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 |
|
A39 F1 I1 R1
|
15 |
59.3 |
3695894 |
97.1% |
3588713 |
75.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
REL606 |
3,388,714 |
G→T |
M331I (ATG→ATT) |
gspF → |
general secretory pathway component, cryptic |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | REL606 | 3,388,714 | 0 | G | T | 98.3%
| 224.9
/ ‑3.6
| 60 | M331I (ATG→ATT) | gspF | general secretory pathway component, cryptic |
| Reads supporting (aligned to +/- strand): ref base G (0/1); new base T (26/33); total (26/34) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.64e-01 |
ACGTTCGCCAGGGTAACAGCATTCATCTTTCGCTGGAACAAACCGCAATTTTCCCGCCGATGATGCTCTACATGGTGGCCTCTGGCGAAAAAAGCGGGCAGCTCGGCACATTAATGGTCAGAGCCGCAGATAACCAGGAGACACTC > REL606/3388641‑3388786
|
ccGTCCGCCAGGGTAACAGCATTCATTTTTCGCTGGAACAACCCGCAATTTTCCCGCCGATGATGCTCTACAttgt < 1:336770/75‑1 (MQ=255)
ttCGCCAGGGTAACAGCATTCATCTTTCGCTGGAACAACCCGCAATTTTCCCGCCGATGATGCTCTACATTGTGGc < 2:760401/76‑1 (MQ=255)
ttCGCCAGGGTAACAGCATTCATCTTTCGCTGGAACAAACCGCAATTTTCCCGCCGATGATGCTCTACATTGTGGc > 2:1779400/1‑76 (MQ=255)
tCGCCAGGGTAACAGCATTCATCTTTCGCTGGAACAAACCGCAATTTTCCCGCCGATGATGCTCTACATTGTGGcc > 1:319107/1‑76 (MQ=255)
tCGCCAGGGTAACAGCATTCATCTTTCGCTGGAACAAACCGCAATTTTCCCGCCGATGATGCTCTACATTGTGGcc > 1:569753/1‑76 (MQ=255)
cGCCAGGGTAACAGCATTCATCTTTCGCTGGAACAAACCGCAATTTTCCCGCCGATGATGCTCTACATTGTGGCct > 1:129405/1‑76 (MQ=255)
ccAGGGTAACAGCATTCATCTTTCGCTGGAACAACCCGCAATTTCCCCGCCGATGATGCTCTACATTGTGGCctct < 1:1654619/76‑1 (MQ=255)
ccAGGGTAACAGCATTCATCTTTCGCTGGAACAAACCGCAATTTTCCCGCCGATGATGCTCTACATTGTGGCctct < 1:160261/76‑1 (MQ=255)
ccAGGGAAACACCATTCATCTTCCGCTGGAACAAACCGCAATTTCCCCGCCGATGATGCTCTACATTGTGGCctct < 2:545107/76‑1 (MQ=255)
ggTAACAGCATTCATCTTTCGCGGAAACAACCCGCAATTTTCCCGCCGATGATGCTCTACATTGTGGCCTCTGGCg < 1:1559200/76‑1 (MQ=38)
gTAACAGCATTCATCTTTCGCTGGAACAAACCGCAATTTTCCCGCCGATGATGCTCTACATTGTGGCCTCTGGCGa > 1:1277618/1‑76 (MQ=255)
gTAACAGCATTCATCTTTCGCTGGAACAAAACGCAATTTTCCCGCCGATGATGCTCTACATTGTGGCCTCTGGCGa > 1:1472060/1‑76 (MQ=39)
tAACAGCATTCATCTTTCGCTGGAACAAACCGCAATTTTCCCGCCGATGATGCTCTACATTGTGGCCTCTGGCGaa > 1:629241/1‑76 (MQ=255)
aaCAGCATTCATCTTTCGCTGGAACAAACCGCAATTTTCCCGCCGATGATGCTCTACATTGTGGCCTCTGGCGaaa > 2:467036/1‑76 (MQ=255)
aaCAGCATTCATCTTTCGCTGGAACAAACCGCAATTTTCCCGCCGATGATGCTCTACATTGTGGCCTCTGGCGaaa > 1:1729099/1‑76 (MQ=255)
gCATTCATCTTTCGCTGGAACAAACCGCAATTTTCCCGCCGATGATGCTCTACATTGTGGCCTCTGGCGAAAAAAg > 1:1533798/1‑76 (MQ=255)
