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 F21 I0 R2
|
308 |
27.9 |
1975068 |
96.7% |
1909890 |
67.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
3,824,362 |
A→T |
100% |
pseudogene (495/687 nt) |
rph → |
ECK3633:JW3618:b3643; ribonuclease PH |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,824,362 | 0 | A | T | 100.0%
| 110.3
/ NA
| 36 | pseudogene (495/687 nt) | rph | ECK3633:JW3618:b3643; ribonuclease PH |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base T (20/16); total (20/16) |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
TGGAAAACGGCAAGCTGAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATG > W3110S.gb/3824301‑3824428
|
tggAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCTGTATtgta < 1:202890/68‑2 (MQ=255)
gAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACgg > 1:1602653/1‑71 (MQ=255)
aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCg < 1:1028506/70‑1 (MQ=255)
aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCg < 1:1245785/70‑1 (MQ=255)
aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCg < 1:1536246/70‑1 (MQ=255)
aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCg < 1:1536805/70‑1 (MQ=255)
aaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCg < 1:1589900/69‑1 (MQ=255)
aTGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCg < 1:1061724/49‑1 (MQ=25)
gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGAc > 1:970191/1‑66 (MQ=255)
gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGAc > 1:1075599/1‑66 (MQ=255)
gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGAc > 1:1106804/1‑66 (MQ=255)
gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGAc > 1:725329/1‑66 (MQ=255)
gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGAc > 1:1368874/1‑66 (MQ=255)
gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc > 1:1050529/1‑71 (MQ=255)
gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc > 1:754364/1‑71 (MQ=255)
gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc > 1:204644/1‑71 (MQ=255)
gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc > 1:1761762/1‑71 (MQ=255)
gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc > 1:1068694/1‑71 (MQ=255)
cGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa > 1:1721534/1‑49 (MQ=25)
cGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa > 1:286859/1‑49 (MQ=25)
cGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa > 1:982567/1‑49 (MQ=25)
cGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa > 1:554109/1‑49 (MQ=25)
cGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa > 1:921775/1‑49 (MQ=25)
cGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa > 1:1309580/1‑49 (MQ=25)
cGCAGTTTATGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa > 1:1511493/1‑49 (MQ=19)
tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa > 1:1814428/1‑71 (MQ=255)
tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa > 1:964083/1‑71 (MQ=255)
cTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa < 1:661770/70‑1 (MQ=255)
cTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa < 1:1367448/70‑1 (MQ=255)
cTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa < 1:808008/70‑1 (MQ=255)
cTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa < 1:604600/70‑1 (MQ=255)
cTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa < 1:333101/70‑1 (MQ=255)
cTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa < 1:306397/70‑1 (MQ=255)
tGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa < 1:623003/69‑1 (MQ=255)
tCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATg < 1:951522/71‑1 (MQ=255)
tCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATg < 1:520148/71‑1 (MQ=255)
|
TGGAAAACGGCAAGCTGAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATG > W3110S.gb/3824301‑3824428
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
