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 |
|
A6 F1 I2 R1
|
67 |
27.9 |
1239648 |
95.3% |
1181384 |
112.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
2,313,622 |
G→A |
W45* (TGG→TGA) |
rcsD → |
phosphotransfer intermediate protein in two‑component regulatory system with RcsBC |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 2,313,622 | 0 | G | A | 81.1%
| 72.1
/ 13.5
| 37 | W45* (TGG→TGA) | rcsD | phosphotransfer intermediate protein in two‑component regulatory system with RcsBC |
| Reads supporting (aligned to +/- strand): ref base G (3/4); new base A (16/14); total (19/18) |
| Fisher's exact test for biased strand distribution p-value = 6.93e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.93e-01 |
AATGCGTCAGAAAGAGACAACGGCCACGACCCGCTTTTCACTCCTACCGGGGAGCATTACCCGCTTCTTTTTACTGTTGATCATTGTGTTACTGGTGACGATGGGTGTAATGGTACAAAGCGCCGTTAACGCCTGGCTGAAAGATAAAAGTTACCAGATTGTCGACATTACCCATGCTATCCAAAAGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCTCCCCCTCCTCCGGCGA > NC_000913/2313487‑2313750
|
aaTGCGTCAGAAAGAGACAACGGCCACGACCCGCTTTTCACTCCTACCGGGGAGCATTACCCGCTTCTTTTTACTGTTGATCATTGTGTTACTGGTGACGATGGGTGTAATGGTACAAAGCGCCGTTAACGCCTGACTg < 2:337094/139‑1 (MQ=255)
aTGCGTCAGAAAGAGACAACGGCCACGACCCGCTTTTCACTCCTACCGGGGAGCATTACCCGCTTCTTTTTACTGTTGATCATTGTGTTACTGGTGACGATGGGTGTAATGGTACAAAGCGCCGTTAACGCctgactga > 2:120469/1‑139 (MQ=255)
gTCAGAAAGAGACAACGGCCACGACCCGCTTTTCACTCCTACCGGGGAGCATTACCCGCTTCTTTTTACTGTTGATCATTGTGTTACTGGTGACGATGGGTGTAATGGTACAAAGCGCCGTTAACGCCTGGCTGAAAGa > 1:6604/1‑139 (MQ=255)
aCGGCCACGACCCGCTTTTCACTCCTACCGGGGAGCATTACCCGCTTCTTTTTACTGTTGATCATTGTGTTACTGGTGACGATGGGTGTAATGGTACAAAGCGCCGTTAACGCCTGACTGAAAGATAAAAGTTACCAGa > 2:44619/1‑139 (MQ=255)
cGGCCACGACCCGCTTTTCACTCCTACCGGGGAGCATTACCCGCTTCTTTTTACTGTTGATCATTGTGTTACTGGTGACGATGGGTGTAATGGTACAAAGCGCCGTTAACGCCTGGCTGAAAGATAAAAGTTACCAGAt < 2:341625/139‑1 (MQ=255)
gCCACGAACCGCTTTTCACTCCTACCGGGGAGCATTACCCGCTTCTTTTTACTTTTGATCATTGTGTTACTGGTGACGATGGGTGTAATGGTACAAAGCGCCGTTAACGCCTGGCTGAAAGATAAAAGTTACCAGATTg < 1:603991/139‑1 (MQ=255)
tttCACTCCTACCGGGGAGCATTACCCGCTTCTTTTTACTGTTGATCATTGTGTTACTGGTGACGATGGGTGTAATGGTACAAAGCGCCGTTAACGCCTGACTGAAAGATAAAAGTTACCAGATTGTCGACATTACCCa < 1:120469/139‑1 (MQ=255)
tCACTCCTACCGGGGAGCATTACCCGCTTCTTTTTACTGTTGATCATTGTGTTACTGGTGACGATGGGTGTAATGGTACAAAGCGCCGTTAACGCCTGACTGAAAGATAAAAGTTACCAGATTGTCGACATTACCCATg < 1:44619/139‑1 (MQ=255)