gCATTCATCTTTCGCGGGAACAACCCGCACTTTCCCCGCCGATGATGCTCTACATTGTGGCCTCTGGCGAAAAAAg < 2:313961/76‑1 (MQ=38)
cATTCATCTTTCGCTGGAACAAACCGCAATTTTCCCGCCGATGATGCTCTACATTGTGGCCTCTGGCGAAAAAAGc > 1:1104522/1‑76 (MQ=255)
cATTCATCTTTCGCTGGAACAAACCGCAATTTTCCCGCCGATGATGCTCTACATTGTGGCCTCTGGCGAAAAAAGc > 1:1445247/1‑76 (MQ=255)
tCATCTTTCGCTGGAACAAACCNCAATTTTCCCGCCGATGATGCTCTACATTGTGGCCTCTGGCGAAAAAAGCggg > 2:257442/1‑76 (MQ=39)
caccTTTCGCGAGAACAACCCGCAATTTCCCCGCCGATGATGCTCTACATTGTGGCCTCTGGCGAAAAAAGCGGGc < 2:1605511/73‑1 (MQ=37)
cATTTTTCGCTGGAACAACCCGAAATTTTCCCGCCGATGATGCTCTACATTGTGGCCTCTGGCGAAAAAAGCGGGc < 2:1151496/76‑1 (MQ=37)
cATCTTTCGCTGGAACAACCCGCATTTTTCCCGCCGATGATGCTCTACATTGTGGCCTCTGGCGAAAAAAGCGGGc < 2:62962/76‑1 (MQ=38)
ttCGCTGGAACAACCCGCAATTTCCCCGCCGATGATGCTCTACATTGTGGCCTCTGGCGAAAAAAGCGGGCAGCTc < 2:1830661/76‑1 (MQ=38)
ttCGCTGGAACAAACCGCAATTTTCCCGCCGATGATGCTCTACATTGTGGCCTCTGGCGAAAAAAGCGGGCAGCTc > 2:119356/1‑76 (MQ=255)
ttCGCTGGAACAAACCGCAATTTTCCCGCCGATGATGCTCTACATTGTGGCCTCTGGCGAAAAAAGCGGGCAGCTc > 2:174159/1‑76 (MQ=255)
cGCTGAAACAACCCGCAATTTCCCCGCCGATGATGCTCTACATTGTGGCCTCTGGCGAAAAAAGCGGGCAGCTCgg < 1:1504419/76‑1 (MQ=38)
gAACAACCCGCAATTTCCCCGCCGATGATGCTCTACATTGTGGCCTCTGGCGAAAAAAGCGGGCAGCTCGGCACAt < 1:170316/76‑1 (MQ=38)
gAACAACCCGCAATTTCCCCGCCGATGATGCTCTACATTGTGGCCTCTGGCGAAAAAAGCGGGCAGCTCGGCACAt < 1:1783173/76‑1 (MQ=38)
aCAAACCTCAATTTTCCCGCCGATGATGCTCTACATTGTGGCCTCTGGCGAAAAAAGCGGGCAGCTCGGCACATTa < 2:276987/76‑1 (MQ=255)
aCAAACCACAATTTTCCCGCCGATGATGCTCTACATTGTGGCCTCTGGCGAAAAAAGCGGGCAGCTCGGCACATTa < 2:1006773/76‑1 (MQ=255)
aacccGCATTTTCCCCGCCGATGATGCTCTACATTGTGGCCTCTGGCGAAAAAAGCGGGCAGCTCGGCACATTAAt < 1:1561373/73‑1 (MQ=38)
aacccGCAATTGTCCCGCCGATGATGCTCTACATTGTGGCCTCTGGCGAAAAAAGCGGGCAGCTCGGCACATTAAt < 1:81895/73‑1 (MQ=38)
gCAATTTTCCCGCCGATGATGCTCTACATTGTGGCCTCTGGCGAAAAAAGCGGGCAGCTCGGCACATTAATGGTCa > 1:719962/1‑76 (MQ=255)
cAATTTTCCCGCCGATGATGCTCTACATTGTGGCCTCTGGCGAAAAAAGCGGGCAGCTCGGCACATTAATGGTCag < 2:1328562/76‑1 (MQ=255)
nttttCCCGCCGATGATGCTCTACATTGTGGCCTCTGGCGAAAAAAGCGGGCAGCTCGGCACATTAATGGTCagag > 1:514899/2‑76 (MQ=255)
aTTTCCCCGCCGATGATGCTCTACATTGTGGCCTCTGGCGAAAAAAGCGGGCAGCTCGGCACATTAATGGTCagag < 2:608844/76‑1 (MQ=255)
ttttCCCGCCGATGATGCTCTACATTGTGGCCTCTGGCGAAAAAAGCGGGCAGCTCGGCACATTAATGGTCAGAGc < 1:1835430/76‑1 (MQ=255)
ttccccGCCGATGATGCTCTACATTGTGGCCTCTGGCGAAAAAAGCGGGCAGCTCGGCACATTAATGGTCAGAGcc < 1:84520/73‑1 (MQ=255)
cccGCCGATGATGCTCTACATTGTGGCCTCTGGCGAAAAAAGCGGGCAGCTCGGCACATTAATGGTCAGAGCCGCa < 2:1236047/76‑1 (MQ=255)
