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 |
|
A10 F1 I1 R1
|
77 |
35.1 |
1569012 |
96.6% |
1515665 |
112.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
2,682,157 |
(C)7→8 |
coding (589/3282 nt) |
yphG ← |
DUF4380 domain‑containing TPR repeat protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 2,682,150 | 1 | . | C | 94.7%
| 56.0
/ ‑2.6
| 19 | coding (596/3282 nt) | yphG | DUF4380 domain‑containing TPR repeat protein |
| Reads supporting (aligned to +/- strand): ref base . (0/1); new base C (9/9); total (9/10) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.23e-01 |
TAGCGAGAAATGTCCACTCCAGCGGAGTAGTCCACTTTGTAGTAAGTGCCGGTAGCGATGGGGAAAGCGGAGACGGCCCGTTTGCCGTGATCAAACACCGCCGTTACATCCGGCGGGAAGACGCTCTGATGCCCTT‑CCCCCCCTTTCACTGCCGGGTTGGCCCACCACAAGAAATGACGCGGCGTGGCGTTCCCGTTATAGACGCGGCTGGCGATTTCCAGCGCCGCCCGGTCAGGGCGCAGGGTGAAACCTGTCAT > NC_000913/2682015‑2682271
|
taGCGAGAAATGTCCACTCCAGCGGAGTAGTCCACTTTGTAGTAAGTGCCGGTAGCGATGGGGAAAGCGGAGACGGCCCGTTTGCCGTGATCAAACACCGCCGTTACATCCGGCGGGAAGACGCTCTGATGCCCTT‑ccc < 1:184259/139‑1 (MQ=255)
aaaTGTCCACTCCAGCGGAGTAGTCCACTTTGTAGTAAGTGCCGGTAGCGATGGGGAAAGCGGAGACGGCCCGTTTGCCGTGATCAAACACCGCCGTTACATCCGGCGGGAAGACGCTCTGATGCCCTT‑cccccccctt > 2:124520/1‑136 (MQ=255)
tCCACTCCAGCGGAGTAGTCCACTTTGTAGTAAGTGCCGGTAGCGATGGGGAAAGCGGAGACGGCCCGTTTGCCGTGATCAAACACCGCCGTTACATCCGGCGGGAAGACGCTCTGATGCCCTTCCCCCCCCTTTCACt > 1:297160/1‑139 (MQ=255)
gtCCACTTTGTAGTAAGTGCCGGTAGCGATGGGGAAAGCGGAGACGGCCCGTTTGCCGTGATCAAACACCGCCGTTACATCCGGCGGGAAGACGCTCTGATGCCCTTCCCCCCCCTTTCACTGCCGGGTTGGCccacca < 2:477375/139‑1 (MQ=255)
gtCCACTTTGTAGTAAGTGCCGGTAGCGATGGGGAAAGCGGAGACGGCCCGTTTGCCGTGATCAAACACCGCCGTTACATCCGGCGGGAAGACGCTCTGATGCCCTTCCCCCCCCTTTCACTGCCGGGTTGGCccacca > 2:413292/1‑139 (MQ=255)
cACTTTGTAGTAAGTGCCGGTAGCGATGGGGAAAGCGGAGACGGCCCGTTTGCCGTGATCAAACACCGCCGTTACATCCGGCGGGAAGACGCTCTGATGCCCTTCCCCCCCCTTTCACTGCCGGGTTGGCCCACCACaa > 1:765641/1‑139 (MQ=255)
gCCGGTAGCGATGGGGAAAGCGGAGACGGCCCGTTTGCCGTGATCAAACACCGCCGTTACATCCGGCGGGAAGACGCTCTGATGCCCTTCCCCCCCCTTTCACTGCCGGGTTGGCCCACCACAAGAAATGACGCggcgt > 1:386749/1‑139 (MQ=255)
gCCGGTAGCGATGGGGAAAGCGGAGACGGCCCGTTTGCCGTGATCAAACACCGCCGTTACATCCGGCGGGAAGACGCTCTGATGCCCTT‑ccc < 2:53599/92‑1 (MQ=255)
gCCGGTAGCGATGGGGAAAGCGGAGACGGCCCGTTTGCCGTGATCAAACACCGCCGTTACATCCGGCGGGAAGACGCTCTGATGCCCTT‑ccc > 1:274253/1‑92 (MQ=255)
gCCGGTAGCGATGGGGAAAGCGGAGACGGCCCGTTTGCCGTGATCAAACACCGCCGTTACATCCGGCGGGAAGACGCTCTGATGCCCTT‑ccc < 2:274253/92‑1 (MQ=255)
