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 |
2,342,380 |
A→C |
100% |
L78V (TTG→GTG) |
USA300HOU_2199 ← |
possible HAD superfamily hydrolase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | CP000730 | 2,342,380 | 0 | A | C | 99.8%
| 82.5
/ ‑7.3
| 27 | L78V (TTG→GTG) | USA300HOU_2199 | possible HAD superfamily hydrolase |
| Reads supporting (aligned to +/- strand): ref base A (1/0); major base C (17/8); minor base T (1/0); total (19/8) |
| 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. |
TTATATTGCGCAGAAATATGACGTAATATATCTTCAATATCTTCAAATAAAAATGGTTCGCTCAAGACTTTCTTTTTATATGTTTCTGATTCAACATATTCGCCATTATTCCAAGTGAACATTTTAGAACTCAAATCAGAAAAGATATGTAATGGTTTAAACGTCATATTAACTTGATCCATTTTATCCATGACACTTTGAAATGTACTTCCTGTCAATACAGCAGTGATCACTTCATTATTATTAGTTAGTTTTTCCAACAATTTT > CP000730/2342247‑2342513
|
ttATATTGCGCAGAAATATGACGTAATATATCTTCAATATCTTCAAATAAAAATGGTTCGCTCAAGACTTTCTTTTTATATGTTTCTGATTCAACATATTCGCCATTATTCCAAGTAAACATTTTAGCACTCACATcctaa > 1:235706/1‑137 (MQ=255)
ttGCGCAGAAATATGACGTAATATATCTTCAATATCTTCAAATAAAAATGGTTCGCTCAAGAATTTCTTTTTATATGTTTCTGATTCAACATATTCGCCATTATTCCAAGTGAACATTTTAGAAGTCACATCAGAAAGGat > 1:44888/1‑141 (MQ=255)
gcAGAAATATGACGTAATATATCTTCAATATCTTCAAATAAAAAGGGTTCGCTCAAGACTTTCTTTTTATATGTTTCTGATTCAACATATTCGCCATTATTCCAAGTGAACATTTTAGAACTCACAACAGAAAAGATATGt < 2:146916/141‑1 (MQ=255)
aaTATGACGTAATATATCTTCAATATCTTCAAATAAAAATGGTTCGCTCAAGACTTTCTTTTTATATGTTTCTGATTCAACATATTCGCCATTATTCCAAGTGAACATTTTAGAACTCACATCAGAAAAGATCTGTAATgg > 2:109368/1‑141 (MQ=255)
tatGACGTAATATATCTTCAATATCTTCAAATAAAAATGGTTCGCTCAAGACTTTATTTTTATATGTTTCTGATTCAACATATTCGCCATTATTCCAAGTGAACATTTTAGAACTCACATCAGAAAAGATATGTAATGttt > 1:54662/1‑141 (MQ=255)
aCGTAATATATCTTCAATATCTTCAAATAAAAATGGTTCGCTCAAGACTTTCTTTTTATATGTTTCTGATTCAACATATTCGCCATTATTCCAAGTGAACATTTTAGAACTCACATCAGAAAAGATATGTAATGGTTTaaa > 1:107523/1‑141 (MQ=255)
tatcttcaaATAAAAATGGTTCGCTCAAGACTTTCTTTTTATATGTTTCTGATTCAACATATTCGCCATTATTCCAAGTGAACATTTTAGAACTCACCTCAGAAAAGATATATAATGGTTTAACCGTCATATTAACTTGAt > 2:257982/1‑141 (MQ=255)
ttcaaATAAAAATGGTTCGCTCAAGACTTTCTTTTTATATGTTTCTGATTCAACATATTCGCCATTATTCCAAGTGAACATTTTAGAACTCAAATCAGAAAAGATATGTAGTGGTTTAAACGTCATATTAACTTGATCCAt > 1:267064/1‑141 (MQ=255)
tcaaATAAAAATGGTTCGCTCAAGACTTTCTTTTTATATGTTTCTGATTCAACATATTCGCCATTATTCCAAGTGAACATTTTAGAACTCACATCAGAAAAGATATGTAATGGTTTAAACGTCATCTTAACTTGATCCAtt > 2:225722/1‑141 (MQ=255)
aaTGGTTCGCTCAAGACTTTCTGTTTATATGTTTCTGATTCAACATATTCGCCATTATTCAAACAGAACATTTTAGAAATCACTTCAAAAAAAATATTTACTGGTTTAAACGTCATATTAACTTGATCCATTTTATCCAta > 2:112362/1‑140 (MQ=255)
tCGCTCAAGACTTTCTTTTTATATGTTTCTGATTCAACATATTCGCCATTATTCCAAGTGAACATTTTAGAACTCACATCAGAAAAGATATGTAATGGTTTAAACGTCATATTAACTTGATCCATTTTATCCATGACACtt > 1:247035/1‑141 (MQ=255)
tCGCTCAAGACTTTCTCTTCATATGTTTCTGATTCAACATATTCGCCATTATTCCAAGTGAACATTTTAGAACTCACATCAGAAAAGATATGTAATGGTTTAAACGTCATATTAACTTGATCCATTTTATCCATGACACtt > 1:159714/1‑141 (MQ=255)
