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 |
2,502,882:1 |
+A |
100% |
coding (1406/2106 nt) |
melR_2 → |
Melibiose operon regulatory protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | USA300TCH1516_ALE | 2,502,882 | 1 | . | A | 93.1%
| 93.1
/ 0.3
| 29 | coding (1406/2106 nt) | melR_2 | Melibiose operon regulatory protein |
| Reads supporting (aligned to +/- strand): ref base . (0/2); new base A (15/12); total (15/14) |
| Fisher's exact test for biased strand distribution p-value = 2.24e-01 |
| 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: Variant not supported by required number of reads on each strand. |
| Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch. |
TTAAAAACAAAAATAAAGAAATTAAATATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTC‑AAA‑AA‑CTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCAGGTATATCATCAACACAATTTGTATATAATAACCTGTCTGTAAG > USA300TCH1516_ALE/2502747‑2503017
|
ttaaaaACAAAAATAAAGAAATTAAATATAGTGTGCCTGTTCAAGACTTTTTTTATAGGTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTC‑aaa‑aa > 1:390769/1‑141 (MQ=255)
aaaaaCAAAAATAAAGAAATTAAATCTAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCCTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTC‑aaacaaa > 2:151390/1‑137 (MQ=255)
aaaaCAAAAATAAAGAAATTAAATATAGTGTGACAGTCTATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATAATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTC‑aaa‑aaact > 1:27507/1‑138 (MQ=255)
aaCAAAAATAAAGAAATTAAATATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTC‑aaa‑aaactgc < 1:2866/141‑6 (MQ=255)
tAAAGAAATTAAATATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAA‑AA‑CTGCAACACATc > 1:379073/1‑141 (MQ=255)
gAAATTAAATATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAA‑AA‑CTGCAACACATCTTAt > 1:33923/1‑141 (MQ=255)
ttAAATATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAA‑AA‑CTGCAACACATCTTATCACt > 2:83794/1‑141 (MQ=255)
ttAAATATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATACAAAA‑AA‑CTGCAACACATCTTATCACt > 2:136091/1‑141 (MQ=255)
aaTATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAA‑AA‑CTGCAACACATCTTATCACTaaa < 1:254483/141‑1 (MQ=255)
tataGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAA‑AA‑CTGCAACACATCTTATCACTaaaaa < 1:119495/141‑1 (MQ=255)
aGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAA‑AA‑CTGCAACACATCTTATCACTAAAAACCAACACTatc > 2:227399/1‑141 (MQ=255)
ttttAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAA‑AA‑CTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGac < 1:254194/141‑1 (MQ=255)
ttAGAAACTTATTCAACCGTGGAACAAGTTCATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAA‑AA‑CTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGacac < 2:248354/141‑1 (MQ=255)
tAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCAATTATTACTTTATTGATATTGAAAATTCAAAA‑AA‑CTGCAACACATCTTCTCACTAAAAACCAACTATATCATCAGACTGCCACt > 1:11878/1‑141 (MQ=255)
tAGAAACTTACGCAAACGTAGAACAAGTTTATCCTCTCAAGCAACGTCTTAAATTCCATTATGACTTTATTGAAAAAAAAAAAAAAAAA‑AA‑CTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACt < 2:381135/141‑1 (MQ=255)
aGAAACTTCTTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCCTAAATTCCATTATTTCTTAATTAAGGTGGAAAATTA‑AAATAA‑CTTGAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTc < 1:92721/141‑1 (MQ=255)
aaCTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAA‑AA‑CTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCAtt < 1:55178/141‑1 (MQ=255)
aTTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAA‑AA‑CTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGaa > 1:344010/1‑141 (MQ=255)
tCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAA‑AA‑CTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACa > 2:234880/1‑141 (MQ=255)
aCCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAA‑AA‑CTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGta > 1:375603/1‑141 (MQ=255)
gAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATAGAAAATTAAAAA‑AA‑CTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGaa < 2:165295/141‑1 (MQ=255)
aCAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAA‑AA‑CTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAat > 1:665/1‑141 (MQ=255)
aCAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAA‑AA‑CTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAat > 2:387552/1‑141 (MQ=255)
gTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAA‑AA‑CTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACCCATTTTGAACAGTATAAGAAatttat > 1:82559/1‑141 (MQ=255)
gTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAA‑AA‑CTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTc < 1:162060/141‑1 (MQ=255)
tCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAA‑AA‑CTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCa > 1:256251/1‑141 (MQ=255)
aTGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAA‑AA‑CTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCAgg < 1:207358/141‑1 (MQ=255)
cAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAA‑AA‑CTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCAGGtat > 2:47300/1‑141 (MQ=255)
tcttCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAA‑AA‑CTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCAGGTatat < 2:66697/138‑1 (MQ=255)
cTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAA‑AA‑CTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCAGGTATatcatc < 1:351095/141‑1 (MQ=255)
gtAAGTTCCATTATTCTATTATTGTCATTGAAAATTCAAAA‑AA‑CTACGACTTTCCTTATCACTAAAAACCAACACTATCATCAAACTGACCCTCATTTTGAACAGTATAAGAAATTAATTTTAGATTCAGGTATAtcatca < 2:196302/140‑1 (MQ=255)
ttATTGATATTGAAAATTCAAAA‑AA‑CTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCAGGTATATCATCAACACAATTTGTATataat > 2:184452/1‑141 (MQ=255)
aaTTC‑AAA‑AACCTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCAGGTATATCATCAACACAATTTGTATATAATAACCTGTCTGTAAg < 1:302723/141‑1 (MQ=255)
|
TTAAAAACAAAAATAAAGAAATTAAATATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTC‑AAA‑AA‑CTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCAGGTATATCATCAACACAATTTGTATATAATAACCTGTCTGTAAG > USA300TCH1516_ALE/2502747‑2503017
|
| 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
