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 |
1,827,450 |
G→A |
58.0% |
P231P (CCG→CCA) |
mutS → |
methyl‑directed mismatch repair protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,827,450 | 0 | G | A | 58.0%
| 11.9
/ 35.5
| 50 | P231P (CCG→CCA) | mutS | methyl‑directed mismatch repair protein |
| Reads supporting (aligned to +/- strand): ref base G (8/13); new base A (7/22); total (15/35) |
| Fisher's exact test for biased strand distribution p-value = 3.56e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.84e-01 |
CCAGCAGTTGAATCTGCAATTTGGGACCCGCGATCTGGTCGGTTTTGGCGTCGAGAACGCGCCGCGCGGACTTTGTGCTGCCGGTTGTCTGTTGCAGTATGCGAAAGATACCCAACGTACGACTCT > minE/1827387‑1827512
|
ccAGCAGTTGAATCTGCAATTTGGGACCCGCGATCTGGTCGGTTTTGGCGTCGAGAACGCGCCGCGCgg < 1:1290479/69‑1 (MQ=255)
ccAGCAGTTGAATCTGCAATTTGGGACCCGCGATCTGGTCGGTTTTGGCGTCGAGAACGCGCCGCGCgg < 1:583740/69‑1 (MQ=255)
cagcagTTGAATCTGCAATTTGGGACCCGCGATCTGGTCGGTTTTGGCGTCGAGAACGCGCCGCGCgg < 1:1144777/68‑1 (MQ=255)
tGCAATTTGGGACCCGCGATCTGGTCGGTTTTGGCGTCGAGAACGCGCCGCGCGGACTTTGTGCTGcc > 1:1294568/1‑68 (MQ=255)
tGCAATTTGGGACCCGCGATCTGGTCGGTTTTGGCGTCGAGAACGCGCCGCGCGGACTTTGTGCTGCCg > 1:2119034/1‑69 (MQ=255)
tGCAATTTGGGACCCGCGATCTGGTCGGTTTTGGCGTCGAGAACGCGCCGCGCGGACTTTGTGCTGCCg > 1:800779/1‑69 (MQ=255)
tGCAATTTGGGACCCGCGATCTGGTCGGTTTTGGCGTCGAGAACGCGCCGCGCGGACTTTGTGCTGCCg > 1:2961219/1‑69 (MQ=255)
cgcgATCTGGTCGGTTTTGGCGTCGAGAACGCGCCGCGCGGACTTTGTGCTGCCGGTTGTCTGTTGCAg < 1:1160070/69‑1 (MQ=255)
cgcgATCTGGTCGGTTTTGGCGTCGAGAACGCGCCGCGCGGACTTTGTGCTGCCGGTTGTCTGTTGCAg > 1:2774249/1‑69 (MQ=255)
gcgATCTGGTCGGTTTTGGCGTCGAGAACGCGCCGCGCGGACTTTGTGCTGCCGGTTGTCTGTTGCAGt < 1:2370520/69‑1 (MQ=255)
gcgATCTGGTCGGTTTTGGCGTCGAGAACGCGCCGCGCGGACTTTGTGCTGCCGGTTGTCTGTTGCAGt < 1:507020/69‑1 (MQ=255)
gcgATCTGGTCGGTTTTGGCGTCGAGAACGCGCCGCGCGGACTTTGTGCTGCCGGTTGTCTGTTGCAGt < 1:3295733/69‑1 (MQ=255)
gcgATCTGGTCGGTTTTGGCGTCGAGAACGCGCCGCGCGGACTTTGTGCTGCCGGTTGTCTGTTGCAGt < 1:2645584/69‑1 (MQ=255)
agATCTGGTCGGTTTTGGTGTGGAGCACGCACCACGCGGACTTtg > 1:527084/2‑45 (MQ=255)
