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 |
|
A34 F5 I0 R1
|
408 |
67.6 |
2494072 |
96.8% |
2414261 |
139.8 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
NC_000913 |
1,491,756 |
G→A |
13.3% |
G27D (GGT→GAT) |
ydcA → |
putative periplasmic protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 1,491,756 | 0 | G | A | 13.3%
| 71.6
/ 4.8
| 30 | G27D (GGT→GAT) | ydcA | putative periplasmic protein |
| Reads supporting (aligned to +/- strand): ref base G (10/16); new base A (2/2); total (12/18) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.36e-01 |
ACGGTATCAAAATAAACCAGCGTATAACGTTCAAATCGAACATAAGATTCGATAAACCATGGAGGTTATATGAAAAAACTGGCACTTATTTTGTTTATGGGAACGCTTGTTTCCTTTTATGCCGATGCCGGGCGCAAACCCTGTTCTGGTTCGAAAGGGGGGATCTCACACTGTACGGCAGGCGGCAAATTTGTCTGTAATGATGGTTCTATTAGTGCATCGAAAAAAACATGCACTAACTGAAGTGTAAAAGGGGTGCCATGAGAAAATGAATCTGCTAGTCAAATGCGCG > NC_000913/1491608‑1491899
|
aCGGTATCAAAATAAACCAGCGTATAACGTTCAAATCGAACATAAGATTCGATAAACCATGGAGGTTATATGAAAAAACTGGCACTTATTTTGTTTATGGGAACGCTTGTTTCCTTTTATGCCGATGCCGGGCGCAAACCCTGTTCTgg < 3:316892/149‑1 (MQ=255)
aaaaTAAACCAGCGTATAACGTTCAAATCGAACATAAGATTCGATAAACCATGGAGGTTATATGAAAAAACTGGCACTTATTTTGTTTATGGGAACGCTTGTTTCCTTTTATGCCGATGCCGGGCGCAAACCCTGTTCTGGTTCGAAAg > 1:347848/1‑149 (MQ=255)
aGCGTATAACGTTCAAATCGAACATAAGATTCGATAAACCATGGAGGTTATATGAAAAAACTGGCACTTATTTTGTTTATGGGAACGCTTGTTTCCTTTTATGCCGATGCCGGGCGCAAACCCTGTTCTGGTTCGAAAGGGGGGAtctc < 4:329868/149‑1 (MQ=255)
cAAATCGAACATAAGATTCGATAAACCATGGAGGTTATATGAAAAAACTGGCACTTATTTTGTTTATGGGAACGCTTGTTTCCTTTTATGCCGATGCCGGGCGCAAACCCTGTTCTGGTTCGAAAGGGGGGATCTCACACTGTACGGCa < 4:180851/149‑1 (MQ=255)
tCGAACATAAGATTCGATAAACCATGGAGGTTATATGAAAAAACTGGCACTTATTTTGTTTATGGGAACGCTTGTTTCCTTTTATGCCGATGCCGGGCGCAAACCCTGTTCTGGTTCGAAAGGGGGGATCTCACACTGTACGGCAggcg < 4:450175/149‑1 (MQ=255)
gATTCGATAAACCATGGAGGTTATATGAAAAAACTGGCACTTATTTTGTTTATGGGAACGCTTGTTTCCTTTTATGCCGATGCCGGGCGCAAACCCTGTTCTGGTTCGAAAGGGGGGATCTCACACTGTACGGCAGGCGGCAAATTTGt < 3:84204/149‑1 (MQ=255)
tCGATAAACCATGGAGGTTATATGAAAAAACTGGCACTTATTTTGTTTATGGGAACGCTTGTTTCCTTTTATGCCGATGCCGGGCGCAAACCCTGTTCTGGTTCGAAAGGGGGGATCTCACACTGTACGGCAGGCGGCAAATTTGTCTg < 1:525084/149‑1 (MQ=255)
