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 F1 I2 R1
|
766 |
55.6 |
2631458 |
94.7% |
2491990 |
109.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
1,421,650 |
(C)7→8 |
coding (532/858 nt) |
ydaU → |
Rac prophage, conserved protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 1,421,643 | 1 | . | C | 91.8%
| 161.6
/ 6.0
| 49 | coding (525/858 nt) | ydaU | Rac prophage, conserved protein |
| Reads supporting (aligned to +/- strand): ref base . (1/3); new base C (25/20); total (26/23) |
| Fisher's exact test for biased strand distribution p-value = 3.30e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.96e-01 |
CAGATGTTCAAACAAAACAAGAGAGAAATTTAACAGGTGTTCAAACAGATGTTGAAGTGGTGTTTGAACATGATGTCAACACAAAGGCAACTAATAAAGATACAGATAAAGATCTAAAAACAGATCCCCCCCTAAAT‑‑CCCCCCCGGGGGAATCGAGGTGTCAAAAAGTTTGACCCTCTGGATATTACTTTGCCGAACTGGATTTCTGTCTCGCTTTGGCGTGAGTGGGTTGAATTTCGCCAGGCATTGCGAAAACCGATTCGAA > NC_000913/1421507‑1421770
|
cAGATGTTCAAACAAAACAAGAGAGAAATTTAACAGGTGTTCAAACAGATGTTGAAGTGGTGTTTGAACATGATGTCAACACAAAGGCAACTAATAAAGATACAGATAAAGATCTAAAAACAGATCCCCCCCTAAAT‑‑cc < 2:774026/139‑1 (MQ=255)
gATGTTCAAACAAAACAAGAGAGAAATTTAACAGGTGTTCAAACAGATGTTGAAGTGGTGTTTGAACATGATGTCAACACAAAGGCAACTAATAAAGATACAGATAAAGATCTAAAAACAGATCCCCCCCTAAAT‑‑cccc > 1:854596/1‑139 (MQ=255)
tGTTCAAACAAAACAAGAGAGAAATTTAACAGGTGTTCAAACAGATGTTGAAGTGGTGTTTGAACATGATGTCAACACAAAGGCAACTAATAAAGATACAGATAAAGATCTAAAAACAGATCCCCCCCTAAAT‑‑cccccc < 1:528129/139‑1 (MQ=255)
caaacaaaACAAGAGAGAAATTTAACAGGTGTTCAAACAGATGTTGAAGTGGTGTTTGAACATGATGTCAACACAAAGGCAACTAATAAAGATACAGATAAAGATCTAAAAACAGATCCCCCCCTAAAT‑‑ccccccccgg < 1:1206437/139‑4 (MQ=255)
caaacaaaACAAGAGAGAAATTTAACAGGTGTTCAAACAGATGTTGAAGTGGTGTTTGAACATGATGTCAACACAAAGGCAACTAATAAAGATACAGATAAAGATCTAAAAACAGATCCCCCCCTAAAT‑‑CCCCCCCcgg < 1:203101/139‑1 (MQ=255)
aacaaaacaaGAGAGAAATTTAACAGGTGTTCAAACAGATGTTGAAGTGGTGTTTGAACATGATGTCAACACAAAGGCAACTAATAAAGATACAGATAAAGATCTAAAAACAGATCCCCCCCTAAAT‑‑CCCCCCCcgggg < 2:854596/139‑1 (MQ=255)
acaaGAGAGAAATTTAACAGGTGTTCAAACAGATGTTGAAGTGGTGTTTGAACATGATGTCAACACAAAGGCAACTAATAAAGATACAGATAAAGATCTAAAAACAGATCCCCCCCTAAATC‑CCCCCCCGGGGGAATCg < 1:1278493/139‑1 (MQ=255)
gtTCAAACAGATGTTGAAGTGGTGTTTGAACATGATGTCAACACAAAGGCAACTAATAAAGATACAGATAAAGATCTAAAAACAGATCCCCCCCTAAATC‑CCCCCCCGGGGGAATCGAGGTGTCAAAAAGTTTGACCct < 2:924875/139‑1 (MQ=255)