tACCGGGGAGCATTACCCGCTTCTTTTTACTGTTGATCATTGTGTTACTGGTGACGATGGGTGTAATGGTACAAAGCGCCGTTAACGCCTGACTGAAAGATAAAAGTTACCAGATTGTCGACATTACCCATGCTATCCa > 1:350098/1‑139 (MQ=255)
gCATTACCCGCTTCTTTTTACTGTTGATCATTGTGTTACTGGTGACGATGGGTGTAATGGTACAAAGCGCCGTTAACGCCTGACTGAAAGATAAAAGTTACCAGa < 2:82702/105‑1 (MQ=255)
gCATTACCCGCTTCTTTTTACTGTTGATCATTGTGTTACTGGTGACGATGGGTGTAATGGTACAAAGCGCCGTTAACGCCTGACTGAAAGATAAAAGTTACCAGa > 1:82702/1‑105 (MQ=255)
ttACTGTTGATCATTGTGTTACTGGTGACGATGGGTGTAATGGTACAAAGCGCCGTTAACGCCTGACTGAAAGATAAAAGTTACCAGATTGTCGACATTACCCATGCTATCCAAAAGCGCGTCGATAACTGGCGTTACg < 1:385593/139‑1 (MQ=255)
ttGATCATTGTGTTACTGGTGACGATGGGTGTAATGGTACAAAGCGCCGTTAACGCCTGACTGAAAGATAAAAGTTACCAGATTGTCGACATTAc < 2:588936/95‑1 (MQ=255)
ttGATCATTGTGTTACTGGTGACGATGGGTGTAATGGTACAAAGCGCCGTTAACGCCTGACTGAAAGATAAAAGTTACCAGATTGTCGACATTAc > 1:588936/1‑95 (MQ=255)
ttGATCATTGTGTTACTGGTGACGATGGGTGTAATGGTACAAAGCGCCGTTAACGCCTGACTGAAAGATAAAAGTTACCAGATTGTCGACATTACCCATGCTATCCAAAAGCGCGTCGATAACTGGCGTTACGTGACCt > 1:221689/1‑139 (MQ=255)
ttGATCATTGTGTTACTGGTGACGATGGGTGTAATGGTACAAAGCGCCGTTAACGCCTGACTGAAAGATAAAAGTTACCAGATTGTCGACATTACCCATGCTATCCAAAAGCGCGTCGATAACTGGCGTTACGTGACCt > 2:224856/1‑139 (MQ=255)
tgtTACTGGTGACGATGGGTGTAATGGTACAAAGCGCCGTTAACGCCTGACTGAAAGATAAAAGTTACCAGCTTGTCGACATTAc > 2:514528/1‑85 (MQ=255)
tgtTACTGGTGACGATGGGTGTAATGGTACAAAGCGCCGTTAACGCCTGACTGAAAGATAAAAGTTACCAGATTGTCGACATTAc < 1:514528/85‑1 (MQ=255)
tgtTACTGGTGACGATGGGTGTAATGGTACAAAGCGCCGTTAACGCCTGACTGAAAGATAAAAGTTACCAGATTGTCGACATTACCCATGCTATCCAAAAGCGCGTCGATAACTGGCGTTACGTGAc > 1:510286/1‑127 (MQ=255)
tgtTACTGGTGACGATGGGTGTAATGGTACAAAGCGCCGTTAACGCCTGACTGAAAGATAAAAGTTACCAGATTGTCGACATTACCCATGCTATCCAAAAGCGCGTCGATAACTGGCGTTACGTGAc < 2:510286/127‑1 (MQ=255)
gtTACTGGTGACGATGGGTGTAATGGTACAAAGCGCCGTTAACGCCTGACTGAAAGATAAAAGTTACCAGATTGTCGACATTACCCATGCTATCCAAAAGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTAc < 1:239414/139‑1 (MQ=255)
cTGGTGACGATGGGTGTAATGGTACAAAGCGCCGTTAACGCCTGACTGAAAGATAAAAGTTACCAGATTGTCGACATTACCCATGCTATCCAAAAGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGaca > 2:241486/1‑139 (MQ=255)
gTGACGATGGGTGTAATGGTACAAAGCGCCGTTAACGCCTGACTGAAAGATa < 2:64744/52‑1 (MQ=255)
gTGACGATGGGTGTAATGGTACAAAGCGCCGTTAACGCCTGACTGAAAGATa > 1:64744/1‑52 (MQ=255)
