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 |
|
A7 F123 I0 R1
|
46 |
52.8 |
1143652 |
95.1% |
1087613 |
141.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
CP000730 |
1,064,254 |
Δ1 bp |
100% |
coding (235/1218 nt) |
USA300HOU_1000 ← |
LytR family transcriptional regulator |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | CP000730 | 1,064,253 | 0 | C | . | 92.4%
| 213.3
/ 8.0
| 52 | coding (236/1218 nt) | USA300HOU_1000 | LytR family transcriptional regulator |
| Reads supporting (aligned to +/- strand): ref base C (2/1); new base . (18/30); total (20/32) |
| Fisher's exact test for biased strand distribution p-value = 5.53e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.55e-01 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
TAATCTTATCGTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTCCTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGC > CP000730/1064116‑1064389
|
tAATCTTATCGTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTcttt > 2:259567/1‑138 (MQ=255)
aTCTTATCGTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTCTtttt > 1:227900/1‑141 (MQ=255)
tCTTATCGTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTCtttttt > 2:225528/1‑141 (MQ=255)
aaTAGCCAACTCTAGGAATTTAGTTTATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGCTCAGCATCCTGT‑CTTTTTTTCTTCTTcc < 2:218578/141‑1 (MQ=255)
ccAACTTTAGGAATGTATGTGATATTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAACTCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGt < 2:514387/141‑1 (MQ=255)
aaCTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTa < 2:389464/141‑1 (MQ=255)
aCTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTat < 1:249559/141‑1 (MQ=255)
tttAGGAATTTAGCTGATATTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTatca < 2:161185/141‑1 (MQ=255)
tttAGGAATGCAGCTGAAAGTATCACGTGGAATACTAAGCATGCTAATTTGAGGTTTTGATTGATTAAAAGTAGTGAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTatca < 2:15958/141‑1 (MQ=255)
aGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCg > 1:435037/1‑141 (MQ=255)
aaTGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTACTTTGATGTTTTGCTTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGGGTTCAGCATCCGGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGAtc > 2:418315/1‑140 (MQ=255)
gatcTGATAGGATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTa < 1:45400/138‑1 (MQ=255)
gCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTaag < 1:53584/141‑1 (MQ=255)
gCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTaag < 2:218191/141‑1 (MQ=255)
tGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTTTTCTTCCATCGTTATCATCGATTCATaagaa > 1:218704/1‑141 (MQ=255)
tGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTaagaa > 2:139767/1‑141 (MQ=255)
tGATAATAACACGTGGAATACTAAGCATTCTAAGTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGGGTGTTCAGCATCCGGT‑CTTTTTTTCTTCGTCCATCGTTATCATCGATACCTaagaa < 2:521455/141‑1 (MQ=255)
gTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGTTACCTaagaaaagca > 2:303065/1‑139 (MQ=255)
cGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCTTCGTTATCATCGATACCTAAGAAACGAATagagt > 1:521833/1‑140 (MQ=255)
gAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTGTTCCATGGTTATCATCGATACCTAACAAAAGAATagagttcgg > 2:546180/1‑136 (MQ=255)
aTACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGgtt > 1:329742/1‑141 (MQ=255)
aCTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCGTCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGgttgt < 2:65139/141‑1 (MQ=255)
tAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGgttgttt > 2:173364/1‑140 (MQ=255)
aaGCATTCTAATTTGATGTTTTGATTGATAAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATGTGTACCTAAGATAAGCATAGAGATAGGTCGttct > 2:237695/1‑141 (MQ=255)
aGCATTCCAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGttctt < 1:197640/141‑1 (MQ=255)
cATTCTTATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTTTTCg < 2:67493/141‑1 (MQ=255)
cATTCTAATTTGATGTTTTTATTGATTAAAAGTAGTTNCAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCCTCGTTCTCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCg < 2:564468/141‑1 (MQ=255)
aTTCTAATTTGATGTCTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGGTCTTCgg < 1:356451/141‑1 (MQ=255)
ttCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCggg > 1:20544/1‑141 (MQ=255)
ttAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGAt < 2:513534/140‑1 (MQ=255)
tAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGAtt > 2:409484/1‑141 (MQ=255)
aaTTTGATTTTTTGATGGATTAATAGTAGTTAGTATCATTGCGTCTTATCTAGTGTGTTCAGCATCCTTTCTTTTGTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGAtt < 1:400220/141‑1 (MQ=255)
aTTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGa < 1:259567/141‑1 (MQ=255)
aTTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGa > 1:569236/1‑141 (MQ=255)
gATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATCCCTAAGAAAAGAATAGAGCTAGGTTGTTCATCGGGATTGACttt < 1:313362/141‑1 (MQ=255)
aTGTTTTGATTGATTAAAAGTAGTTAAAGTCATGGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCAGCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTtta < 1:89387/141‑1 (MQ=255)
attTAAAGTAGTTTAATTCATAGCTTCTCATCTAGAGTGTTCAGCATCCTCT‑CTCTTTCTCTTCTCCCATCGTTATCATCGATACCTAAGAAAAGAATAGACATAGGTTGTCCTTCGGGATTGACTTTATTATCTCTTAAg < 2:385678/141‑1 (MQ=255)
ttAAAAGTATTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGt < 1:63343/141‑1 (MQ=255)
ttAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGt < 1:480156/141‑1 (MQ=255)
gtagtTAAAATCATAGCGTCTGCTCTAGAGTGTTCAGCTTCCTGT‑CTTTGTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATGGACTTTATTATCTCTTGAGTTGGAtt < 2:293662/141‑1 (MQ=255)
gtTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTGCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGAc > 1:391625/1‑141 (MQ=255)
gtTAAAATCATAGCGTCTGATCTAGAGTGTTCAGAATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAGAAGAATAGAGATAGGTTGTTCTTCGGGCTTGACTTTATTCTCTCTTGAGTTGGaggaac > 1:189373/1‑136 (MQ=255)
acaaaTCATTGCGTCTGATCTTGAGTGTTCAGCATCCT‑TTCTTTTTTTCGTCTTTCATCGTTATCATCGATACCTAAGAAAAGAATACAGATAGGTTGTTCGTCTGGATTCACTTTCTTATCACTTTAGTTGGATTGACGa < 2:347766/139‑1 (MQ=255)
aaaTCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGAtt < 1:106624/141‑1 (MQ=255)
gCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCAtttt < 1:187631/141‑1 (MQ=255)
gTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTATTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGAAGATTAGCATTTTTg < 1:317039/141‑1 (MQ=255)
tGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCATTTTTGCTg > 1:62039/1‑141 (MQ=255)
aTCTAGAGTGTTCCGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCATTTTTGCTGTc < 1:475339/141‑1 (MQ=255)
gagTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCATTTTTGCTGTCTTgag < 2:227900/141‑1 (MQ=255)
gtgtTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCATTTTTGCTGTCTTGagaa < 1:313660/141‑1 (MQ=255)
cAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTc > 2:350725/1‑141 (MQ=255)
aTCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCATTTTTCTTGTCTTGAGAAGATTCGAAt > 2:561135/1‑141 (MQ=255)
ccTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGc < 1:409484/141‑1 (MQ=255)
|
TAATCTTATCGTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTCCTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGC > CP000730/1064116‑1064389
|
| 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
