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 |
|
A12 F59 I0 R4
|
226 |
76.6 |
2995274 |
95.4% |
2857491 |
127.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
CP006881 |
1,474,968 |
G→T |
39.3% |
S88* (TCA→TAA) |
U712_07575 ← |
Uncharacterized protein ykoA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | CP006881 | 1,474,968 | 0 | G | T | 39.3%
| 28.0
/ 11.0
| 37 | S88* (TCA→TAA) | U712_07575 | Uncharacterized protein ykoA |
| Reads supporting (aligned to +/- strand): ref base G (6/16); new base T (10/5); total (16/21) |
| Fisher's exact test for biased strand distribution p-value = 2.33e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CCGAAACGGGCTGGGACTGATCGCGGAAGATCGAATTGTCGGCACATCGAAGTTTGTCTTTTTCCCGT‑TTAACGAAATGCGTCAAACAAAATAAAAACGCCTTGCTGGCCTAGGACAGCAGGCG‑TTTTTATTTTGAAAAAGAAGCGACCAATGCAATGCATAAAACCGTGATGAACACTGAACCGATAATAGCCAGCACACTGAAGAAAAGGTGAACCTGTTTGTTCTCTTTTCCGCGCTTTTCTAATAGCCGTTTAGAAAAAATGTGCGAAA > CP006881/1474834‑1475106
|
ccGAAACGGGCTGGGACTGATCGCGGAAGATCGAATTGTCGGCACATCGAAGTTTGTCTTTTTCCCGT‑TTAACGAAATGCGTCAAACAAAATAAAAACGCCTTGCTGGCCTAGGCCAGCAGGCG‑TGTTTATTTTGaaa > 1:16270/1‑138 (MQ=255)
ccGAAACGGGCTGGGACTGATCGCGGAAGATCGAATTGTCGGCACATCGAAGTTTGTCTTTTTCCCGT‑TTAACGAAATGCGTCAAACAAAATAAAAACGCCTTGCTGGCCTAGGACAGCAGGCG‑TGTTTTTTTTGaaa > 5:110046/1‑138 (MQ=255)
aaaCGGGCTGGGACTGATCGCGGAAGATCGAATTGTAGGCACATCGAAGTTTGTCTTTTTCCCGT‑TTAACGAAAATCGTCAAACAAAAAAAAAACCCCTTTCTTGCCTAGGACAGCAGGCGTTTTTTATTTTTaaaaa > 6:30438/1‑138 (MQ=255)
aCGGGCTGGGACTGATCGCGGAAGATCGAATTGTCGGCACATCGAAGTTTGTCTTTTTCCCGT‑TTAACGAAATGCGTCAAACAAAATAAAAACGCCTTGCTGGCCTAGGACAGCACGCG‑TGTTTATTTTTaaaaataca > 4:172317/1‑135 (MQ=255)
ggCTGGGACTGATCGCGGAAGATCGAATTGTCGGCACATCGAAGTTTGTCTTTTTCCCGT‑TTAACGAAATTCGTCAAACAAAATAAAAACGCCTTGCTGGCCTAGGACAGCAGGCG‑TTTTTATTTTTAAAAATAAGcca > 2:25879/1‑137 (MQ=255)
ccTGGTACTGATCGCGGAAGAGCGAATTGTCGCCACATCGATTTTTGTCTTTTTCCCGT‑TAAACCAAATGCGACAAACAAAAAAAAAACGCCTTGCTGGCCTAGGACAGCAGGCG‑TTTTTATTTTGAAAAAGAAGCGAc < 5:301232/138‑1 (MQ=255)
