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 I2 R1
|
772 |
77.0 |
3769570 |
91.6% |
3452926 |
105.3 |
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%
| 139.5
/ NA
| 43 | pseudogene (40/678 nt) | yedN | pseudogene, IpaH/YopM family |
| Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (18/25); total (18/25) |
CACATTTTTTTTGAAGTCATTCGATGCGCCTTCTTTTACTGAATTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTCTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATCTTATTATAAATCGAGAAATCTTGAAACCAGAGACTATAATCACCCCATTCGAAATATT > NC_000913/2011867‑2012122
|
cacaTTTTTTTTGAAGTCATTCGATGCGCCTTCTTTTACTGAATTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAAt < 2:1680108/139‑1 (MQ=255)
acaTTTTTTTTGAAGTCATTCGATGCGCCTTCTTTTACTGAATTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAAtt > 1:534438/1‑139 (MQ=255)
aTTTTTTTTGAAGTCATTCGATGCGCCTTCTTTTACTGAATTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTa > 2:545399/1‑139 (MQ=255)
aTTTTTTTTGAAGTCATTCGATGCGCCTTCTTTTACTGAATTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTa > 2:834784/1‑139 (MQ=255)
aTTTTTTTTGAAGTCATTCGATGCGCCTTCTTTTACTGAATTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTa < 2:1324690/139‑1 (MQ=255)
gAAGTCATTCGATGCGCCTTCTTTTACTGAATTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAAtg < 1:545399/139‑1 (MQ=255)
gaGTCATTCGATGCGCCTTCTTTTACTGAATTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAAtgg > 2:683076/2‑139 (MQ=255)
aGTCATTCGATGCGCCTTCTTTTACTGAATTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAAtggg < 1:1656221/139‑1 (MQ=255)
aGTCATTCGATGCGCCTTCTTTTACTGAATTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAAtggg < 2:1423948/139‑1 (MQ=255)
gTCATTCGATGCGCCTTCTTTTACTGAATTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAAtgggt < 1:683076/139‑1 (MQ=255)
cATTCGATGCGCCTTCTTTTACTGAATTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAAtgggtgg < 2:1181845/139‑1 (MQ=255)
gcgcCTTCTTTTACTGAATTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAg < 1:795784/139‑1 (MQ=255)
aaTTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATgggtgggt < 2:133322/117‑1 (MQ=255)
aaTTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATgggtgggt > 1:133322/1‑117 (MQ=255)
ttAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTAt > 1:1689484/1‑139 (MQ=255)
tAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATc < 1:834784/139‑1 (MQ=255)
ccAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGa < 2:534438/139‑1 (MQ=255)
cAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGAt < 2:976215/139‑1 (MQ=255)
gTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATaa > 1:380027/1‑139 (MQ=255)
tGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAAtggg > 1:1646460/1‑88 (MQ=255)
tGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAAtggg < 2:1646460/88‑1 (MQ=255)
tCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAAt > 2:1442155/1‑67 (MQ=255)
tCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAAt < 1:1442155/67‑1 (MQ=255)
gTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATa < 1:664395/107‑1 (MQ=255)
gTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATa > 2:664395/1‑107 (MQ=255)
gTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAAcc < 2:36194/112‑1 (MQ=255)
gTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAAcc > 1:36194/1‑112 (MQ=255)
gTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATCTTATTATAAATCGAGAAATCTTg > 2:1506109/1‑139 (MQ=255)
cGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATCTTATTATAAATCGAGAAATCTTGAAACCaga < 1:1506109/139‑1 (MQ=255)
gTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGaa < 1:856552/58‑1 (MQ=255)
gTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGaa > 2:856552/1‑58 (MQ=255)
tAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATCTTATTATAAATCGAGAAATCTTGAAACCAgaga < 2:380027/139‑1 (MQ=255)
tCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATc < 1:239852/98‑1 (MQ=255)
tCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATc > 2:239852/1‑98 (MQ=255)
ctGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATCTTATTATAAATCGAGAAATCTTGAAAGCAGAGACTATAATCACCCCATTCg > 2:1048773/1‑139 (MQ=255)
aaTATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATCTTATTATAAATCGAGAAATCTTGAAACCAGAGACTATAATCACCCCATTCGAAat < 1:1048773/139‑1 (MQ=255)
atTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATCTTATTATAAATCGAGAAATCTTGAAACCAGAGACTATAATCACCCCATTCGAAATAtt < 2:1689484/139‑1 (MQ=255)
ttAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATc < 1:1025380/80‑1 (MQ=255)
ttAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATc > 2:1025380/1‑80 (MQ=255)
gTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATCTTATTATAAATCGAGAAATCTTGAAACCAGAGACt > 2:467803/1‑112 (MQ=255)
gTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATCTTATTATAAATCGAGAAATCTTGAAACCAGAGACt < 1:467803/112‑1 (MQ=255)
gTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATCTTATTATAAATCGAGAAATCTTGAAACCAGAGACTATAATCAcc < 1:925377/121‑1 (MQ=255)
gTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATCTTATTATAAATCGAGAAATCTTGAAACCAGAGACTATAATCAcc > 2:925377/1‑121 (MQ=255)
|
CACATTTTTTTTGAAGTCATTCGATGCGCCTTCTTTTACTGAATTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTCTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATCTTATTATAAATCGAGAAATCTTGAAACCAGAGACTATAATCACCCCATTCGAAATATT > NC_000913/2011867‑2012122
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