gACTTTCTTTTTATATGTTTCTGATTCAACATATTCGCCATTATTCCAAGTGAACATTTTAGAACTCACATCAGAAAAGATATGTAATGGTTTAAACGTCATATTAACTTGATCCATTTTATCCATGACACTTTGAAATGt > 2:159613/1‑141 (MQ=255)
tttatttTTATATGTTTCTGATTCAACATAATAGCCATTATTCCAAACGCAGATAGTAATACACATATCAGAAAAGATATGTAATGGTTTAAACGTCATATTAACTTGATCCATTTTATCCATGACACTTTGAAATGTACt > 2:60490/1‑141 (MQ=255)
ttttATATGTTTCTGATTCAACCTATTCGCCATTATTCCAAGTTAACATTTTAGAACTCACATCAGAAAATATATGTAATGGTTTAAACGTCATATTAACTTGATCCATTTTATCCATGACTCTTTGAAATGTACTTCCTg < 1:141428/141‑1 (MQ=255)
tgtataTGTTTCTGATTCAACATATTCTCCATTATTCCAAGTGAACATTTTAGAACTCACATCAGAAAAGATATGTAATGGTTTAAACGTCATATTAACTTGATCCATTTTATCCATGACACTTTGAAATGTACTTCCTGt < 1:257982/139‑1 (MQ=255)
ttATATGTTTCTGATTCAACATATTCGCCATTATTCCAAGTGAACATTTTAGAACTCACATCAGAAAAGATATGTAATGGTTTAAACGTCATATTAACTTGATCCATTTTATCCATGACACTTTGAAATGTACTTCCTGTc < 1:285112/141‑1 (MQ=255)
cTGATTCAACATATTCGCCATTATTCCAGGTGAACATTTTAGAACTCACATCAGAAAAGATATGTAATGGTTTAAACGTCATATTAACTTGATCCACTTTATCCATGACACTTTGAAATGTACTTCCTGTCAATAcagcag < 1:161746/141‑1 (MQ=255)
tGATTCAACATATTCGCCATTATTCCAAGTGAACATTTTAGAACTCACATCAGAAAAGATATGTAATGGTTTAAACGTCATATTAACTTGATCCATTTTATCCATGACACTTTGAAATGTACTTCCTGTCAATACAGCAGt < 2:155657/141‑1 (MQ=255)
acAACAGAGTCGCCATTATTCCAAGTGAACATTTTAGAACTCACATCAGAAAAGATATGTAATGGTTTAAACGTCATATTAACTTGATCCATTTTATCCATGACACTTTGAAATGTACTTCCTGTCAATACAGCAGTGAta > 2:2853/2‑140 (MQ=255)
aCATATTCGCCATTATTCCAAGTGAACATTTTAGAACTCACATCAGAAAAGATATGTAATGGTTTAAACGTCATATTAACTTGATCCATTTTATCCATGACACTTTGAAATGTACTTCCTGTCAATACAGCAGTGATCACt > 1:46222/1‑141 (MQ=255)
ttCGCCATTATTCCAAGTGAACATTTTAGAACTCACATCAGAAAAGATATGTAATGGTTTAAACGTCATATTAACTTGATCCATTTTATCCATGACACTTTGAAATGTACTTCCTGTCAATACAGCAGTGATCACTTCatt > 1:200632/1‑141 (MQ=255)
gCCATTATTCCAAGTGAACATTTTAGAACTCACATCAGAAAAGATATGTAATGGTTTAAACGTCATATTAACTTGATCCATTTTATCCATGACACTTTGAAATGTACTTCCTGTCAATACAGCAGTGATCACTTCattatt > 1:253276/1‑141 (MQ=255)
cAACTGAACATCTTAGAACTCACATCAGAAAAGATATGTAATGGATTAAACGTCATATTAACTTGATCCATTTTACCCATTACCCCTTAAAATGTACTTCCTGTCAATACAGCAGTGATCACTTCATTATTATtagttagt < 2:230152/141‑1 (MQ=255)
gAACATTTTAGAACTCACATCAGAAAAGATATGTAATGGTTTAAACGTCATATTAACTTGATCCATTTTATCCATGACACTTTGAAATGTACTTCCTGTCAATACAGCAGTGATCACTTCATTATTATTAGTTAGTTTTTc > 2:252260/1‑141 (MQ=255)
tAGAACTCACATCAGAAAAGATATGTAATGGTTTAAACGTCATATTAACTTGATCCATTTTATCCATGACACTTTGAAATGTACTTCCTGTCAATACAGCAGTGATCACTTCATTATTATTAGTTAGTTTTTCCAACAAtt > 1:1984/1‑141 (MQ=255)
gAACTCACATCAGAAAAGATATGTAATGGTTTAAACGTCATATTAACTTGATCCATTTTATCCATGACACTTTGAAATGTACTTCCTGTCAATACAGCAGTGATCACTTCATTATTATTAGTTAGTTTTTCCAACAAtttt < 2:84463/141‑1 (MQ=255)
|
TTATATTGCGCAGAAATATGACGTAATATATCTTCAATATCTTCAAATAAAAATGGTTCGCTCAAGACTTTCTTTTTATATGTTTCTGATTCAACATATTCGCCATTATTCCAAGTGAACATTTTAGAACTCAAATCAGAAAAGATATGTAATGGTTTAAACGTCATATTAACTTGATCCATTTTATCCATGACACTTTGAAATGTACTTCCTGTCAATACAGCAGTGATCACTTCATTATTATTAGTTAGTTTTTCCAACAATTTT > CP000730/2342247‑2342513
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