gtTCAAACAGATGTTGAAGTGGTGTTTGAACATGATGTCAACACAAAGGCAACTAATAAAGATACAGATAAAGATCTAAAAACAGATCCCCCCCTAAATC‑CCCCCCCGGGGGAATCGAGGTGTCAAAAAGTTTGACCct < 1:66199/139‑1 (MQ=255)
ttCAAACAGATGTTGAAGTGGTGTTTGAACATGATGTCAACACAAAGGCAACTAATAAAGATACAGATAAAGATCTAAAAACAGATCCCCCCCTAAAt > 2:721613/1‑98 (MQ=255)
ttCAAACAGATGTTGAAGTGGTGTTTGAACATGATGTCAACACAAAGGCAACTAATAAAGATACAGATAAAGATCTAAAAACAGATCCCCCCCTAAAt < 1:721613/98‑1 (MQ=255)
aaGTGGTGTTTGAACATGATGTCAACACAAAGGCAACTAATAAAGATACAGATAAAGATCTAAAAACAGATCCCCCCCTAAATC‑CCCCCCCGGGGGAATCg > 2:62923/1‑101 (MQ=255)
aaGTGGTGTTTGAACATGATGTCAACACAAAGGCAACTAATAAAGATACAGATAAAGATCTAAAAACAGATCCCCCCCTAAATC‑CCCCCCCGGGGGAATCg < 1:62923/101‑1 (MQ=255)
ggtgTTTGAACATGATGTCAACACAAAGGCAACTAATAAAGATACAGATAAAGATCTAAAAACAGATCCCCCCCTAAATC‑CCCCCCCGGGGGAATCGAGGTGTCAAAAAGTTTg < 1:1021876/114‑1 (MQ=255)
ggtgTTTGAACATGATGTCAACACAAAGGCAACTAATAAAGATACAGATAAAGATCTAAAAACAGATCCCCCCCTAAATC‑CCCCCCCGGGGGAATCGAGGTGTCAAAAAGTTTg > 2:1021876/1‑114 (MQ=255)
ggtgTTTGAACATGATGTCAACACAAAGGCAACTAATAAAGATACAGATAAAGATCTAAAAACAGATCCCCCCCTAAATC‑CCCCCCCGGGGGAATCGAGGTGTCAAAAAGTTTGACCCTCTGGATATTACTTTGCCGaa > 2:1077024/1‑139 (MQ=255)
gtgtTTGAACATGATGTCAACACAAAGGCAACTAATAAAGATACAGATAAAGATCTAAAAACAGATCCCCCCCTAAATC‑CCCCCCCGGGGGAATCGAGGTGTCAAAAAGTTTg < 1:563024/113‑1 (MQ=255)
gtgtTTGAACATGATGTCAACACAAAGGCAACTAATAAAGATACAGATAAAGATCTAAAAACAGATCCCCCCCTAAATC‑CCCCCCCGGGGGAATCGAGGTGTCAAAAAGTTTg > 2:563024/1‑113 (MQ=255)
gtgtTTGAACATGATGTCAACACAAAGGCAACTAATAAAGATACAGATAAAGATCTAAAAACAGATCCCCCCCTAAATC‑CCCCCCCGGGGGAATCGAGGTGTCAAAAAGTTTg < 1:395324/113‑1 (MQ=255)
gtgtTTGAACATGATGTCAACACAAAGGCAACTAATAAAGATACAGATAAAGATCTAAAAACAGATCCCCCCCTAAATC‑CCCCCCCGGGGGAATCGAGGTGTCAAAAAGTTTg > 2:395324/1‑113 (MQ=255)
tgatgTCAACACAAAGGCAACTAATAAAGATACAGATAAAGATCTAAAAACAGATCCCCCCCTAAATC‑CCCCCCCGGGGGAATCGAGGTGTCAAAAAGTTTGACCct < 1:164208/107‑1 (MQ=255)
tgatgTCAACACAAAGGCAACTAATAAAGATACAGATAAAGATCTAAAAACAGATCCCCCCCTAAATC‑CCCCCCCGGGGGAATCGAGGTGTCAAAAAGTTTGACCct > 2:164208/1‑107 (MQ=255)
tgatgTCAACACAAAGGCAACTAATAAAGATACAGATAAAGATCTAAAAACAGATCCCCCCCTAAATC‑CCCCCCCGGGGGAAACGAAGTGTCAAAAAGTTTGACCCTCTGGATATTACCTTGCCGTACCGGAGTTCTGt > 1:1044389/1‑139 (MQ=255)
