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 F2 I75 R1
|
71 |
32.8 |
2150506 |
93.3% |
2006422 |
83.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
3,758,726 |
G→C |
A1062P (GCC→CCC) |
rhsA → |
RHS element protein RhsA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,758,726 | 0 | G | C | 97.5%
| 113.9
/ ‑3.8
| 40 | A1062P (GCC→CCC) | rhsA | RHS element protein RhsA |
| Reads supporting (aligned to +/- strand): ref base G (1/0); new base C (25/14); total (26/14) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.93e-01 |
CGGCTGACCACAATACAGAACGACAGAACCCGCATCCAGACGATTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCGCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATGCGCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGT > NZ_CP009273/3758639‑3758806
|
cGGCTGACCACAATACAGAACGACAGAACCCGCATCCAGACGATTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACcccc < 1:308424/90‑1 (MQ=255)
ccACAATACAGAACGACAGAACCCGCATCCAGACGATTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTg < 2:1026360/90‑1 (MQ=255)
cAGAACGACAGAACCCGCATCCAGACGATTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCg > 2:776029/1‑90 (MQ=18)
gAACGACAGAACCCGCATCCAGACGATTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGaa > 1:1009097/1‑90 (MQ=18)
gAACGACAGAACCCGCATCCAGACGATTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGaa > 1:859031/1‑90 (MQ=18)
gAACGACAGAACCCGCATCCAGACGATTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGaa > 1:60039/1‑90 (MQ=18)
gAACGACAGAACCCGCATCCAGACGATTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACAGGTGAGCTGGCGaa < 2:529135/90‑1 (MQ=255)
cGACAGAACCCGCATCCAGACGATTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAAc < 2:961929/90‑1 (MQ=18)
cGACAGAACCCGCATCCAGACGATTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAAc > 1:786075/1‑90 (MQ=18)
cGACAGAACCCGCATCCAGACGATTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAAc > 1:512848/1‑90 (MQ=18)
aCAGAACCCGCATCCAGACGATTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGc > 1:47424/1‑90 (MQ=18)
aCAGAACCCGCATCCAGACGATTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGc > 2:794712/1‑90 (MQ=18)
aCAGAACCCGCATCCAGACGATTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGc > 1:971309/1‑90 (MQ=18)
aCAGAACCCGCATCCAGACGATTTATCAGCCGAGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGc < 1:31796/90‑1 (MQ=11)
aCCCGCATCCAGACGATTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTTGCGAAAACGCAgcgc > 1:604227/1‑90 (MQ=255)
ccGCATCCAGACGATTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGcgccg < 2:197110/90‑1 (MQ=18)
cGCATCCAGACGATTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGcgccgc < 1:271427/90‑1 (MQ=18)
gCATCCAGACGATTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCa > 1:24585/1‑90 (MQ=18)
cATCCAGACGATTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGAGCCGCAg > 2:579002/1‑90 (MQ=255)
ccAGACGATTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCt > 1:548153/1‑90 (MQ=18)
aTTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGAt > 1:731512/1‑90 (MQ=25)
ttATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGTCGAAAACGCAGCGCCGCAGCCTGGCGGATgc > 1:706622/1‑90 (MQ=255)
ttATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATgc < 1:601744/90‑1 (MQ=37)
gCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATGCGCTTca > 1:866062/1‑90 (MQ=255)
cGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGAt < 2:1072276/80‑1 (MQ=21)
cGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGAt > 1:1072276/1‑80 (MQ=19)
ggAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATGCGCTTCAGCAGt > 1:902948/1‑90 (MQ=255)
cTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATGCGCTTCAGCAGTCcgg < 2:937132/90‑1 (MQ=255)
ttCACGCCACTCATCAGAGTTGAAACCGCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATGCGCTTCAGCAGTCcggc > 1:787888/1‑90 (MQ=255)
tCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGAGCCGCAGCCTGGCGGATGCGCTTCAGCAGTCcggcg < 1:579002/90‑1 (MQ=255)
cGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATGCGCTTCAGCAGTCCGgcggcg > 1:359207/1‑90 (MQ=255)
catcaGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATGCGCTTCAGCAGTCCGGCGGCGAAGACgg > 1:627754/1‑90 (MQ=255)
atcaGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATGCGCTTCAGCAGTCCGGCGGCGAAGACGGt < 2:24585/90‑1 (MQ=255)
atcaGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATGCGCTTCAGCAGTCCGGCGGCGAAGACGGt < 2:786075/90‑1 (MQ=255)
atcaGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATGCGCTTCAGCAGTCCGGCGGCGAAGACGGt < 2:512848/90‑1 (MQ=255)
gagTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATGCGCTTCAGCAGTCCGGCGGCGAAGACGGTGGCa > 1:422544/1‑90 (MQ=255)
gTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATGCGCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAgt > 2:785709/1‑90 (MQ=255)
gTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATGCGCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAgt > 1:940975/1‑90 (MQ=255)
gTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATGCGCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAgc > 2:808618/1‑89 (MQ=255)
gAAACCCCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATGCGCTTCAGCAGTCCGGCGGCGa > 2:1008705/1‑74 (MQ=255)
gAAACCCCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATGCGCTTCAGCAGTCCGGCGGCGa < 1:1008705/74‑1 (MQ=255)
|
CGGCTGACCACAATACAGAACGACAGAACCCGCATCCAGACGATTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCGCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATGCGCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGT > NZ_CP009273/3758639‑3758806
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CGGATCGCACGCTTTCGGGATTGGACACGGAAACTCACGCTGCAAATCCGCTACCAACTGGTGCCACTCTGCACGCGGTTGCGCTTCCACCAGCGGGATCAACTGCGCCAGCACGTCATCAACATCCGCCTGAATCGCCACGTGCGGCTGCTTGATTTTACCCAGCTCTGCACGGTCGATATCGACATGAATGATTT > NZ_CP009273/3845044‑3845240
|