gATAAACCATGGAGGTTATATGAAAAAACTGGCACTTATTTTGTTTATGGGAACGCTTGTTTCCTTTTATGCCGATGCCGGGCGCAAACCCTGTTCTGGTTCGAAAGGGGGGATCTCACACTGTACGGCAGGCGGCAAATTTGTCTGTa < 1:329293/149‑1 (MQ=255)
aTAAACCATGGAGGTTATATGAAAAAACTGGCACTTATTTTGTTTATGGGAACGCTTGTTTCCTTTTATGCCGATGCCGGGCGCAAACCCTGTTCTGGTTCGAAAGGGGGGATCTCACACTGTACGGCAGGCGGCAAATTTGTCTGTaa < 3:477359/149‑1 (MQ=255)
ccATGGTGGTTATATGAAAAAACTGGCACTTATTTTGTTTATGGGAACGCTTGTTTCCTTTTATGCCGATGCCGGGCGCAAACCCTGTTCTGGTTCGAAAGGGGGGATCTCACACTGTACGGCAGGCGGCAAATTTGTCTGTAatgatg > 2:442342/1‑149 (MQ=255)
ttATATGAAAAAACTGGCACTTATTTTGTTTATGGGAACGCTTGTTTCCTTTTATGCCGATGCCGGGCGCAAACCCTGTTCTGGTTCGAAAGGGGGGATCTCACACTGTACGGCAGGCGGCAAATTTGTCTGTAATGATGGTTCTATTa < 2:354079/149‑1 (MQ=255)
aaaCTGGCACTTATTTTGTTTATGGGAACGCTTGTTTCCTTTTATGCCGATGCCGGGCGCAAACCCTGTTCTGGTTCGAAAGGGGGGAtctc < 2:538821/92‑1 (MQ=255)
aaaCTGGCACTTATTTTGTTTATGGGAACGCTTGTTTCCTTTTATGCCGATGCCGGGCGCAAACCCTGTTCTGGTTCGAAAGGGGGGAtctc > 1:538821/1‑92 (MQ=255)
ggCACTTATTTTGTTTATGGGAACGCTTGTTTCCTTTTATGCCGATGCCGGGCGCAAACCCTGTTCTGGTTCGAAAGGGGGGATCTCACACTGTACGGCAGGCGGCAAATTTGTCTGTAATGATGGTTCTATTAGTGCATCGaaaaaaa < 2:347848/149‑1 (MQ=255)
cTTATTTTGTTTATGGGAACGCTTGTTTCCTTTTATGCCGATGCCGGGCGCAAACCCTGTTCTGGTTCGAAAGGGGGGATCTCGTACTGTACGGCAGGCGGCAAATTTGTCTGTAATGATGGTTCTATTAGTGCATCGAAAAAAACATg > 3:409459/1‑149 (MQ=255)
aTGGGAACGCTTGTTTCCTTTTATGCCGATGCCGGGCGCAAACCCTGTTCTGGTTCGAAAGGGGGGATCTCACACTGTACGGCAGGCGGCAAATTTGTCTGTAATGATGGTTCTATTAGTGCATCGAAAAAAACATGCACTAACTGAAg > 3:108129/1‑149 (MQ=255)
gggAACGCTTGTTTCCTTTTATGCCGATGCCGGGCGCAAACCCTGTTCTGATTCGAAAGGGGGGATCTCACACTGTACGGCAGGCGGCAAATTTGTCTGTAATGATGGTTCTATTAg > 2:50678/1‑117 (MQ=255)
gggAACGCTTGTTTCCTTTTATGCCGATGCCGGGCGCAAACCCTGTTCTGATTCGAAAGGGGGGATCTCACACTGTACGGCAGGCGGCAAATTTGTCTGTAATGATGGTTCTATTAg < 1:50678/117‑1 (MQ=255)
gggAACGCTTGTTTCCTTTTATGCCGATGCCGGGCGCAAACCCTGTTCTGATTCGAAAGGGGGGATCTCACACTGTACGGCAGGCGACAAATTTGTCTGTAATGATGGTTCTATTAg < 3:138595/117‑1 (MQ=255)
gggAACGCTTGTTTCCTTTTATGCCGATGCCGGGCGCAAACCCTGTTCTGATTCGAAAGGGGGGATCTCACACTGTACGGCAGGCGACAAATTTGTCTGTAATGATGGTTCTATTAg > 4:138595/1‑117 (MQ=255)
cGCTTGTTTCCTTTTATGCCGATGCCGGGCGCAGACCCTGTTCTGGTTCGAAAGGGGGGATCTCATACTGTACGGCAGGCGGCAAATTTGTCTGTAATGATGGTTCTATTAGTGCATCGAAAAAAACATGCACTAACTGAAGTGTaaaa < 4:409459/149‑1 (MQ=255)
gCTTGTTTCCTTTTATGCCGATGCCGGGCGCAAACCCTGTTCTGGTTCGAAAGGGGGGATCTCACACTGTACGGCAGGCGGCAAATTTGTCTGTAATGATGGTTCTATTAGTGCATCGAAAAAAACATGCACTAACTGAAGTGTAAAAg > 2:168943/1‑149 (MQ=255)