gTGACGATGGGTGTAATGGTACAAAGCGCCGTTAACGCCTGACTGAAAGATAAAAGTTACCAGATTGTCGACATTACCCATGCTATCCAAAAGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGa < 1:535654/127‑1 (MQ=255)
gTGACGATGGGTGTAATGGTACAAAGCGCCGTTAACGCCTGACTGAAAGATAAAAGTTACCAGATTGTCGACATTACCCATGCTATCCAAAAGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGa > 2:535654/1‑127 (MQ=255)
aCGATGGGTGTAATGGTACAAAGCGCCGTTAACGCCTGACTGAAAGATAAAAGTTACCAGATTGTCGAc > 1:333036/1‑69 (MQ=255)
aCGATGGGTGTAATGGTACAAAGCGCCGTTAACGCCTGACTGAAAGATAAAAGTTACCAGATTGTCGAc < 2:333036/69‑1 (MQ=255)
cGATGGGTGTAATGGTACAAAGCGCCGTTAACGCCTGGCTGAAAGATAAAAGTTACCAGATTGTCGACATTACCCATGCTATCCAAAAGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATc < 2:500342/125‑1 (MQ=255)
cGATGGGTGTAATGGTACAAAGCGCCGTTAACGCCTGGCTGAAAGATAAAAGTTACCAGATTGTCGACATTACCCATGCTATCCAAAAGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATc > 1:500342/1‑125 (MQ=255)
cAAAGCGCCGTTAACGCCTGACTGAAAGATAAAAGTTACCAGATTGt > 2:607252/1‑47 (MQ=255)
cAAAGCGCCGTTAACGCCTGACTGAAAGATAAAAGTTACCAGATTGt < 1:607252/47‑1 (MQ=255)
cAAAGCGCCGTTAACGCCTGACTGAAAGATAAAAGTTACCAGATTGTCGACATTACCCATGCTATCCAAAAGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGacaa < 2:244614/116‑1 (MQ=255)
cAAAGCGCCGTTAACGCCTGACTGAAAGATAAAAGTTACCAGATTGTCGACATTACCCATGCTATCCAAAAGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGacaa > 1:244614/1‑116 (MQ=255)
cgcCGTTAACGCCTGACTGAAAGATAAAAGTTACCAGATTGTCGACATTACCCATGCTATCCAAAAGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCTCCCCCtcctcc > 2:53597/1‑139 (MQ=255)
ccGTTAACGCCTGGCTGAAAGATAAAAGTTACCAGATTGTCGACATTACCCATGCTATCCAAAAGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCTCCCCCTCCTCCgg > 2:159924/1‑139 (MQ=255)
cGTTAACGCCTGACTGAAAGATAAAAGTTACCAGATTGTCGACATTACCCATGCTATCCAAAAGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCTCCCCCTCCTCCGGc > 2:397853/1‑139 (MQ=255)
ttAACGCCTGGCTGAAAGATAAAAGTTACCAGATTGTCGACATTACCCATGCTATCCAAAAGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCTCCCCCTCCTCCGGCGa < 2:6604/139‑1 (MQ=255)
|
AATGCGTCAGAAAGAGACAACGGCCACGACCCGCTTTTCACTCCTACCGGGGAGCATTACCCGCTTCTTTTTACTGTTGATCATTGTGTTACTGGTGACGATGGGTGTAATGGTACAAAGCGCCGTTAACGCCTGGCTGAAAGATAAAAGTTACCAGATTGTCGACATTACCCATGCTATCCAAAAGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCTCCCCCTCCTCCGGCGA > NC_000913/2313487‑2313750
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
