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 F1 I1 R1
|
770 |
51.4 |
2439994 |
93.8% |
2288714 |
110.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
2,012,001 |
C→T |
pseudogene (40/678 nt) |
yedN ← |
pseudogene, IpaH/YopM family |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 2,012,001 | 0 | C | T | 100.0%
| 127.9
/ NA
| 40 | pseudogene (40/678 nt) | yedN | pseudogene, IpaH/YopM family |
| Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (19/21); total (19/21) |
CATTTTTTTTGAAGTCATTCGATGCGCCTTCTTTTACTGAATTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTCTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATCTTATTATAAATCGAGAAATCTTGAAACCAGAGACTATAATCACCCCATTCGAAATATTCTGAGTGCAAT > NC_000913/2011869‑2012133
|
caTTTTTTTTGAAGTCATTCGATGCGCCTTCTTTTACTGAATTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAAttt > 2:37515/1‑139 (MQ=255)
aaTTTTTTTTGTAGTCATCCGATGCTCCTTCTTTTACTGAATTAGCCCAGTCGCTGAAACCTTTGCAGAGTCTCGAATCTGTATTCTTCGTAAAGTAGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAAttt > 1:214510/2‑139 (MQ=255)
aTTTTTTTTGAAGTCATTCGATGCGCCTTCTTTTACTGAATTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTa < 1:37515/139‑1 (MQ=255)
aaGTCATTCGATGCGCCTTCTTTTACTGAATTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAAtgg < 2:854686/139‑1 (MQ=255)
cATTCGATGCGCCTTCTTTTACTGAATTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTa < 2:546897/125‑1 (MQ=255)
cATTCGATGCGCCTTCTTTTACTGAATTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTa > 1:546897/1‑125 (MQ=255)
cttcttTTACTGAATTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAg > 2:243605/1‑135 (MQ=255)
cttcttTTACTGAATTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAg < 1:243605/135‑1 (MQ=255)
aaTTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCt > 1:1186887/1‑139 (MQ=255)
aaTTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCt > 1:504188/1‑139 (MQ=255)
aaTTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCt > 1:7215/1‑139 (MQ=255)
ttAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAGCTTTAATTTATGCCGAAtggg > 2:773688/1‑110 (MQ=255)
ttAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAAtggg < 1:773688/110‑1 (MQ=255)
ttAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTAt > 1:853454/1‑139 (MQ=255)
ttAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTAt < 2:341374/139‑1 (MQ=255)
cAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTCTCATGAt < 2:504188/139‑1 (MQ=255)
gTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAAtggg < 1:919638/102‑1 (MQ=255)
gTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAAtggg > 2:919638/1‑102 (MQ=255)
gTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATgggtgggt > 2:1083690/1‑107 (MQ=255)
gTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATgggtgggt < 1:1083690/107‑1 (MQ=255)
gTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATaa > 2:1004753/1‑139 (MQ=255)
gCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAAc < 2:1186887/139‑1 (MQ=255)
gCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAAc < 2:7215/139‑1 (MQ=255)
cTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAAcc < 2:853454/139‑1 (MQ=255)
cTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAAcc > 2:865565/1‑121 (MQ=255)
cTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAAcc < 1:865565/121‑1 (MQ=255)
ggAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAAtggg < 2:1119891/78‑1 (MQ=255)
ggAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAAtggg > 1:1119891/1‑78 (MQ=255)
gTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGAt < 2:1138371/91‑1 (MQ=255)
gTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGAt > 1:1138371/1‑91 (MQ=255)
gTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATCTTATTATAAATCGAGAAATCTTg > 2:505294/1‑139 (MQ=255)
gTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATc < 1:489502/107‑1 (MQ=255)
gTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATc > 2:489502/1‑107 (MQ=255)
tAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATCTTATTATAAATCGAGAAATCTTGAAACCAgaga < 1:505294/139‑1 (MQ=255)
ctGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATCTTATTATAAATCGAGAAATCTTGAAACCa > 2:912754/1‑117 (MQ=255)
ctGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATCTTATTATAAATCGAGAAATCTTGAAACCa < 1:912754/117‑1 (MQ=255)
cAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATCTTATTATAAATCGAGAAATCTTGAAACCag < 1:1129560/115‑1 (MQ=255)
cAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATCTTATTATAAATCGAGAAATCTTGAAACCag > 2:1129560/1‑115 (MQ=255)
tAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATCTTATTATAAATCGAGAAATCTTGAAACCAGAGACTATAATCACCCCATTCGAAATATTCt < 1:1004753/139‑1 (MQ=255)
taAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATCTTATTATAAATCGAGAAATCTTGAAACCAGAGACTATAATCACCCCATTCGAAATATTCTGAGTGCAAt < 1:283803/139‑1 (MQ=255)
|
CATTTTTTTTGAAGTCATTCGATGCGCCTTCTTTTACTGAATTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTCTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATCTTATTATAAATCGAGAAATCTTGAAACCAGAGACTATAATCACCCCATTCGAAATATTCTGAGTGCAAT > NC_000913/2011869‑2012133
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
