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 |
2,561,951 |
G→A |
65.4% |
A157A (GCC→GCT) |
lldR ← |
DNA‑binding transcriptional repressor |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,561,951 | 0 | G | A | 65.4%
| 33.1
/ 27.3
| 52 | A157A (GCC→GCT) | lldR | DNA‑binding transcriptional repressor |
| Reads supporting (aligned to +/- strand): ref base G (8/10); new base A (18/16); total (26/26) |
| Fisher's exact test for biased strand distribution p-value = 7.71e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GCTTCACTGAGGATTGCAGGACATCGAAGAAACCGCGCATGGTTTGCAGCAGCACGATGTTATGTGAGGCTTCGGCAATCGCCAGATGAAAACGAACGTCCGCTTGTGAGGCGATA > minE/2561884‑2561999
|
gCTTCACTGAGGATTGCAGGACATCGAAGAAACCGCGCATGGTTTGCAGCAGCACGATGTTATGTGAgg > 1:3004532/1‑69 (MQ=255)
aGGATTGCAGGACATCGAAGAAACCGCGCATGGTTTGCAGCAGCACGATGTTATGTGAGGCTTCGGCaa > 1:1139805/1‑69 (MQ=255)
aGGATTGCAGGACATCGAAGAAACCGCGCATGGTTTGCAGCAGCACGATGTTATGTGAGGCTTCGGCaa > 1:460194/1‑69 (MQ=255)
aGGATTGCAGGACATCGAAGAAACCGCGCATGGTTTGCAGCAGCACGATGTTATGTGAGGCTTCGGCaa > 1:2861526/1‑69 (MQ=255)
aGGATTGCAGGACATCGAAGAAACCGCGCATGGTTTGCAGCAGCACGATGTTATGTGAGGCTTCGGCaa > 1:1438114/1‑69 (MQ=255)
aGGATTGCAGGACATCGAAGAAACCGCGCATGGTTTGCAGCAGCACGATGTTATGTGAGGCTTCGGCaa > 1:864236/1‑69 (MQ=255)
aGGATTGCAGGACATCGAAGAAACCGCGCATGGTTTGCAGCAGCACGATGTTATGTGAGGCTTCGGCaa > 1:159272/1‑69 (MQ=255)
aGGATTGCAGGACATCGAAGAAACCGCGCATGGTTTGCAGCAGCACGATGTTATGTGAGGCTTCGGCa > 1:1411732/1‑68 (MQ=255)
cATCGAAGAAACCGCGCATGGTTTGCAGCAGCACGATGTTATGTGAGGCTTCGGCAATCGCCAGATGaa < 1:2239404/69‑1 (MQ=255)
cATCGAAGAAACCGCGCATGGTTTGCAGCAGCACGATGTTATGTGAGGCTTCGGCAATCGCCAGATGaa < 1:3264253/69‑1 (MQ=255)
cATCGAAGAAACCGCGCATGGTTTGCAGCAGCACGATGTTATGTGAGGCTTCGGCAATCGCCAGATGaa < 1:1261891/69‑1 (MQ=255)
gaagaaACCGCGCATGGTTTGCAGCAGCACGATGTTATGTGAGGCTTCGGCAATCGCCAGATGAAaacg < 1:579311/69‑1 (MQ=255)
gaagaaACCGCGCATGGTTTGCAGCAGCACGATGTTATGTGAGGCTTCGGCAATCGCCAGATGAAaacg < 1:1678752/69‑1 (MQ=255)