ttGTTTCCTTTTATGCCGATGCCGGGCGCAAACCCTGTTCTGGTTCGAAAGGGGGGATCTCACACTGTACGGCAGGCGGCAAATTTGTCTGTAATGATGGTTCTATTAGTGCATCGAAAAAAACATGCACTAACTGAAGTGTAAAAggg < 3:66256/149‑1 (MQ=255)
ttttATGCCGATGCCGGGCGCAAACCCTGTTCTGGTTCGAAAGGGGGGATCTCACACTGTACGGCAGGCGGCAAATTTGTCTGTAATGATGGTTCTATTAGTGCATCGAAAAAAACATGCACTAACTGAAGTGTAAAAGGGGTGCCATg > 1:140043/1‑149 (MQ=255)
ccgatgccgGGCGCAAACCCTGTTCTGGTTGGAAAGGGGGGATCTCACACTGTACGGCAGGCGGCAAATTTGTCTGTAATGATGGTTCTATTAGTGCATCGAAAAAAACATGCACTAACTGAAGTGTAAAAGGGGTGCCATGAGAAAAt < 4:163623/149‑1 (MQ=255)
cgGGCGCAAACCCTGTTCTGGTTCGAAAGGGGGGATCTCACACTGTACGGCAGGCGGCAAATTTGTCTGTAATGATGGTTCTATTAGTGCATCGAAAAAAACa < 2:417963/103‑1 (MQ=255)
cgGGCGCAAACCCTGTTCTGGTTCGAAAGGGGGGATCTCACACTGTACGGCAGGCGGCAAATTTGTCTGTAATGATGGTTCTATTAGTGCATCGAAAAAAACa > 1:417963/1‑103 (MQ=255)
gcgcAAACCCTGTTCTGGTTCGAAAGGGGGGATCTCACACTGTACGGCAGGCGGCAAATTTGTCTGTAATGATGGTTCTATTAGTGCATCGAAAAAAACATGCACTAACTGAAGTGTAAAAGGGGTGCCATGAGAAAATGAATCTGCTa < 1:495673/149‑1 (MQ=255)
gcgcAAACCCTGTTCTGGTTCGAAAGGGGGGATCTCACACTGTACGGCAGGCGGCAAATTTGTCTGTAATGATGGTTCTATTAGTGCATCGAAAAAAACATGCACTAACTGAAGTGTAAAAGGGGTGCCATGAGAAAATGAATCTGCTa < 1:168943/149‑1 (MQ=255)
ttCTGGTTCGAAAGGGGGGATCTCACACTGTACGGCAGGCGGCAAATTTGTCTGTAATGATGGTTCTATTAGTGCATCGAAAAAAACATGCACTAACTGAAGTGTAAAAGGGGTGCCATGAGAAAATGAATCTGCTAGTCAAATGcgcg > 3:258419/1‑149 (MQ=255)
ttCTGGTTCGAAAGGGGGGATCTCACACTGTACGGCAGGCGGCAAATTTGTCTGTAATGATGGTTCTATTAGTGCATCGAAAAAAACATGCACTAACTGAAGTGTAAAAGGGGTGCCATGAGAAAATGAATCTGCTAGTCAAATGcgcg > 2:332461/1‑149 (MQ=255)
gTTCGAAAGGGGGGATCTCACACTGTACGGCAGGCGGCAAATTTGTCTGTAATGATGGTTCTATTAGTGCATCGAAAAAAACATGCACTAACTGAAGTGTAAAAgg > 4:111026/1‑106 (MQ=255)
gTTCGAAAGGGGGGATCTCACACTGTACGGCAGGCGGCAAATTTGTCTGTAATGATGGTTCTATTAGTGCATCGAAAAAAACATGCACTAACTGAAGTGTAAAAgg < 3:111026/106‑1 (MQ=255)
|
ACGGTATCAAAATAAACCAGCGTATAACGTTCAAATCGAACATAAGATTCGATAAACCATGGAGGTTATATGAAAAAACTGGCACTTATTTTGTTTATGGGAACGCTTGTTTCCTTTTATGCCGATGCCGGGCGCAAACCCTGTTCTGGTTCGAAAGGGGGGATCTCACACTGTACGGCAGGCGGCAAATTTGTCTGTAATGATGGTTCTATTAGTGCATCGAAAAAAACATGCACTAACTGAAGTGTAAAAGGGGTGCCATGAGAAAATGAATCTGCTAGTCAAATGCGCG > NC_000913/1491608‑1491899
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
