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 |
|
A15 F177 I0 R1
|
51 |
26.9 |
575130 |
96.6% |
555575 |
140.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
CP000730 |
1,797,772 |
G→C |
100% |
R7G (CGC→GGC) |
USA300HOU_1679 ← |
sensor histidine kinase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | CP000730 | 1,797,772 | 0 | G | C | 98.1%
| 61.6
/ ‑6.4
| 21 | R7G (CGC→GGC) | USA300HOU_1679 | sensor histidine kinase |
| Reads supporting (aligned to +/- strand): ref base G (1/0); new base C (10/10); total (11/10) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
CTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATCAACAATT > CP000730/1797661‑1797907
|
cTAGAGCTTGTTCGTGTTTTTCTGATCAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATCAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAgg < 1:174972/141‑1 (MQ=255)
cTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAgg < 1:272703/141‑1 (MQ=255)
tatagCTTGTTCGTGTTTTTCTGATAAAACATATGTTATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGt < 1:6747/138‑1 (MQ=255)
ttGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTcc < 1:75983/141‑1 (MQ=255)
ttttCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATAATTGTTCTTTAGGTCTTTCCAATTTATAGc > 1:110171/1‑141 (MQ=255)
ttCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATGATTAATATACTGCTTATCAATAACATTAAACGGTGATGAAAGTTAATCATTGTTATTTAAGCCATCGCAAGTTATAGCCt > 2:115617/1‑141 (MQ=255)
tAAAACCTACGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTATGTCTTTCCAATTTATAACCTAAGCCa > 2:232947/1‑141 (MQ=255)
aaaaCATATGTGATTGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGCGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCAc < 1:192447/141‑1 (MQ=255)
aTGGAAGCTTGAATAATACTACCTAATCGAACAATACTGATACTTAATATACTGCTTATCAATAACATTAAGTCGTCGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTtaa < 2:273664/141‑1 (MQ=255)
aTGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTtaa < 2:236566/141‑1 (MQ=255)
aTGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGGGGTGAAACTACATCATTGTTCTTTAGGTCTTTCCAATGTATAGCCTAAGCAACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTAtc > 2:157094/1‑141 (MQ=255)
gTAACAAAACGGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTAtctt > 2:33718/1‑141 (MQ=255)
aaCAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTAtcttct < 2:268872/141‑1 (MQ=255)
aCTGATAATTAATATACTGCTTATCAATAACATTACGCCCTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTAGTGGCTTCTTAGAATTATCTTCTAATTTa > 2:117857/1‑141 (MQ=255)
tGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAACCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTACTTTTTAATTTAtc > 2:64786/1‑141 (MQ=255)
cTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGa < 2:113284/141‑1 (MQ=255)
taaaTAACATTAATGCGTGGTGAAACTTAATCATTGTTCTTTAGGTATTTCCAATTTAAAGCCTAAGCCACGCACAGTTTTAATAAGTTCTACCTCCTCAGGTCAATCTACTAATTTATCTCTTAAATGACTGATATGTaa > 2:129556/3‑140 (MQ=255)
tCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTACTTTATCTCTTAAATGACTGATATGTAc > 2:269051/1‑141 (MQ=255)
aaTAACATTAAGCCGTGGTGAAAATTCATGATTGGTCTTTATGGCTTTCCAATTTAGAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACAt > 2:167090/1‑141 (MQ=255)
tAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATCAACAAtt > 1:246849/1‑141 (MQ=255)
tAAGCCGTGGTGAAACCTCCTCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATCAACAAtt < 1:235653/141‑1 (MQ=255)
|
CTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATCAACAATT > CP000730/1797661‑1797907
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