gCCGGTAGCGATGGGGAAAGCGGAGACGGCCCGTTTGCCGTGATCAAACACCGCCGTTACATCCGGCGGGAAGACGCTCTGATGCCCTT‑ccc > 1:53599/1‑92 (MQ=255)
cGGTAGCGATGGGGAAAGCGGAGACGGCCCGTTTGCCGTGATCAAACACCGCCGTTACATCCGGCGGGAAGACGCTCTGATGCCCTTCCCCCCCCTTTCACTGCCGGGTTGGcc > 2:603865/1‑114 (MQ=255)
cGGTAGCGATGGGGAAAGCGGAGACGGCCCGTTTGCCGTGATCAAACACCGCCGTTACATCCGGCGGGAAGACGCTCTGATGCCCTTCCCCCCCCTTTCACTGCCGGGTTGGCCCACCACAAGAAATGACGCggcgtgg > 2:468035/1‑139 (MQ=255)
cGGTAGCGATGGGGAAAGCGGAGACGGCCCGTTTGCCGTGATCAAACACCGCCGTTACATCCGGCGAGAAGACGCTCTGATGCCCTTCCCCCCCCTTTCACTGCCGGGTTGGcc < 1:603865/114‑1 (MQ=255)
tAGCGATGGGGAAAGCGGAGACGGCCCGTTTGCCGTGATCAAACACCGCCGTTACATCCGGCGGGAAGACGCTCTGATGCCCTTCCCCCCCCTTTCACTGCCGGGTTGGCCCACCACAAGAAATGACGCggcgtggcgt < 1:360162/139‑1 (MQ=255)
cGATGGGGAAAGCGGAGACGGTCCGTTTGCCGTGATCAAACACCGCCGTTACATCCGGCGGGAAGACGCTCTGATGCCCTTCCCCCCCCTTTCACTGCCGGGTTGGCCCACCACAAGAAATGACGCGGCGTGGCGTTcc < 2:455834/139‑1 (MQ=255)
tGGGGAAAGCGGAGACGGCCCGTTTGCCGTGATCAAACACCGCCGTTACATCCGGCGGGAAGACGCTCTGATGCCCTTCCCCCCCCTTTCACTGCCGGGTTGGCCCACCACAAGAAATGACGCGGCGTGGCGTTCCCGt < 2:386749/139‑1 (MQ=255)
cGGCCCGTTTGCCGTGATCAAACACCGCCGTTACATCCGGCGGGAAGACGCTCTGATGCCCTTCCCCCCCCTTTCACTGCCGGGTTGGCCCACCACAAGAAATGACGCGGCGTGGCGTTCCCGTTATAGACGCGGCTgg < 1:413292/139‑1 (MQ=255)
gccgTTACATCCGGCGGGAAGACGCTCTGATGCCCTTCCCCCCCCTTTCACTGCCGGGTTGGCCCACCACAAGAAATGACGCGGCGTGGCGTTCCCGTTATAGACGCGGCTGGCGATTTCCAGCGCCGCCCGGTCAggg > 2:373164/1‑139 (MQ=255)
gccgTTACATCCGGCGGGAAGACGCTCTGATGCCCTTCCCCCCCCTTTCACTGCCGGGTTGGCCCACCACAAGAAATGACGCGGCGTGGCGTTCCCGTTATAGACGCGGCTGGCGATTTCCAGCGCCGCCCGGTCAggg > 1:410316/1‑139 (MQ=255)
gccgTTACATCCGGCGGGAAGACGCTCTGATGCCCTT‑ccccccccttt > 1:623271/1‑44 (MQ=255)
gccgTTACATCCGGCGGGAAGACGCTCTGATGCCCTT‑CCCCCCCcttt < 2:623271/48‑2 (MQ=255)
cgTTACATCCGGCGGGAAGACGCTCTGATGCCCTTCCCCCCCCTTTCACTGCCGGGTTGGCCCACCACAAGAAATGACGCGGCGTGGCGTTCCCGTTATAGATGCGGCTGGCGATTTCCAGCGCCGCCCGGTCAGGgcg < 2:765641/139‑1 (MQ=255)
tCCGGCGGGAAGACGCTCTGATGCCCTTCCCCCCCCTTTCACTGc < 2:214338/45‑1 (MQ=255)
tCCGGCGGGAAGACGCTCTGATGCCCTTCCCCCCCCTTTCACCGc > 1:214338/1‑45 (MQ=255)
gACGCTCTGATGCCCTTCCCCCCCCTTTCACTGCCGGGTTGGCCCACCACAAGAAATGACGCGGCGTGGCGTTCCCGTTATAGACGCGGCTGGCGATTTCCAGCGCCGCCCGGTCAGGGCGCAGGGTGAAACCTGtcat < 2:297160/139‑1 (MQ=255)
|
TAGCGAGAAATGTCCACTCCAGCGGAGTAGTCCACTTTGTAGTAAGTGCCGGTAGCGATGGGGAAAGCGGAGACGGCCCGTTTGCCGTGATCAAACACCGCCGTTACATCCGGCGGGAAGACGCTCTGATGCCCTT‑CCCCCCCTTTCACTGCCGGGTTGGCCCACCACAAGAAATGACGCGGCGTGGCGTTCCCGTTATAGACGCGGCTGGCGATTTCCAGCGCCGCCCGGTCAGGGCGCAGGGTGAAACCTGTCAT > NC_000913/2682015‑2682271
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
