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 |
|
A5 F17 I0 R1
|
87 |
56.5 |
4283937 |
98.6% |
4223961 |
62.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
349,140 |
C→T |
11.1% |
intergenic (+344/‑96) |
prpB → / → prpC |
2‑methylisocitrate lyase/2‑methylcitrate synthase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 349,140 | 0 | C | T | 11.1%
| 125.6
/ 6.7
| 45 | intergenic (+344/‑96) | prpB/prpC | 2‑methylisocitrate lyase/2‑methylcitrate synthase |
| Reads supporting (aligned to +/- strand): ref base C (28/12); new base T (2/3); total (30/15) |
| Fisher's exact test for biased strand distribution p-value = 3.15e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.38e-01 |
CGCATAGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACAATCTCGACCCTAC > W3110S.gb/349081‑349210
|
cGCATAGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGtgaa < 1:2631785/71‑1 (MQ=32)
cGCATAGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGtgaa < 1:1740045/71‑1 (MQ=32)
aTAGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGtgaactg < 1:3900272/71‑1 (MQ=34)
aGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGtgaa > 1:2682017/1‑66 (MQ=33)
gCATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGaactgaactg > 1:122120/1‑68 (MQ=35)
gCATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAg > 1:3741411/1‑71 (MQ=34)
cATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGTGtgaa < 1:3183506/59‑1 (MQ=16)
tCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTc < 1:500653/71‑1 (MQ=34)
ccGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGtgaa > 1:1905004/1‑56 (MQ=33)
cAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGAt > 1:1988228/1‑70 (MQ=35)
aaCCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGAt > 1:4006576/1‑69 (MQ=35)
aaCCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATaa < 1:2963751/71‑1 (MQ=34)
aaCCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATaa < 1:2490333/71‑1 (MQ=34)
aCCGATGCCTGATGCGCCTCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAg < 1:1599134/71‑1 (MQ=255)
cGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGAc > 1:3823205/1‑71 (MQ=34)
aTGCCTGATGCGCCGCTGACGCGACTTATCAGGCTTACGGGGTGAACTGAACTGTAGGTCGGATa > 1:3242136/1‑65 (MQ=25)
aTGCCTGATGCGCCGCTGACGCGACTTATCAGGCTTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGc < 1:1911281/71‑1 (MQ=21)
gCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCa > 1:4081717/1‑70 (MQ=35)
ccTGATGCGCCGCTGACGCGACTTATCAGGCTTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCAt < 1:3818646/70‑1 (MQ=25)
ccTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATa < 1:4099595/71‑1 (MQ=34)
gATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAg > 1:2176453/1‑61 (MQ=35)
aTGCGCCGCTGACGCGACTTATCAGGCTTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGc < 1:1942846/69‑1 (MQ=25)
aTGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGt > 1:4202901/1‑71 (MQ=34)
cgccgcTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAg > 1:756619/1‑47 (MQ=38)
cgccgcTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCg > 1:741681/1‑70 (MQ=35)
gacgcTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGc > 1:272640/3‑70 (MQ=25)
gcTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATcc > 1:3002997/1‑71 (MQ=34)
gcTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATcc > 1:2510620/1‑71 (MQ=34)
cTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATcc > 1:1623212/1‑70 (MQ=35)
gACGCGACTTATCAGGCCTACGGGGTgaactgaact < 1:3703002/36‑1 (MQ=40)
gACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGa > 1:3629806/1‑70 (MQ=35)
aCGCGACTTATCAGGCTTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGac > 1:4199158/1‑70 (MQ=25)
aCGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTc < 1:1895830/42‑1 (MQ=38)
aCGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGac < 1:1179856/70‑1 (MQ=35)
gcgACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGacaa > 1:2699203/1‑70 (MQ=35)
cgACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGa > 1:1316328/1‑47 (MQ=38)
gACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGAcaacaa > 1:4242261/1‑71 (MQ=38)
ttATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACAAtct > 1:1696580/1‑71 (MQ=255)
aTCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACAAtctc > 1:401922/1‑70 (MQ=255)
aTCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACAAtctc > 1:796012/1‑70 (MQ=255)
tCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTc > 1:1630122/1‑51 (MQ=35)
cAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACAATCTCGa > 1:4029330/1‑70 (MQ=255)
aGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACAATCTCGAcc > 1:25972/1‑71 (MQ=255)
aGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACAATCTCGAc > 1:1307964/1‑70 (MQ=255)
aGGCCTACGAGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACAATCTCGAcc > 1:1109138/1‑71 (MQ=255)
cTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACAATCTCGACCCTAc < 1:300604/71‑1 (MQ=255)
|
CGCATAGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACAATCTCGACCCTAC > W3110S.gb/349081‑349210
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