cTGGGACTGATCGCGGAAGATCGAATTGTCGGCACATCGAAGTTTGTCTTTTTCCCGT‑TTAACGAAATGCGTCAAACAAAATAAAAACGCCTTGCTGGCCTAGGACAGCAGGCG‑TTTTTATTTTGAAAAAGAACCGAc > 4:367515/1‑138 (MQ=255)
cTGGGACTGATCGCGGAAGATCGAATTGTCGGCACATCGAAGTTTGTCTTTTTCCCCT‑TTAACGAAATGCGTCAAACAAAATAAAAACGCCTTGCTGGCCTAGGACAGCAGGCG‑TTTTTTTTTTTTAAAAAAAGCGccc > 8:191579/1‑139 (MQ=255)
gACTGACCCCGCAAGATCTAATTGCCGGCACATCGAAGTTTGTCTTTTTCCCGT‑TAAACGAAATGCGTCAAACAAAAAAAAAACGCCTTGCTGGCCTAGGACAGCAGGCG‑TTTTTATTTTGAAAAAGAAGCGACcaatg < 7:244886/139‑1 (MQ=255)
cTGATCGCGTAATATCTAATTGTCGGCACATCTAATTTTGTATTTTACCCTT‑TAAACTAAATGCGAAAAAAAAAAAAAAAACGCCTTGCTGGCCTAGGACAGCAGGCG‑TTTTTATTTTGAAAAAGAAGCGACcaatgca < 1:292307/139‑1 (MQ=255)
cTGATCGCGTAAGATCGAATTGTCGGCACATCTAATTTTGTCTTTTTCCCTT‑TTAACTAAATGCGTCAAAAAAAAAAAAAACGCATTGCTGGCCTAGGACAGCAGGCG‑TTTTTATTTTGAAAAAGAAGCGACcaatgca < 2:136378/139‑1 (MQ=255)
cTGATCGCGGAAGATCGAATTGTCGGCACATCGAAGTTTGTCTTTTACCCGT‑TTAACTAAATGCGTCAAACAAAATAAAAACGCCTTGCTGGCCTAGGACAGCAGGCG‑TTTTTATTTTGAAAAAGAAGCGACcaatgca < 7:11957/139‑1 (MQ=255)
aTCGCGGAAGATCGAATTGTCGGCACATCGAAGTTTGTCTTTTTCCCGT‑TTAACGAAATGCGTCAAACAAAATAAAAACGCCTTGCTGGCCTAGGACAGCAGGCG‑TTTTTTTTTTGTAAAAGAAGCGCCcaaaggaatt > 8:312473/1‑138 (MQ=255)
aTCGCGGAAGATCGAATTGTCGGCACATCGAAGTTTGTCTTTTTCCCGT‑TTAACGAAATGCGTCAAACAAAATAAAAACGCCTTGCTGGCCTAGGACAGCAGGCG‑TGTTTTTTTTTAAAAATAAGCGACcaaagcaatg > 2:292307/1‑139 (MQ=255)
aTCGCGGAAGATCGAATTGTCGGCACATCGAAGTTTGTCTTTTTCCCGT‑TTAACGAAAAGCGTCAAACAAAAAAAAAACGCCTTGCTGGCCTAGGACATCAGGCG‑GTGTTTTTTTGAAAAAGAAGCGACcaaaacaat > 2:67307/1‑138 (MQ=255)
aaGATCGAATTGTCGGCACATCGAAGTTTGTCTTTTTCCCGT‑TTAACGAAATGCGTCAAACAAAATAAAAACGCCTTGCTGGCCTAGGACAGCAGGCG‑TTTTTATTTTGAAAAAGAAGCGACCAATGCAATGCATaaaa < 8:282802/139‑1 (MQ=255)
gATCTAATTGTCGTCACATCGAAGTTTGTCTTTTTCCCGT‑TTAACGAAATGCGCCAAACAAAATAAAAACGCCTTGCTGGCATAGGACAGCAGGCG‑TTTTTATTTTGAAAAAGAAGCGACCAATGCAATGCATAAAAcc < 3:361107/139‑1 (MQ=255)
