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 F1 I0 R1
|
92 |
46.1 |
3712835 |
96.9% |
3597737 |
60.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
3,824,380 |
2 bp→AA |
100% |
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%
| 153.8
/ NA
| 55 | pseudogene (513/687 nt) | rph | ECK3633:JW3618:b3643; ribonuclease PH |
| Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (27/28); total (27/28) |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
| * | W3110S.gb | 3,824,381 | 0 | G | A | 100.0%
| 151.0
/ NA
| 55 | pseudogene (514/687 nt) | rph | ECK3633:JW3618:b3643; ribonuclease PH |
| Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (27/28); total (27/28) |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
GAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATGAACGTAGTGATGACCG > W3110S.gb/3824317‑3824444
||
gAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGc > 1:35930/1‑70 (MQ=255)
aaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGAt > 1:2383292/1‑71 (MQ=255)
aaccaaccCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATc > 1:561224/1‑71 (MQ=255)
aaccaaccCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATc < 1:1369396/71‑1 (MQ=255)
aaccaaccCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGCAAACGGTGAAGCAATTTGCGATc < 1:3040459/71‑1 (MQ=255)
ccAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTg > 1:982169/1‑71 (MQ=255)
acccGATGAAAGGGATGGTAGCCTCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa < 1:2997136/69‑1 (MQ=255)
cccGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa > 1:1442181/2‑70 (MQ=255)
aTGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt > 1:3180695/1‑71 (MQ=255)
aTGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt > 1:2976517/1‑71 (MQ=255)
gAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGAt > 1:3111530/1‑58 (MQ=255)
gAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGAt > 1:3188225/1‑58 (MQ=255)
aaGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTg < 1:2008313/69‑1 (MQ=255)
aGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGat > 1:1902413/1‑69 (MQ=255)
ggATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGa < 1:3107361/70‑1 (MQ=255)
gATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGAt > 1:2606752/1‑52 (MQ=255)
tGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa < 1:1200285/56‑1 (MQ=255)
tGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGaa < 1:3053789/65‑1 (MQ=255)
gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg < 1:1056643/52‑1 (MQ=255)
aGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCg > 1:3464116/1‑71 (MQ=255)
cGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCg > 1:803879/1‑68 (MQ=255)
gTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACg < 1:1465297/49‑1 (MQ=25)
gTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACg < 1:1328060/49‑1 (MQ=25)
tttCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCag < 1:877753/66‑1 (MQ=255)
ttCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGaa > 1:1482834/1‑52 (MQ=255)
tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg < 1:1654586/40‑1 (MQ=16)
tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa > 1:3590080/1‑42 (MQ=19)
tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATa > 1:3547008/1‑44 (MQ=21)
tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGa > 1:45078/1‑50 (MQ=255)
tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa > 1:515962/1‑71 (MQ=255)
tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa > 1:2270233/1‑71 (MQ=255)
tGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACa > 1:3711375/1‑71 (MQ=255)
tGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACa > 1:418140/1‑71 (MQ=255)
gTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCa < 1:2964650/60‑1 (MQ=255)
tCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATg < 1:3533300/71‑1 (MQ=255)
cGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa > 1:948157/1‑37 (MQ=12)
aTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAAc > 1:910156/1‑69 (MQ=255)
aTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAAc > 1:662375/1‑69 (MQ=255)
aTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAAc > 1:1109122/1‑69 (MQ=255)
aTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg < 1:1591543/70‑1 (MQ=255)
aTTGTAAACGGTGAAGCAATTTGCAATCTGGAATACGTTg < 1:706472/40‑1 (MQ=19)
ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGtt < 1:2181588/38‑1 (MQ=21)
ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGaa < 1:2172751/41‑1 (MQ=25)
ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCg < 1:1670337/51‑1 (MQ=255)
ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCg < 1:3385335/51‑1 (MQ=255)
ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCa < 1:1188343/53‑1 (MQ=255)
ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGt < 1:458719/70‑1 (MQ=255)
tgtaAACGGTGAAGCAATTTGCGATCTGGAATACGTTg < 1:229250/38‑1 (MQ=21)
taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCaga > 1:2828120/3‑52 (MQ=255)
taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtg < 1:664290/69‑1 (MQ=255)
taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt < 1:2129204/68‑1 (MQ=255)
cGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgatga > 1:3638070/1‑71 (MQ=255)
gtgAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAgaga < 1:650955/46‑1 (MQ=37)
tgAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCagag < 1:2925823/45‑1 (MQ=37)
tgAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCg < 1:1299847/70‑1 (MQ=255)
||
GAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATGAACGTAGTGATGACCG > W3110S.gb/3824317‑3824444
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