gaagaaACCGCGCATGGTTTGCAGCAGCACGATGTTATGTGAGGCTTCGGCAATCGCCAGATGAAaacg < 1:1238603/69‑1 (MQ=255)
gaagaaACCGCGCATGGTTTGCAGCAGCACGATGTTATGTGAGGCTTCGGCAATCGCCAGATGAAaacg < 1:228173/69‑1 (MQ=255)
gaagaaACCGCGCATGGTTTGCAGCAGCACGATGTTATGTGAGGCTTCGGCAATCGCCAGATGAAaacg < 1:1320019/69‑1 (MQ=255)
gaagaaACCGCGCATGGTTTGCAGCAGCACGATGTTATGTGAGGCTTCGGCAATCGCCAGATGAAaacg < 1:2795586/69‑1 (MQ=255)
gaaACCGCGCATGGTTTGCAGCAGCACGATGTTATGTGAGGCTTCGGCAATCGCCAGATGAAaacgaac < 1:1685031/69‑1 (MQ=255)
cgcgCATGGTTTGCAGCAACACAATGTTATGTGAAGCTTCGGCAATCGCCAGATGAAaacgaac > 1:766880/1‑64 (MQ=255)
cgcgCATGGTTTGCAGCAACACAATGTTATGTGAAGCTTCGGCAATCGCCAGATGAAaacgaac > 1:2403425/1‑64 (MQ=255)
cgcgCATGGTTTGCAGCAACACAATGTTATGTGAAGCTTCGGCAATCGCCAGATGAAaacgaac > 1:2625245/1‑64 (MQ=255)
cgcgCATGGTTTGCAGCAACACAATGTTATGTGAAGCTTCGGCAATCGCCAGATGAAaacgaac > 1:2648586/1‑64 (MQ=255)
cgcgCATGGTTTGCAGCAACACAATGTTATGTGAAGCTTCGGCAATCGCCAGATGAAaacgaac > 1:2689719/1‑64 (MQ=255)
cgcgCATGGTTTGCAGCAACACAATGTTATGTGAAGCTTCGGCAATCGCCAGATGAAaacgaac > 1:1299573/1‑64 (MQ=255)
cgcgCATGGTTTGCAGCAACACAATGTTATGTGAAGCTTCGGCAATCGCCAGATGAAaacgaac > 1:3175380/1‑64 (MQ=255)
cgcgCATGGTTTGCAGCAACACAATGTTATGTGAAGCTTCGGCAATCGCCAGATGAAaacgaac > 1:382436/1‑64 (MQ=255)
cgcgCATGGTTTGCAGCAACACAATGTTATGTGAAGCTTCGGCAATCGCCAGATGAAaacgaac > 1:481361/1‑64 (MQ=255)
cgcgCATGGTTTGCAGCAACACAATGTTATGTGAAGCTTCGGCAATCGCCAGATGAAaacgaac > 1:2137769/1‑64 (MQ=255)
cgcgCATGGTTTGCAGCAACACAATGTTATGTGAAGCTTCGGCAATCGCCAGATGAAaacgaac > 1:164735/1‑64 (MQ=255)
cgcgCATGGTTTGCAGCAACACAATGTTATGTGAAGCTTCGGCAATCGCCAGATGAAaacgaac > 1:1780525/1‑64 (MQ=255)
cgcgCATGGTTTGCAGCAACACAATGTTATGTGAAGCTTCGGCAATCGCCAGATGAAaacgaac > 1:178405/1‑64 (MQ=255)
cgcgCATGGTTTGCAGCAACACAATGTTATGTGAAGCTTCGGCAATCGCCAGATGAAaacgaac > 1:1907620/1‑64 (MQ=255)
cgcgCATGGTTTGCAGCAACACAATGTTATGTGAAGCTTCGGCAATCGCCAGATGAAaacgaac > 1:1478204/1‑64 (MQ=255)
cgcgCATGGTTTGCAGCAACACAATGTTATGTGAAGCTTCGGCAATCGCCAGATGAAaacgaac > 1:2013543/1‑64 (MQ=255)