gATCCATTTGTCGCCACATCTATTTTTGTTTTTATCCGCT‑TTAACAACATCGCTCAAAAAAAAAAAACACGCCTTGCTGGCCTAGGACAGCAGGCG‑TTTTTATTTTTAAAAAGAAGCGACCAATGCAATGCATAAAAcc < 5:320312/139‑1 (MQ=255)
aTCGAATTGTCAGCACATCGAAGTTTGTCTTTTTCCCGT‑TTAACGAAATGCGTCAAACAAAATAAAAACGCCTTGCTGGCCTAGGACAGCAGGCG‑TGTTTTTTTTGAAAAAAAACCGCCCAAAGCAAAGCCAAAAACCg > 5:280877/1‑139 (MQ=255)
aaTTGTCGGCACATCGAAGTTTGTCTTTTTCCCGT‑TTAACGAAATGCGTCAAACAAAATAAAAACGCCTTGCTGGCCTAGGACAGCAGGCG‑TTTTTATTTTTTAAAAACATCGACCAATTCAATTCAAAAAAcccgtgt > 8:254620/1‑134 (MQ=255)
attgggggCACTTCCAATTTTGTCTTTTCACCTT‑TTAAAAAACTCGCAAAAACAAAATAAAACCGCCTTGCTGGCCTTGGACAGCAGGCG‑TTTTTTTTTTTAAAAAGAAGCGACCAATGCAATGCATAAAACCGtgat < 7:190155/132‑1 (MQ=255)
aTTGTCGGCACATCTAAGTTGGTCTTTTTCCCGT‑TAAACGAAATGCTCCAAACAAAATAAAAACGCCTTGCTGGCCTAGGACAGCAGGCG‑TTTTTATTTTGAAAAAGAAGCGACCAATGCAATGCATAAAACCGtgat < 1:213456/138‑1 (MQ=255)
caTCGAAGTTTGTCTTTTTCCCTT‑TTAACTAAATGCGTAAAACAAAATAAAAACGCCTTGCTGGCCTAGGACAGCAGGCT‑TTTTTATTTTTAAAAAGAAGCGACCAATGCAATGCATAAAACCGTGATGAACACTGAAc < 1:25879/139‑1 (MQ=255)
actctaaGTTTGTCTTTTTCCCGT‑TAAACGAAAGGCGTCAAAAAAAAAAAACACGCCTTGCTGGCCTAGGACAGCAGGCG‑TTTTTATTTTGAAAAAGAAGCGACCAATGCAATGCATAAAACCGTGATGAACACTGAAc < 7:243676/134‑1 (MQ=255)
cctgtggTCTTTATCCCGT‑TTAACCAAAGGCGACAAACAAAAAAAAACCGCCTGGCTGGCCTAGGACAGCAGGCG‑TTTTTATTTTGAAAACGAAGCGACCACTGCAATGCATAAAACCGTGATGAACACTGAACCGata < 6:293591/133‑1 (MQ=255)
aaGTTTGGATTTTTCCCGT‑TAAACGAAATGCGACAAACAAAAAAAAAACGCCTTGCTGGCCTAGGACAGCAGGCG‑TTTTTATTTTGAAAAAGAAGCGACCAATGCAATGCATAAAACCGTGATGAACACTGAACCGata < 6:110046/139‑1 (MQ=255)
attttCCCGTATAAACCAACTGCGACAAACAAAAAAAAACCGCCTGGCTGGCCTAGGCCAGCTGGCG‑TTTTTATTTTGAAAAAGACGCGACCAATGCAATGCATAAAACCGTGATGAACACTGAACCGATAATAGCCAg < 2:113387/138‑1 (MQ=255)
cccTT‑TTAACAAATTGCCTAAAAAAAAATAAAAACGCCTTGCTGGCCTAGGACAGCAGGAG‑TTTTTATTTTTAAAAAGAAGCGACCAATGCAATGCATAAAACCGTGATGAACACTGAACCGATAATAGCCAGCacac < 5:235360/138‑1 (MQ=255)
ccagT‑TTAACTAAATGCGTAAAAAAAAATAAAAACTCCTTGCTGGCCTAGGAAAGCTGGCG‑TTTTTATTTTGAAAAAGAAGCGACCAATGCAATGCATAAAACCGTGATGAACACTGAACCGATAATAGCCAGCacac < 6:279444/135‑1 (MQ=255)
