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 F169 I0 R1
|
75 |
34.0 |
794130 |
95.7% |
759982 |
140.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
USA300TCH1516_ALE |
1,440,085 |
G→T |
100% |
intergenic (‑45/+126) |
cspA_2 ← / ← USA300TCH1516_01338 |
Cold shock protein CspA/hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | USA300TCH1516_ALE | 1,440,085 | 0 | G | T | 99.6%
| 34.5
/ ‑7.3
| 17 | intergenic (‑45/+126) | cspA_2/USA300TCH1516_01338 | Cold shock protein CspA/hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base G (0/1); new base T (7/8); total (7/10) |
| 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. |
TACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATA > USA300TCH1516_ALE/1439957‑1440195
|
tACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACaaaa < 2:74134/141‑1 (MQ=255)
ctcCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCTTAATCTGTAACCTCCAAGACTTAAATTCATTCAATATGCTTTTTCTCATATTACAAAAAATACATGCAAAGTTCa > 1:15414/1‑141 (MQ=255)
ccTTCCACTTCGATCAAGCCGAATCCTTTTTCATCGTTAATCCATTTAACTGTACCTGGTTTCATAATCTCAAACCTCCAAGACTAAATGTCATTCCATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACt < 2:194986/141‑1 (MQ=255)
aGCCGAATCCTTTTTCAGCATTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCATTATGCTTATTCTCATATTTCAAAAAATACAGGCAAATTTCACTCAAAAATACttgtcaa > 1:36245/1‑136 (MQ=255)
gCCGAATCCTTTTTCTGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACCCATATATTCTTTGCAat > 1:294704/1‑141 (MQ=255)
tCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACATCCAAGACTAAAATTCATTCAATATGCTTATTATCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTGGCATTATGGaa > 1:360477/1‑141 (MQ=255)
ccTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGaat > 2:396006/1‑141 (MQ=255)
aGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCt > 1:181229/1‑141 (MQ=255)
cGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGc < 1:102952/141‑1 (MQ=255)
tAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATAAAAATAATAAAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTa < 2:146991/141‑1 (MQ=255)
ttAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGtat < 1:183835/141‑1 (MQ=255)
ttAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGtat < 1:183787/141‑1 (MQ=255)
taCCCCCAATACTAAAATTCATTCCATCTGCTTATTCTAATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGCAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGcaa < 1:380729/140‑1 (MQ=255)
aaCCTCCAAGACTAAAGTTCAATCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCTGGTATTACCAAATTGcaa > 1:203339/1‑141 (MQ=255)
cTCCAAGACTAAATTTCATTCTATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGcaatac < 1:119120/141‑1 (MQ=255)
cTCAAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGcaatac < 2:274897/141‑1 (MQ=255)
caGACAAACATACATGCAAGATGCGTATGCGTATATTACAAAAAATACATGCAAATCTCACTCAAAGATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGcaatacaata < 2:271618/140‑1 (MQ=255)
|
TACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATA > USA300TCH1516_ALE/1439957‑1440195
|
| 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