agATCTGGTCGGTTTTGGTGTGGAGAACGCACCACGCGGACTTtg > 1:2341533/2‑45 (MQ=255)
agATCTGGTCGGTTTTGGTGTGGAGAACGCACCACGCGGACTTtg > 1:2366894/2‑45 (MQ=255)
agATCTGGTCGGTTTTGGTGTGGAGAACGCACCACGCGGACTTtg > 1:2529267/2‑45 (MQ=255)
agATCTGGTCGGTTTTGGTGTGGAGAACGCACCACGCGGACTTtg > 1:144784/2‑45 (MQ=255)
agATCTGGTCGGTTTTGGTGTGGAGAACGCACCACGCGGACTTtg > 1:737654/2‑45 (MQ=255)
agATCTGGTCGGTTTTGGTGTGGAGAACGCACCACGCGGACTTtg > 1:1004352/2‑45 (MQ=255)
agATCTGGTCGGTTTTGGTGTGGAGAACCCACcacgcg > 1:1091939/2‑38 (MQ=16)
cTGGTCGGTTTTGGCGTCGAGAACGCGCCGCGCGGACTTTGTGCTGCCGGTTGTCTGTTGCAg > 1:1964172/1‑63 (MQ=255)
cTGGTCGGTTTTGGCGTCGAGAACGCGCCGCGCGGACTTTGTGCTGCCGGTTGTCTGTTGCAg > 1:3353190/1‑63 (MQ=255)
cTGGTCGGTTTTGGCGTCGAGAACGCGCCGCGCGGACTTTGTGCTGCCGGTTGTCTGTTGCAg > 1:3048850/1‑63 (MQ=255)
ttttGGTTTGGAGAACGCACCACGCGGACTTTGTGCTGCCGGTTGTCTGTTGCAGTATGCGAAAGATa < 1:1455769/68‑1 (MQ=255)
ttttGGTGTGGAGAACGCACCACGCGGACTTTTTGCTGCCGGTTGTCTGTTGCAGTATGCGAAAGATa < 1:3276514/68‑1 (MQ=255)
ttttGGTGTGGAGAACGCACCACGCGGACTTTGTGCTGCCGGTTGTCTGTTGCAGTATGCGAAAGATa < 1:968293/68‑1 (MQ=255)
ttttGGTGTGGAGAACGCACCACGCGGACTTTGTGCTGCCGGTTGTCTGTTGCAGTATGCGAAAGATa < 1:2058237/68‑1 (MQ=255)
ttttGGTGTGGAGAACGCACCACGCGGACTTTGTGCTGCCGGTTGTCTGTTGCAGTATGCGAAAGATa < 1:1303624/68‑1 (MQ=255)
ttttGGTGTGGAGAACGCACCACGCGGACTTTGTGCTGCCGGTTGTCTGTTGCAGTATGCGAAAGATa < 1:797977/68‑1 (MQ=255)
ttttGGTGTGGAGAACGCACCACGCGGACTTTGTGCTGCCGGTTGTCTGTTGCAGTATGCGAAAGATa < 1:1439114/68‑1 (MQ=255)
ttttGGTGTGGAGAACGCACCACGCGGACTTTGTGCTGCCGGTTGTCTGTTGCAGTATGCGAAAGATa < 1:558665/68‑1 (MQ=255)
ttttGGTGTGGAGAACGCACCACGCGGACTTTGTGCTGCCGGTTGTCTGTTGCAGTATGCGAAAGATa < 1:1513068/68‑1 (MQ=255)
ttttGGTGTGGAGAACGCACCACGCGGACTTTGTGCTGCCGGTTGTCTGTTGCAGTATGCGAAAGATa < 1:3336366/68‑1 (MQ=255)
ttttGGTGTGGAGAACGCACCACGCGGACTTTGTGCTGCCGGTTGTCTGTTGCAGTATGCGAAAGATa < 1:1566501/68‑1 (MQ=255)
ttttGGTGTGGAGAACGCACCACGCGGACTTTGTGCTGCCGGTTGTCTGTTGCAGTATGCGAAAGATa < 1:3288434/68‑1 (MQ=255)
ttttGGTGTGGAGAACGCACCACGCGGACTTTGTGCTGCCGGTTGTCTGTTGCAGTATGCGAAAGATa < 1:3231235/68‑1 (MQ=255)
ttttGGTGTGGAGAACGCACCACGCGGACTTTGTGCTGCCGGTTGTCTGTTGCAGTATGCGAAAGATa < 1:1627914/68‑1 (MQ=255)