cgcgCATGGTTTGCAGCAACACAATGTTATGTGAAGCTTCGGCAATCGCCAGATGAAaacgaac > 1:811426/1‑64 (MQ=255)
cgcgCATGGTTTGCAGCAACACAATGTTATGTGAAGCTTCGGCAATCGCCAGATGAAaacgaac > 1:2349771/1‑64 (MQ=255)
gTTTGCAGCAGCACGATGTTATGTGAGGCTTCGGCAATCGCCAGATGAAAACGAACGTCCGCTTGTGAg > 1:2665685/1‑69 (MQ=255)
gcaacaCAATGTTATGTGAAGCTTCGGCAATCGCCAGATGAAAACGAACGTCCGCTTGTGAGGCGaga < 1:695380/68‑3 (MQ=255)
gcaacaCAATGTTATGTGAAGCTTCGGCAATCGCCAGATGAAAACGAACGTCCGCTTGTGAGGCGaga < 1:1111163/68‑3 (MQ=255)
gcaacaCAATGTTATGTGAAGCTTCGGCAATCGCCAGATGAAAACGAACGTCCGCTTGTGAGGCGaga < 1:950059/68‑3 (MQ=255)
gcaacaCAATGTTATGTGAAGCTTCGGCAATCGCCAGATGAAAACGAACGTCCGCTTGTGAGGCGaga < 1:581141/68‑3 (MQ=255)
gcaacaCAATGTTATGTGAAGCTTCGGCAATCGCCAGATGAAAACGAACGTCCGCTTGTGAGGCGaga < 1:797324/68‑3 (MQ=255)
gcaacaCAATGTTATGTGAAGCTTCGGCAATCGCCAGATGAAAACGAACGTCCGCTTGTGAGGCGaga < 1:877092/68‑3 (MQ=255)
gcaacaCAATGTTATGTGAAGCTTCGGCAATCGCCAGATGAAAACGAACGTCCGCTTGTGAGGCGaga < 1:790659/68‑3 (MQ=255)
gcaacaCAATGTTATGTGAAGCTTCGGCAATCGCCAGATGAAAACGAACGTCCGCTTGTGAGGCGaga < 1:3341/68‑3 (MQ=255)
gcaacaCAATGTTATGTGAAGCTTCGGCAATCGCCAGATGAAAACGAACGTCCGCTTGTGAGGCGaga < 1:2808090/68‑3 (MQ=255)
gcaacaCAATGTTATGTGAAGCTTCGGCAATCGCCAGATGAAAACGAACGTCCGCTTGTGAGGCGaga < 1:2597336/68‑3 (MQ=255)
gcaacaCAATGTTATGTGAAGCTTCGGCAATCGCCAGATGAAAACGAACGTCCGCTTGTGAGGCGaga < 1:2355790/68‑3 (MQ=255)
gcaacaCAATGTTATGTGAAGCTTCGGCAATCGCCAGATGAAAACGAACGTCCGCTTGTGAGGCGaga < 1:2331824/68‑3 (MQ=255)
gcaacaCAATGTTATGTGAAGCTTCGGCAATCGCCAGATGAAAACGAACGTCCGCTTGTGAGGCGaga < 1:2210136/68‑3 (MQ=255)
gcaacaCAATGTTATGTGAAGCTTCGGCAATCGCCAGATGAAAACGAACGTCCGCTTGTGAGGCGaga < 1:1670561/68‑3 (MQ=255)
gcaacaCAATGTTATGTGAAGCTTCGGCAATCGCCAGATGAAAACGAACGTCCGCTTGTGAGGCGaga < 1:1484263/68‑3 (MQ=255)
gcaacaCAATGTTATGTGAAGCTTCGGCAATCGACAGATGAAAACGAACGTCCGCTTGTGAGGCGaga < 1:197938/68‑3 (MQ=255)
|
GCTTCACTGAGGATTGCAGGACATCGAAGAAACCGCGCATGGTTTGCAGCAGCACGATGTTATGTGAGGCTTCGGCAATCGCCAGATGAAAACGAACGTCCGCTTGTGAGGCGATA > minE/2561884‑2561999
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