aaTAAAAACGCCTTGCTGGCCTAGGACAGCAGGCG‑TTTTTAATTTTAAAAACAACCCACCCATTAAAAGCATAAAAACGTGAAGAAAACTGAAACCCTAAAAAACAGCCCACAGAAGAAAATGTGAACCTGTTTGTtca > 2:223265/1‑138 (MQ=255)
cGCCTTGCTGGCCTAGGACAGCAGGCG‑TTTTTATTTTGAAAAAGAAGCGACCAATGCAATGCATAAAACCGTGATGAACACTGAACCGATAATAGCCAGCACACTGAAGAAAAGGTGAACCTGTTTGTTCTCTTTTCcg < 8:196510/139‑1 (MQ=255)
gCTGGCCAAGCACAGCAGGTG‑TTTTTATTTTTAAAAAGAAGCGACCAATGCAATGCATAAAACCGTGATGAACACTGAACCGATAATAGCCAGCACACTGAAGAAAAGGTGAACCTGTTTGTTCTCTTTTCCGCGCtt < 5:30438/138‑1 (MQ=255)
ggACAGCAGGCG‑TGTTTATTTTTAAAAATAAGCGACCAAAGCAATGCATAAAAACGTGATGAAAACTGCACCGATAATAGCCAGCACACAGAAGAAAAGGTGAACCTGTTTGTTCTCTTTTACGCGCATTTCTAATatc > 2:57764/1‑137 (MQ=255)
agcagGCG‑TTTTTATTTTGAAAAAGAAGCGACCAATGCAATGCATAAAACCGTGATGAACACTGAACCGATAATAGCCAGCACACTGAAGAAAAGGTGAACCTGTTTGTTCTCTTTTCCGCGCTTTTCTAATAGCCGtt < 7:278138/139‑1 (MQ=255)
cagGCG‑TGTTTATTTTTAAAAAGAATCGACCAATGCAATGCATAAAACCGTGATGAACACTGAACCGATAATAGCCAGCACACTGCAGAAAAGGTGAACCGGTTTGTTCTCTTTTGCGCGCTTTTCTAATATCCGTTTa > 4:274029/1‑139 (MQ=255)
g‑TTTTTATTTTTAAAAACAAGCGCCCAAAGCAATGCATAAAAACGTGATGAACACGGAAACGATAATATCCAGCACACTGAAGAAAAGGTGTACCTGTTTGTTCTCTTTTAACCGCGTTTGTAATAGGCGTTTAGaaa > 3:348698/1‑138 (MQ=255)
tGAAAAAGAAGCGACCAAAGCAATGCATAAAACCGTGATGAACACTGAACCGATAATAGCCAGCACACTGAAGAAAAGGTGAACCTGTTTGTTCTCTTTTC‑‑CGCTTTTCTAATAGCCGTTTAGAAAAAATGTGCGaaa < 7:254620/138‑1 (MQ=255)
gAAAAAGAAGCGACCAATGCAATGCATAAAACCGTGATGAACACTGAACCGATAATAGCCAGCACACTGAAGAAAAGGTGAACCTGTTTGTTCTCTTTTCCGCGCTTTTCTAATAGCCGTTTAGAAAAAATGTGCGaa < 5:26902/138‑1 (MQ=255)
|
CCGAAACGGGCTGGGACTGATCGCGGAAGATCGAATTGTCGGCACATCGAAGTTTGTCTTTTTCCCGT‑TTAACGAAATGCGTCAAACAAAATAAAAACGCCTTGCTGGCCTAGGACAGCAGGCG‑TTTTTATTTTGAAAAAGAAGCGACCAATGCAATGCATAAAACCGTGATGAACACTGAACCGATAATAGCCAGCACACTGAAGAAAAGGTGAACCTGTTTGTTCTCTTTTCCGCGCTTTTCTAATAGCCGTTTAGAAAAAATGTGCGAAA > CP006881/1474834‑1475106
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
