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 F21 I0 R1
|
476 |
35.3 |
2812105 |
96.7% |
2719305 |
61.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
2,968,686 |
A→G |
100% |
I123M (ATA→ATG) |
mutH → |
methyl‑directed mismatch repair protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 2,968,686 | 0 | A | G | 82.2%
| 63.6
/ 7.8
| 28 | I123M (ATA→ATG) | mutH | methyl‑directed mismatch repair protein |
| Reads supporting (aligned to +/- strand): ref base A (5/0); new base G (15/8); total (20/8) |
| Fisher's exact test for biased strand distribution p-value = 2.81e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.85e-01 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
AACGGGCAATAGCGGGGTGACCTGGGAAACCAGCCACGTGCGCCACAAACTCAAACGCGTACTGTGGATACCGGTTGAAGGCGAGCGCAGCATCCCGCTGGCGCAGCGTCGCGTTGGATCACCGTTGCTGTGGAGCC > W3110S.gb/2968617‑2968753
|
aaCGGGCAATAGCGGGGTGACCTGGGAAACCAGCCACGTGCGCCACAAACTCAAACGCGTACTGTGGATAc > 1:1567814/1‑71 (MQ=255)
aTAGCGGGGTGACCTGGGAAACCAGCCACGTGCGCCACAAACTCAAACGCGTACTGTGGATGCCGGTTg < 1:2591661/69‑1 (MQ=255)
aGCGGGGTGACCTGGGAAACCAGCCACGTGCGCCACAAACTCAAACGCGTACTGTGGATGCCGGTTGAAgg > 1:581701/1‑71 (MQ=255)
aGCGGGGTGACCTGGGAAACCAGCCACGTGCGCCACAAACTCAAACGCGTACTGTGGATGCCGGTTGAAgg > 1:2109686/1‑71 (MQ=255)
aGCGGGGTGACATGGGAAACCAGCCACGTGCGCCACAAACTCAAACGCGTACTGTGGATACCGGTTGAAgg > 1:2679135/1‑71 (MQ=255)
aGCGGCGTGACCTGGGTAACCAGCCACGTGCGCCACAAACTCAAACGCGTACTGTGGATGCCGGTTGAAg > 1:1268075/1‑70 (MQ=255)
gCGGGGTGACCTGGGAAACCAGCCACGTGCGCCACAAACTCAAACGCGTACTGTGGATGCCGGTTGAAgg > 1:723533/1‑70 (MQ=255)
gCGGGGTGACCTGGGAAACCAGCCACGTGCGCCACAAACTCAAACGCGTACTGTGGATGCCGGTTGAAg > 1:2027541/1‑69 (MQ=255)
gCGGGGTGACCTGGGAAACCAGCCACGTGCGCCACAAACTCAAACGCGTACTGTGGATGCCGGTTGAAGGc > 1:2033745/1‑71 (MQ=255)
aCCTGGGAAACCAGCCACGTGCGCCACAAACTCAAACGCGTACTGTGGATGCCGGTTGAAGGCGAGCgcag < 1:40946/71‑1 (MQ=255)
aCCAGCCACGTGCGCCACAAACTCAAACGCGTACTGTGGATACCGGTTGAAGGCGAGCGCAGCATCCCGCt > 1:1851891/1‑71 (MQ=255)
ccAGCCACGTGCGCCACAAACTCAAACGCGTACTGTGGATGCCGGTTGa < 1:829233/49‑1 (MQ=255)
ccAGCCACGTGCGCCACAAACTCAAACGCGTACTGTGGATGCCGGTTGAAGGCGAGCGCAGCATCCCGCTg > 1:1677690/1‑71 (MQ=255)
ccACGTGCGCCACAAACTCAAACGCGTACTGTGGATGCCGGTTGAAGGCGAGCGCAGCATCCCGCTGgcgc < 1:2261901/71‑1 (MQ=255)
cGTGCGCCACAAACTCAAACGCGTACTGTGGATGCCGGTTGAAGGCGAGCGCAGCATCCCGCTGGCGCAGc > 1:1638054/1‑71 (MQ=255)
gcgcCACAAACTCAAACGCGTACTGTGGATGCCGGTTGAAGGCGAGCGCAGCATCCCGCTGGCGCAGCGTc > 1:1087948/1‑71 (MQ=255)
cacaAACTCAAACGCGTACTGTGGATGCCGGTTGAAGGCGAGCGCAGCATCCCGCTGGCGCAGCGTCGCGt > 1:914552/1‑71 (MQ=255)
caAACTCAAACGCGTACTGTGGATGCCGGTTGAAGGCGAGCGCAGCATCCCGCTGGCGCAGCGTCGCGTTg > 1:1911348/1‑71 (MQ=255)
caAACTCAAACGCGTACTGTGGATGCCGGTTGAAGGCGAGCGCAGCATCCCGCTGGCGCAGCGTCGCGTTg > 1:2729326/1‑71 (MQ=255)
aaaCTCAAACGCGTACTGTGGATGCCGGTTGAAGGCGAGCGCAGCATCCCGCTGGCGCAGCGTCGCGTTgg < 1:2602291/71‑1 (MQ=255)
aaaCTCAAACGCGTACTGTGGATGCCGGTTGAAGGCGAGCGCAGCATCCCGCTGGCGCAGCGTCGCGTTgg < 1:2621648/71‑1 (MQ=255)
aaaCTCAAACGCGTACTGTGGATGCCGGTTGAAGGCGAGCGCAGCATCCCGCTGGCGCAGCGTCGCGTTgg < 1:515289/71‑1 (MQ=255)
aaCTCAAACGCGTACTGTGGATACCGGTTGAAGGCGAGCGCAGCATCCCGCTGGCGCAGCGTCGCGTTGGa > 1:569272/1‑71 (MQ=255)
cTCAAACGCGTACTGTGGATACCGGTTGAAGGCGAGCGCAGCATCCCGCTGGCGCAGCGTCGCGTTGGa > 1:505795/1‑69 (MQ=255)
cAAACGCGTACTGTGGATGCCGGTTGAAGGCGAGCGCAGCATCCCGCTGGCGCAGCGTCGCGTTGGATCAc > 1:1771255/1‑71 (MQ=255)
cgTACTGTGGATGCCGGTTGAAGGCGAGCGCAGCATCCCGCTGGCGCAGCGTCGCGt < 1:2188932/57‑1 (MQ=255)
gtgGATGCCGGTTGAAGGCGAGCGCAGCATCCCGCTGGCGCAGCGTCGCGTTGGATCACCGTTGCtgtg > 1:1601111/1‑69 (MQ=255)
gATGCCGGTTGAAGGCGAGCGCAGCATCCCGCTGGCGCAGCGTCGCGTTGGATCACCGTTGCTGTGGAGcc > 1:2538918/1‑71 (MQ=255)
aCCGGTTGAAGGCGAGCGCAGCATCCCGCTGGCGCAGCGTCGCGt > 1:181654/1‑45 (MQ=255)
aCCGGTTGAAGGCGAGCGCAGCATCCCGCTGGCGCAGCGTCGCGt > 1:178322/1‑45 (MQ=255)
|
AACGGGCAATAGCGGGGTGACCTGGGAAACCAGCCACGTGCGCCACAAACTCAAACGCGTACTGTGGATACCGGTTGAAGGCGAGCGCAGCATCCCGCTGGCGCAGCGTCGCGTTGGATCACCGTTGCTGTGGAGCC > W3110S.gb/2968617‑2968753
|
| 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