cAACACAAAGGCAACTAATAAAGATACAGATAAAGATCTAAAAACAGATCCCCCCCTAAAT‑‑CCCCCCCGGGGGAATCGAg < 2:77173/80‑1 (MQ=255)
cAACACAAAGGCAACTAATAAAGATACAGATAAAGATCTAAAAACAGATCCCCCCCTAAAT‑‑CCCCCCCGGGGGAATCGAg > 1:77173/1‑80 (MQ=255)
aGGCAACTAATAAAGATACAGATAAAGATCTAAAAACAGATCCCCCCCTAAATC‑CCCCCCCGGGGGAATCGAGGTTTCAAAAAGTTTGACCCTCTGGATATTACTTTGCCGAACTGGATTTCTGTCTCGCTTTGGCg > 2:809429/1‑137 (MQ=255)
aGGCAACTAATAAAGATACAGATAAAGATCTAAAAACAGATCCCCCCCTAAATC‑CCCCCCCGGGGGAATCGAGGTGTCAAAAAGTTTGACCCTCTGGATATTACTTTGCCGAACTGGATTTCTGTCTCGCTTTGGCg < 1:809429/137‑1 (MQ=255)
aCTAATAAAGATACAGATAAAGATCTAAAAACAGATCCCCCCCTAAATC‑CCCCCCCGGGGGAATCGAGGTGTCAAAAAGTTTGAACCTCTGGATATTACTTTGCCGAACCGGATTTCTGTCTCGCTTTGGCggtggtgg > 2:19425/1‑132 (MQ=255)
taaAGATACAGATAAAGATCTAAAAACAGATCCCCCCCTAAATC‑CCCCCCCGGGGGAATCGAGGTGTCAAAAAGTTTGACCCTCTGGATATTACTTTGCCGAACTGGATTTCTGTCTCGCTTTGGCGTGAGTGGGTTGa > 1:546057/1‑139 (MQ=255)
cAGGTAAAGATCTAAAAACAGATCCCCCCCTAAATC‑CCCCCCCGGGGGAATCGAGGTGTCAAAAAGTTTGACCCTCTGGATATTACTTTGCCGAACTGGATTTCTGTCTCGCt > 1:894291/1‑113 (MQ=255)
cAGATAAAGATCTAAAAACAGATCCCCCCCTAAATC‑CCCCCCCGGGGGAATCGAGGTGTCAAAAAGTTTGACCCTCTGGATATTACTTTGCCGAACTGGATTTCTGTCTCGCt < 2:894291/113‑1 (MQ=255)
aGATAAAGATCTAAAAACAGATCCCCCCCTAAATC‑CCCCCCCGGGGGAATCGAGGTGTCAAAAAGTTTGACCCTCTGGATATTACTTTGCCGAACTGGATTTCTGTCTCGCTTTGGCGTGAGTGGGTTGAATTTCGCCa > 1:979991/1‑139 (MQ=255)
aGATAAAGATCTAAAAACAGATCCCCCCCTAAATC‑CCCCCCCGGGGGAATCGAGGTGTCAAAAAGTTTGACCCTCTGGATATTACTTTGCCGAACTGGATTTCTGTCTCGCTTTGGCGTGAGTGGGTTGAATTTCGCCa > 1:1165038/1‑139 (MQ=255)
aTAAAGATCTAAAAACAGATCCCCCCCTAAATC‑CCCCCCCGGGGGAATCGAGGTGTCAAAAAGTTTGACCctc < 1:259118/73‑1 (MQ=255)
aTAAAGATCTAAAAACAGATCCCCCCCTAAATC‑CCCCCCCGGGGGAATCGAGGTGTCAAAAAGTTTGACCctc > 2:259118/1‑73 (MQ=255)
aGATCTAAAAACAGATCCCCCCCTAAATC‑CCCCCCCGGGGGAATCGAGGTGTCAAAAAGTTTg < 1:505601/63‑1 (MQ=255)
aGATCTAAAAACAGATCCCCCCCTAAATC‑CCCCCCCGGGGGAATCGAGGTGTCAAAAAGTTTg > 2:505601/1‑63 (MQ=255)
cTAAAAACAGATCCCCCCCTAAATC‑CCCCCCCGGGGGAATCGAGGTGTCAAAAAGTTTGACCctct > 1:757911/1‑66 (MQ=255)
cTAAAAACAGATCCCCCCCTAAATC‑CCCCCCCGGGGGAATCGAGGTGTCAAAAAGTTTGACCctct < 2:757911/66‑1 (MQ=255)
aaaaaCAGATCCCCCCCTAAATC‑CCCCCCCGGGGGAATCGAGGTGTCAAAAAGTTTGACCCTCTGGa < 1:1093466/67‑1 (MQ=255)
aaaaaCAGATCCCCCCCTAAATC‑CCCCCCCGGGGGAATCGAGGTGTCAAAAAGTTTGACCCTCTGGa > 2:1093466/1‑67 (MQ=255)