cccGCCGATGATGCTCTACATTGTGGCCTCTGGCGAAAAAAGCGGGCAGCTCGGCACATTAATGGTCAGAGCCGCa > 2:42069/1‑76 (MQ=255)
ccgccgATGATGCTCTACATTGTGGCCTCTGGCGAAAAAAGCGGGCAGCTCGGCACATTAATGGTCAGAGCCGCAg < 1:1313660/76‑1 (MQ=255)
cgccgATGATGCTCTACATTGTGGCCTCTGGCGAAAAAAGCGGGCAGCTCGGCACATTAATGGTCAGAGCCGCAGa > 1:1554703/1‑76 (MQ=255)
gccgATGATGCTCTACATTGTGGCCTCTGGCGAAAAAAGCGGGCAGCTCGGCACATTAATGGTCAGAGCCGCAGAt < 2:1682873/76‑1 (MQ=255)
ccgATGATGCTCTACATTGTGGCCTCTGGCGAAAAAAGCGGGCAGCTCGGCACATTAATGGTCAGAGCCGCAGATa > 1:32253/1‑76 (MQ=255)
ccgATGATGCTCTACATTGTGGCCTCTGGCGAAAAAAGCGGGCAGCTCGGCACATTAATGGTCAGAGCCGCAGATa < 2:200403/76‑1 (MQ=255)
cgATGATGCTCTACATTGTGGCCTCTGGCGAAAAAAGCGGGCAGCTCGGCACATTAATGGTCAGAGCCGCAGATaa < 2:73583/76‑1 (MQ=255)
cgATGATGCTCTACATTGTGGCCTCTGGCGAAAAAAGCGGGCAGCTCGGCACATTAATGGTCAGAGCCGCAGATaa < 2:1332004/76‑1 (MQ=255)
atgatgCTCTACATTGTGGCCTCTGGCGAAAAAAGCGGGCAGCTCGGCACATTAATGGTCAGAGCCGCAGATAAcc < 1:435003/76‑1 (MQ=255)
tgatgCTCTACATTGTGGCCTCTGGCGAAAAAAGCGGGCAGCTCGGCACATTAATGGTCAGAGCCGCAGATAACCa > 2:761098/1‑76 (MQ=255)
tgatgCTCTACATGGTGGCCTCTGGCGAAAAAAGCGGGCAGCTCGGCACATTAATGGTCAGAGCCGCAGATAACCa < 1:1666896/76‑1 (MQ=255)
gatgCTCTACATTGTGGCCTCTGGCGAAAAAAGCGGGCAGCTCGGCACATTAATGGTCAGAGCCGCAGATAACCAg < 1:121647/76‑1 (MQ=255)
gatgCTCTACATTGTGGCCTCTGGCGAAAAAAGCGGGCAGCTCGGCACATTAATGGTCAGAGCCGCAGATAACCAg < 1:1133978/76‑1 (MQ=255)
atgCTCTACATTGTGGCCTCTGGCGAAAAAAGCGGGCAGCTCGGCACATTAATGGTCAGAGCCGCAGATAACCAgg > 2:1071783/1‑76 (MQ=255)
atgCTCTACATTGTGGCCTCTGGCGAAAAAAGCGGGCAGCTCGGCACATTAATGGTCAGAGCCGCAGATAACCAgg < 1:1128382/76‑1 (MQ=255)
tgCTCTACATTGTGGCCTCTGGCGAAAAAAGCGGGCAGCTCGGCACATTAATGGTCAGAGCCGCAGATAACCAGga > 1:1398210/1‑76 (MQ=255)
ctACATTGTGGCCTCTGGCGAAAAAAGCGGGCAGCTCGGCACATTAATGGTCAGAGCCGCAGATAACCAGGAGaca > 2:1113670/1‑76 (MQ=255)
tACATTGTGGCCTCTGGCGAAAAAAGCGGGCAGCTCGGCACATTAATGGTCAGAGCCGCAGATAACCAGGAGacac > 2:1333818/1‑76 (MQ=255)
tACATTGTGGCCTCTGGCGAAAAAAGCGGGCAGCTCGGCACATTAATGGTCAGAGCCGCAGATAACCAGGAGacac < 1:1620874/76‑1 (MQ=255)
aCATTGTGGCCTCTGGCGAAAAAAGCGGGCAGCTCGGCACATTAATGGTCAGAGCCGCAGATAACCAGGAGACACt < 1:431100/76‑1 (MQ=255)
cATTGTGGCCTCTGGCGAAAAAAGCGGGCAGCTCGGCACATTAATGGTCAGAGCCGCAGATAACCAGGAGACACTc > 1:646078/1‑76 (MQ=255)
|
ACGTTCGCCAGGGTAACAGCATTCATCTTTCGCTGGAACAAACCGCAATTTTCCCGCCGATGATGCTCTACATGGTGGCCTCTGGCGAAAAAAGCGGGCAGCTCGGCACATTAATGGTCAGAGCCGCAGATAACCAGGAGACACTC > REL606/3388641‑3388786
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
