
| Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch. |
CACTTTCATGTTCCCAACTGGCATAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATC‑‑AAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGTAATTCCTTCAGGAATAT > W3110S.gb/2777350‑2777484
|
cACTTTCATGTTCCCAACTGGCATAGCCGCCCAGAGAATGACTGCCCACACTGCCATGTCCTCCGCGATc > 1:2494885/1‑70 (MQ=255)
cACTTTCATGTTCCCAACTGGCATAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATc > 1:1467499/1‑70 (MQ=255)
tCATGTTCCCAACTGGCATAGCCGCCCAGAGAATAACTGCCCACACTGACATGTCCTCCGCGATC‑‑aaaaac > 1:1894528/1‑69 (MQ=255)
aTGTTCCCAACTGGCATAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCCATC‑‑aaaaacc < 1:322469/70‑4 (MQ=255)
cAACTGGCATAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCA‑AAAACCGATAtgtg < 1:2597504/71‑1 (MQ=255)
cAACTGGCATAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCA‑AAAACCGATAtgtg < 1:1624919/71‑1 (MQ=255)
gCATAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCA‑AAAACCGATATGTGAATggg < 1:166099/71‑1 (MQ=255)
gCATAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCA‑AAAACCGATATGTGAATggg < 1:1638561/71‑1 (MQ=255)
gCATAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCA‑AAAACCGATATGTGAATgg < 1:2823866/70‑1 (MQ=255)
gCATAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCA‑AAAACCGATATGTGAATgg < 1:1706529/70‑1 (MQ=255)
gCATAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCA‑AAAACCGATATGTGAATgg < 1:1213691/70‑1 (MQ=255)
gCATAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCA‑AAAACCGATATGTGAATgg < 1:83914/70‑1 (MQ=255)
gccgccCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCA‑AAAACCGATATGTGAATGGGAATAg > 1:1577670/1‑71 (MQ=255)
gccgccCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCA‑AAAACCGATATGTGAATGGGAATAg > 1:1653245/1‑71 (MQ=255)
gccgccCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCA‑AAAACCGATATGTGAATGGGAATAg > 1:585641/1‑71 (MQ=255)
gccgccCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATC‑‑AAAACCGATATGTGAATGGGAATAg > 1:2338051/1‑70 (MQ=255)
ccgccCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATC‑‑AAAACCGATATGTGAATGGGAATAGcc < 1:363223/71‑1 (MQ=255)
agagAATAACTGCCCACACTGCCATGTCCTCCGCGATCA‑AAAACCGATATGTGAATggg < 1:2482132/59‑1 (MQ=255)
agagAATAACTGCCCACACTGCCATGTCCTCCGCGATCA‑AAAACCGATATGTGAATggg < 1:2430397/59‑1 (MQ=255)
agagAATAACTGCCCACACTGCCATGTCCTCCGCGATCA‑AAAACCGATATGTGAATggg < 1:3432996/59‑1 (MQ=255)
agagAATAACTGCCCACACTGCCATGTCCTCCGCGATCA‑AAAACCGATATGTGAATggg < 1:3666899/59‑1 (MQ=255)
agagAATAACTGCCCACACTGCCATGTCCTCCGCGATCA‑AAAACCGATATGTGAATggg < 1:521574/59‑1 (MQ=255)
gagaATAACTGCCCACACTGCCATGTCCTCCGCGATC‑‑aaaaa > 1:275616/1‑41 (MQ=255)
gagaATAACTGCCCACACTGCCATGTCATCCGCGATCA‑AAAACCGATATGTGAATGGGAATAGCCCATaa > 1:2971531/1‑70 (MQ=255)
agaATAACTGCCCACACTGCCATGTCCTCCGCGATCA‑AAAACCGATAtgtg < 1:2718460/51‑1 (MQ=255)
gaATAACTGCCCACACTGCCATGTCCTCCGCGATCA‑AAAACCGATAtgtg < 1:2060866/50‑1 (MQ=255)
aCTGCCCACACTGCCATGTCCTCCGCGATCA‑AAAACCGATATGTGAATGGGAATAGCCCATAAAAg > 1:3320128/1‑66 (MQ=255)
aCTGCCCACACTGCCATGTCCTCCGCGATCA‑AAAACCGATATGTGAATGGGAATAGCCCATAAAAg > 1:1017638/1‑66 (MQ=255)
aCTGCCCACACTGCCATGTCCTCCGCGATCA‑AAAACCGATATGTGAATGGGAATAGCCCATAAAAg > 1:1920622/1‑66 (MQ=255)
aCTGCCCACACTGCCATGTCCTCCGCGATCA‑AAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGcc > 1:2940566/1‑70 (MQ=255)
acacTTCCATGTCCTCCGCGATC‑‑AAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGt < 1:612617/71‑1 (MQ=255)
acacTGCCATGTCCTCCGCGATC‑‑AAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGt < 1:531338/71‑1 (MQ=255)
cTGCCATGTCCTCCGCGATCA‑AAAACCGATATGTGAATGGGAATa > 1:1144199/1‑45 (MQ=255)
cTGCCATGTCCTCCGCGATCA‑AAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGTaa > 1:208177/1‑71 (MQ=255)
cTGCCATGTCCTCCGCGATCA‑AAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGTaa > 1:736545/1‑71 (MQ=255)
ccATGTCCTCCGCGATCAAAAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGTAAt < 1:2031746/70‑1 (MQ=255)
ccATGTCCTCCGCGATCAAAAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGTAAt < 1:446483/70‑1 (MQ=255)
ccATGTCCTCCGCGATCA‑AAAACCGATATGTGAATggg < 1:183442/38‑1 (MQ=38)
cATGTCCTCCGCGATC‑‑AAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGTAATTCCt > 1:3441373/1‑71 (MQ=255)
tGTCCTCCGCGATCA‑AAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAg < 1:842599/57‑1 (MQ=255)
tGTCCTCCGCGATCA‑AAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAg < 1:1238095/57‑1 (MQ=255)
tcctccGCGATCA‑AAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGTAATTCCtt > 1:1002051/1‑69 (MQ=255)
tcctccGCGATCA‑AAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGTAATTCCtt > 1:1148462/1‑69 (MQ=255)
cgcgATCA‑AAAACCGATATGTGAATGGGAATAGCCCATAAAAg > 1:2268929/1‑43 (MQ=255)
cgATCA‑AAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGt < 1:3656260/54‑1 (MQ=39)
cgATCA‑AAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGTAATTCCTTCAGGAatat < 1:1129696/71‑1 (MQ=255)
cgATCA‑AAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGTAATTCCTTCAGGAatat < 1:2729006/71‑1 (MQ=255)
|
CACTTTCATGTTCCCAACTGGCATAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATC‑‑AAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGTAATTCCTTCAGGAATAT > W3110S.gb/2777350‑2777484
|
| 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