aaaaaCAGATCCCCCCCTAAATC‑CCCCCCCGGGGGAATCGAGGTGTCAAAAAGTTTGACCCTCTGGATATTACTTTGCCGAACTGGATTTCTGTCTCGCTTTGGCGTGAGTGGGt < 2:587053/115‑1 (MQ=255)
aaaaaCAGATCCCCCCCTAAATC‑CCCCCCCGGGGGAATCGAGGTGTCAAAAAGTTTGACCCTCTGGATATTACTTTGCCGAACTGGATTTCTGTCTCGCTTTGGCGTGAGTGGGt > 1:587053/1‑115 (MQ=255)
gATCCCCCCCTAAATCCCCCCCCCGGGGGAATCGAGGTGTCAAAAAGTTTGACCct > 2:1119031/1‑56 (MQ=255)
gATCCCCCCCTAAATCCCCCCCCCGGGGGAATCGAGGTGTCAAAAAGTTTGACCct < 1:1119031/56‑1 (MQ=255)
aTCCCCCCCTAAATC‑CCCCCCCGGGGGAATCGAGGTGTCAAAAAGTTTGACCct < 2:187789/54‑1 (MQ=255)
aTCCCCCCCTAAATC‑CCCCCCCGGGGGAATCGAGGTGTCAAAAAGTTTGACCct > 1:187789/1‑54 (MQ=255)
aTCCCCCCCTAAATC‑CCCCCCCGGGGGAATCGAGGTGTCAAAAAGTTTGACCCTCTGGATATTACTTTGCCGAACTGGATTTCTGTCTCGCTTTGGc < 2:1129593/97‑1 (MQ=255)
aTCCCCCCCTAAATC‑CCCCCCCGGGGGAATCGAGGTGTCAAAAAGTTTGACCCTCTGGATATTACTTTGCCGAACTGGATTTCTGTCTCGCTTTGGc > 1:1129593/1‑97 (MQ=255)
aTCCCCCCCTAAATC‑CCCCCCCGGGGGAATCGAGGTGTCAAAAAGTTTGACCCTCTGGATATTACTTTGCCGAACTGGATTTCTGTCTCGCTTTGGCGTGAGTGGGTTGAATTTCGCCAGGCATTGCGAAAACCGAt < 2:1263719/137‑1 (MQ=255)
aTCCCCCCCTAAATC‑CCCCCCCGGGGGAATCGAGGTGTCAAAAAGTTTGACCCTCTGGATATTACTTTGCCGAACTGGATTTCTGTCTCGCTTTGGCGTGAGTGGGTTGAATTTCGCCAGGCATTGCGAAAACCGAt > 1:1263719/1‑137 (MQ=255)
aTCCCCCCCTAAATC‑CCCCCCCGGGGGAATCGAGGTGTCAAAAAGTTTGACCCTCTGGATATTACTTTGCCGAACTGGATTTCTGTCTCGCTTTGGCGTGAGTGGGTTGAATTTCGCCAGGCATTGCGAAAACCGATTc > 1:964373/1‑139 (MQ=255)
aTCCCCCCCTAAATC‑CCCCCCCGGGGGAATCGAGGTGTCAAAAAGTTTGACCCTCTGGATATTACTTTGCCGAACTGGATTTCTGTCTCGCTTTGGCGTGAGTGGGTTGAATTTCGCCAGGCATTGCGAAAACCGATTc > 2:1188228/1‑139 (MQ=255)
aTCCCCCCCTAAATC‑CCCCCCCGGGGGAATCGAGGTGTCAAAAAGTTTGACCCTCTGGATATTACTTTGCCGAACTGGATTTCTGTCTCGCTTTGGCGTGAGTGGGTTGAATTTCGCCAGGCATTGCGAAAACCGATTc > 1:66804/1‑139 (MQ=255)
ccccccTAAATC‑CCCCCCCGGGGGAATCGAGGTGTCAAAAAGTTTGACCCTCTGGATATTACTTTGCCGAACTGGATTTCTGTCTCGCTTTGGCGTGAGTGGGTTGAATTTCGCCAGGCATTGCGAAAACCGATTCGaa < 1:1077024/139‑1 (MQ=255)
|
CAGATGTTCAAACAAAACAAGAGAGAAATTTAACAGGTGTTCAAACAGATGTTGAAGTGGTGTTTGAACATGATGTCAACACAAAGGCAACTAATAAAGATACAGATAAAGATCTAAAAACAGATCCCCCCCTAAAT‑‑CCCCCCCGGGGGAATCGAGGTGTCAAAAAGTTTGACCCTCTGGATATTACTTTGCCGAACTGGATTTCTGTCTCGCTTTGGCGTGAGTGGGTTGAATTTCGCCAGGCATTGCGAAAACCGATTCGAA > NC_000913/1421507‑1421770
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