CGGATCGCACGCTTTCGGGATTGGACACGGAAACTCACGCTGCAAATCCGCTACCAACTGGTGCCACTCTGCACGCGGTTGCGCTTCCACCAGCGGGGTC > SRR3722213.1023375/1‑100 (MQ=60)
CTTTCGGGATTGGACACGGAAACTCACGCTGCAAATCCGCTACCAACTGGTGCCACTCTGCACGCGGTTGCGCTTCCACCAGCGGGGTCAACTGCGCCAG < SRR3722213.442209/100‑1 (MQ=60)
TTCGGGATTGGACACGGAAACTCACGCTGCAAATCCGCTACCAACTGGTGCCACTCTGCACGCGGTTGCGCTTCCACCAGCGGGGTCAACTGCGCCAGCA < SRR3722213.671365/100‑1 (MQ=60)
agataataacgggtctcgtgggctcggagatgtgtataagagacaGGTGCCACTCTGCACGCGGTTGCGCTTCCACCAGCGGGGTCAACTGCGCCAGCAC < SRR3722213.624238/55‑1 (MQ=60)
GACACGGAAACTCACGCTGCAAATCCGCTACCAACTGGTGCCACTCTGCACGCGGTTGCGCTTCCACCAGCGGGGTCAACTGCGCCAGCACGTCATCAAC < SRR3722213.511053/100‑1 (MQ=60)
GACACGGAAACTCACGCTGCAAATCCGCTACCAACTGGTGCCACTCTGCACGCGGTTGCGCTTCCACCAGCGGGGTCAACTGAGCCAGCACGTCATCAAC < SRR3722213.3884/100‑1 (MQ=60)
CTGCAAATCCGCTACCAACTGGTGCCACTCTGCACGCGGTTGCGCTTCCACCAGCGGGGTCAACTGCGCCAGCACGTCATCAACATCCGCCTGAATCTCC > SRR3722213.320827/1‑100 (MQ=60)
ATCCGCTACCAACTGGTGCCACTCTGCACGCGGTTGCGCTTCCACCAGCGGGGTCAACTGCGCCAGCACGTCATCAACATCCGCCTGAATCGCCACGTGC > SRR3722213.205911/1‑100 (MQ=60)
GCTACCAACTGGTGCCACTCTGCACGCGGTTGCGCTTCCACCAGCGGGGTCAACTGCGCCAGCACGTCATCAACATCCGCCTGAATCGCCACGTGCGGCT > SRR3722213.996991/1‑100 (MQ=60)
CAACTGGTGCCACTCTGCACGCGGTTGCGCTTCCACCAGCGGGGTCAACTGCGCCAGCACGTCATCAACATCCGCCTGAATCGCCACGTGCGGCTGCTTG > SRR3722213.646930/1‑100 (MQ=60)
AACTGGTGCCACTCTGCACGCGGTTGCGCTTCCACCAGCGGGGTCAACTGCGCCAGCACGTCATCAACATCCGCCTGAATCGCCACGTGCGGCTGCTTGA > SRR3722213.706746/1‑100 (MQ=60)
CTGGTGCCACTCTGCACGCGGTTGCGCTTCCACCAGCGGGGTCAACTGCGCCAGCACGTCATCAACATCCGCCTGAATCGCCACGTGCGGCTGCTTGATT < SRR3722213.431594/100‑1 (MQ=60)
GTGCCACTCTGCACGCGGTTGCGCTTCCACCAGCGGGGTCAACTGCGCCAGCACGTCATCAACATCCGCCTGAATCGCCACGTGCGGCTGCTTGATTTTA > SRR3722213.44441/1‑100 (MQ=60)
GTGCCACTCTGCACGCGGTTGCGCTTCCACCAGCGGGGTCAACTGCGCCAGCACGTCATCAACATCCGCCTGAATCGCCACGTGCGGCTGCTTGATTTTA > SRR3722213.967948/1‑100 (MQ=60)
CCACTCTGCACGCGGTTGCGCTTCCACCATCGGGGTCAACTGCGCCAGCACGTCATCAACATCCGCCTGAATCGCCACGTGCGGCTGCTTGATTTTACCC < SRR3722213.447629/100‑1 (MQ=60)
ACTCTGCACGCGGTTGCGCTTCCACCAGCGGGGTCAACTGCGCCAGCACGTCATCAACATCCGCCTGAATCGCCACGTGCGGCTGCTTGATTTTACCCct > SRR3722213.664618/1‑98 (MQ=60)
CGCGGTTGCGCTTCCACCAGCGGGGTCAACTGCGCCAGCACGTCATCAACATCCGCCTGAATCGCCACGTGCGGATGCTTGATTTTACCCAGCTCTGCAC < SRR3722213.474207/100‑1 (MQ=60)
CACCAGCGGGGTCAACTGCGCCAGCACGTCATCAACATCCGCCTGAATCGCCACGTGCGGCTGCTTGATTTTACCCAGCTCTGCACGGTCGATATCGACA < SRR3722213.10071/100‑1 (MQ=60)
CACCAGCGGGGTCAACTGCGCCAGCACGTCATCAACATCCGCCTGAATCGCCACGTGCGGCTGCTTGATTTTACCCAGCTCTGCACGGTCGATATCGACA < SRR3722213.992497/100‑1 (MQ=60)
GTCAACTGCGCCAGCACGTCATCAACATCCGCCTGAATCGCCACGTGCGGCTGCTTGATTTTACCCAGCTCTGCACGGTCGATATCGACATGAATGATTT < SRR3722213.513300/100‑1 (MQ=60)
|
CGGATCGCACGCTTTCGGGATTGGACACGGAAACTCACGCTGCAAATCCGCTACCAACTGGTGCCACTCTGCACGCGGTTGCGCTTCCACCAGCGGGATCAACTGCGCCAGCACGTCATCAACATCCGCCTGAATCGCCACGTGCGGCTGCTTGATTTTACCCAGCTCTGCACGGTCGATATCGACATGAATGATTT > NZ_CP009273/3845044‑3845240
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
