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 F28 I1 R1
|
354 |
41.7 |
3110465 |
93.1% |
2895842 |
61.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
W3110S.gb |
3,824,380 |
2 bp→AA |
pseudogene (513‑514/687 nt) |
rph → |
ECK3633:JW3618:b3643; ribonuclease PH |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,824,380 | 0 | G | A | 100.0%
| 240.1
/ NA
| 72 | pseudogene (513/687 nt) | rph | ECK3633:JW3618:b3643; ribonuclease PH |
| Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (36/36); total (36/36) |
| * | W3110S.gb | 3,824,381 | 0 | G | A | 98.6%
| 240.0
/ ‑5.3
| 72 | pseudogene (514/687 nt) | rph | ECK3633:JW3618:b3643; ribonuclease PH |
| Reads supporting (aligned to +/- strand): ref base G (0/0); major base A (35/36); minor base T (1/0); total (36/36) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATGAACGTA > W3110S.gb/3824342‑3824434
||
gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATActt < 1:2203861/59‑3 (MQ=255)
gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt < 1:2601794/59‑1 (MQ=255)
gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt < 1:1999957/59‑1 (MQ=255)
gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt < 1:2212399/59‑1 (MQ=255)
gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt < 1:2312875/59‑1 (MQ=255)
gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt < 1:2316446/59‑1 (MQ=255)
gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt < 1:758566/59‑1 (MQ=255)
gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt < 1:240887/59‑1 (MQ=255)
gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt < 1:2517901/59‑1 (MQ=255)
gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt < 1:1067019/59‑1 (MQ=255)
gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt < 1:992770/59‑1 (MQ=255)
gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt < 1:286509/59‑1 (MQ=255)
gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt < 1:2943398/59‑1 (MQ=255)
gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt < 1:621762/59‑1 (MQ=255)
gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt < 1:3071721/59‑1 (MQ=255)
gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt < 1:60478/59‑1 (MQ=255)
gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt < 1:526826/59‑1 (MQ=255)
gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt < 1:342116/59‑1 (MQ=255)
gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt < 1:375279/59‑1 (MQ=255)
gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt < 1:1842413/59‑1 (MQ=255)
gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt < 1:889302/59‑1 (MQ=255)
gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt < 1:1614660/59‑1 (MQ=255)
gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt < 1:1652320/59‑1 (MQ=255)
gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt < 1:801929/59‑1 (MQ=255)
gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt < 1:800760/59‑1 (MQ=255)
gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt < 1:76619/59‑1 (MQ=255)
gctgTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc > 1:5040/4‑65 (MQ=255)
gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc > 1:778138/1‑65 (MQ=255)
gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc > 1:454230/1‑65 (MQ=255)
gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc > 1:752554/1‑65 (MQ=255)
gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc > 1:405409/1‑65 (MQ=255)
gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc > 1:2346688/1‑65 (MQ=255)
gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc > 1:3051156/1‑65 (MQ=255)
gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc > 1:1677756/1‑65 (MQ=255)
gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc > 1:2513316/1‑65 (MQ=255)
gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc > 1:1630998/1‑65 (MQ=255)
gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc > 1:2112518/1‑65 (MQ=255)
gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc > 1:2744166/1‑65 (MQ=255)
gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc > 1:2924726/1‑65 (MQ=255)
tGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt < 1:2999632/45‑1 (MQ=25)
aaaCGGTGAAGCATTTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa > 1:2308537/2‑63 (MQ=255)
aaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa > 1:846169/2‑63 (MQ=255)
aaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa > 1:2675516/2‑63 (MQ=255)
aaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa > 1:3022367/2‑63 (MQ=255)
aaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa > 1:2402396/2‑63 (MQ=255)
aaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa > 1:188916/2‑63 (MQ=255)
aaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa > 1:1288207/2‑63 (MQ=255)
aaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa > 1:125598/2‑63 (MQ=255)
aaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa > 1:939163/2‑63 (MQ=255)
aaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa > 1:666524/2‑63 (MQ=255)
aaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa > 1:2343414/2‑63 (MQ=255)
aaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa > 1:1760280/2‑63 (MQ=255)
aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg < 1:821167/64‑1 (MQ=255)
aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg < 1:866328/64‑1 (MQ=255)
aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg < 1:2597848/64‑1 (MQ=255)
aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg < 1:1755263/64‑1 (MQ=255)
aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg < 1:1186184/64‑1 (MQ=255)
aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg < 1:1222828/64‑1 (MQ=255)
aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg < 1:1699489/64‑1 (MQ=255)
aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg < 1:2341791/64‑1 (MQ=255)
aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg < 1:332111/64‑1 (MQ=255)
aCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTa > 1:2348629/1‑65 (MQ=255)
aCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTa > 1:2339913/1‑65 (MQ=255)
aCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTa > 1:1798565/1‑65 (MQ=255)
aCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTa > 1:384983/1‑65 (MQ=255)
aCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTa > 1:1748284/1‑65 (MQ=255)
aCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTa > 1:306879/1‑65 (MQ=255)
aCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTa > 1:1503753/1‑65 (MQ=255)
aCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTa > 1:1320493/1‑65 (MQ=255)
aCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTa > 1:1295806/1‑65 (MQ=255)
aCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTa > 1:1290353/1‑65 (MQ=255)
aCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTa > 1:3073809/1‑65 (MQ=255)
||
GTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATGAACGTA > W3110S.gb/3824342‑3824434
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