ttttGGTGTGGAGAACGCACCACGCGGACTTTGTGCTGCCGGTTGTCTGTTGCAGTATGCGAAAGATa < 1:1992132/68‑1 (MQ=255)
ttttGGTGTGGAGAACGCACCACGCGGACTTTGTGCTGCCGGTTGTCTGTTGCAGTATGCGAAAGATa < 1:2477186/68‑1 (MQ=255)
ttttGGTGTGGAGAACGCACCACGCGGACTTTGTGCTGCCGGTTGTCTGTTGCAGTATGCGAAAGATa < 1:2670197/68‑1 (MQ=255)
ttttGGTGTGGAGAACGCACCACGCGGACTTTGTGCTGCCGGTTGTCTGTTGCAGTATGCGAAAGATa < 1:2886735/68‑1 (MQ=255)
ttttGGTGTGGAGAACGCACCACGCGGACTTTGTGCTGCCGGTTGTCTGTTGCAGTATGCGAAAGATa < 1:2897094/68‑1 (MQ=255)
ttttGGTGTGGAGAACGCACCACGCGGACTTTGTGCTGCCGGTTGTCTGTTGCAGTATGCGAAAGATa < 1:2984517/68‑1 (MQ=255)
ttttGGTGTGGAGAACGCACCAAGCGGACTTTGTGCTGCCGGTTGTCTGTTGCAGTATGCGAAAGATa < 1:2380528/68‑1 (MQ=255)
tttGGTGTGGAGAACGCACCACGCGGACTTTGTGCTGCCGGTTGTCTGTTGCAGTATGCGAAAGATa < 1:693709/67‑1 (MQ=255)
ttGGCGTCGAGAACGCGCCGCGCGGACTTTGTGCTGCCGGTTg < 1:1370694/43‑1 (MQ=255)
ggCGTCGAGAACGCGCCGCGCGGACTTTGTTCTGCCGGTTGTCTGTTGCAGTATGCGAAAGATACCCa < 1:2820505/68‑1 (MQ=255)
ggCGTCGAGAACGCGCCGCGCGGACTTTGTGCTGCCGGTTGTCTGTTGCAGTATGCGAAAGATACCCa < 1:3411074/68‑1 (MQ=255)
ggCGTCGAGAACGCGCCGCGCGGACTTTGTGCTGCCGGTTGTCTGTTGCAGTATGCGAAAGATACCCa < 1:2611801/68‑1 (MQ=255)
ggCGTCGAGAACGCGCCGCGCGGACTTTGTGCTGCCGGTTGTCTGTTGCAGTATGCGAAAGATACCCa < 1:91638/68‑1 (MQ=255)
cgcgccgcgcGGACTTTGTGCTGCCGGTTGTCTGTTGCAGTATGCGAAAGATACCCAACGTACGActct > 1:1630564/1‑69 (MQ=255)
cgcgccgcgcGGACTTTGTGCTGCCGGTTGTCTGTTGCAGTATGCGAAAGATACCCAACGTACGActct > 1:2677343/1‑69 (MQ=255)
cgcgccgcgcGGACTTTGTGCTGCCGGTTGTCTGTTGCAGTATGCGAAAGATACCCAACGTACGActct > 1:2627046/1‑69 (MQ=255)
cgcgccgcgcGGACTTTGTGCTGCCGGTTGTCTGTTGCAGTATGCGAAAGATACCCAACGTACGActct > 1:1979932/1‑69 (MQ=255)
cgcgccgcgcGGACTTTGTGCTGCCGGTTGTCTGTTGCAGTATGCGAAAGATACCCAACGTACGActct > 1:868506/1‑69 (MQ=255)
cgcgccgcgcGGACTTTGTGCTGCCGGTTGTCTGTTGCAGTATGCGAAAGATACCCAACGTACGActc > 1:599848/1‑68 (MQ=255)
|
CCAGCAGTTGAATCTGCAATTTGGGACCCGCGATCTGGTCGGTTTTGGCGTCGAGAACGCGCCGCGCGGACTTTGTGCTGCCGGTTGTCTGTTGCAGTATGCGAAAGATACCCAACGTACGACTCT > minE/1827387‑1827512
|
| 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
