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 F3 I0 R1
|
560 |
56.4 |
4650532 |
94.9% |
4413354 |
59.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
3,359,906 |
T→C |
28.8% |
M285T (ATG→ACG) |
gltD → |
glutamate synthase, 4Fe‑4S protein, small subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,359,906 | 0 | T | C | 28.8%
| 96.6
/ 49.0
| 66 | M285T (ATG→ACG) | gltD | glutamate synthase, 4Fe‑4S protein, small subunit |
| Reads supporting (aligned to +/- strand): ref base T (20/27); new base C (8/11); total (28/38) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CCGTTCCTCATCGCCAACACCAAACAGTTAATGGGCTTTGGTGAAACCCGCGACGAACCGTTCGTCAGCATGGAAGGCAAACGCGTGGTGGTCCTTGGCGGTGGCGACACTGCGATGGACTGCGTGCGTA > W3110S.gb/3359836‑3359965
|
ccGTTCCTCATCGCCAACACCAAACAGTTAATGGGCTTTGGTGAAACCCGCGACGAACCGTTCGTCAGCAt > 1:1038056/1‑71 (MQ=255)
cGTTCCTCATCGCCAACACCAAACAGTTAATGGGCTTTGGTGAAACCCGCGACGAACCGTTCGTCAGCATg > 1:2271936/1‑71 (MQ=255)
gTTCCTCATCGCCAACACCAAACAGTTAATGGGCTTTGGTGAAACCCGCGACGAACCGTTCGTCAGCATg < 1:2614029/70‑1 (MQ=255)
tCATCGCCAACACCAAACAGTTAATGGGCTTTGGTGAAACCCGCGACGAACCGTTCGTCAGCACGGaa < 1:4247388/68‑1 (MQ=255)
cATCGCCAACACCAAACAGTTAATGGGCTTTGGTGAAACCCGCGACGAACCGTTCGTCAGCATGGAAGGc > 1:1176295/1‑70 (MQ=255)
ccAACACCAAACAGTTAATGGGCTTTGGTGAAACCCGCGACGAACCGTTCGTCAGCATGGAAGGCAAAcgc > 1:256508/1‑71 (MQ=255)
cAACACCAAACAGTTAATGGGCTTTGGTGAAACCCGCGACGAACCGTTCGTCAGCATGGAAGGCAAAcgcg < 1:1928044/71‑1 (MQ=255)
acacCAAACAGTTAATGGGCTTTGGTGAAACCCGCGACGAACCGTTCGTCAGCATGGAAGGCAAACGCgtg < 1:4404987/71‑1 (MQ=255)
acacCAAACAGTTAATGGGCTTTGGTGAAACCCGCGACGAACCGTTCGTCAGCATGGAAGGCAAACGCgtg < 1:943930/71‑1 (MQ=255)
acacCAAACAGTTAATGGGCTTTGGTGAAACCCGCGACGAACCGTTCGTCAGCATGGAAGGCAAACGCgtg < 1:2375154/71‑1 (MQ=255)
acacCAAACAGTTAATGGGCTTTGGTGAAACCCGCGACGAACCGTTCGTCAGCACGGAAGGCAAACGCgtg < 1:2008556/71‑1 (MQ=255)
cacCAAACAGTTAATGGGCTTTGGTGAAACCCGCGACGAACCGTTCGTCAGCACGGAAg > 1:4210147/1‑59 (MQ=255)
acaaaaCAGTTAATGGGCTTTGGTGAAACCCGCGACGAACCGTTCGTCAGCATGGAAGGCaaa > 1:2990798/4‑63 (MQ=255)
acCAAACAGTTAATGGGCTTTGGTGAAACCCGCGACGAACCGTTCGTCAGCATGGAAGGCAAACGCgtggt > 1:4214245/1‑71 (MQ=255)
acCAAACAGTTAATGGGCTTTGGTGAAACCCGCGACGAACCGTTCGTCAGCATGGAAGGCAAACGCgtggt > 1:2305725/1‑71 (MQ=255)
acCAAACAGTTAATGGGCTTTGGTGAAACCCGCGACGAACCGTTAGTCAGCACGGAAGGCAAACGCgtggt > 1:668858/1‑71 (MQ=255)
ccAAACAGTTAATGGGCTTTGGTGAAACCCGCGACGAACCGTTCGTCAGCACGGAAGGCAAACGCgtggtg > 1:4014540/1‑71 (MQ=255)
aaaCAGTTAATGGGCTTTGGTGAAACCCGCGACGAACCGTTCGTCAGCATGGAAGGCAAACGCGtggtgg < 1:317458/70‑1 (MQ=255)
aCAGTTAATGGGCTTTGGTGAAACCCGCGACGAACCGTTCGTCAGCATGGAAGGCAAACGCGTGGTGGTcc < 1:2176280/71‑1 (MQ=255)
cAGTTAATGGGCTTTGGTGAAACCCGCGACGAACCGTTCGTCAGCATGGAAGGCAAACGCGTGGTGGTCCt < 1:3545667/71‑1 (MQ=255)
aGTTAATGGGCTTTGGTGAAACCCGCGACGAACCGTTCGTCAGCATGGAAGGCAAACGCGTGGTGGTCCtt < 1:4006399/71‑1 (MQ=255)
gTTAATGGGCTTTGGTGAAACCCGCGACGAACCGTTCGTCAGCATGGAAgg < 1:3957459/51‑1 (MQ=255)
tAATGGGCTTTGGTGAAACCCGCGACGAACCGTTCGTCAGCATGGa > 1:146508/1‑46 (MQ=255)
tAATGGGCTTTGGTGAAACCCGCGAAGAACCGTTCGTCAGCACGGaa > 1:1268793/1‑47 (MQ=255)
aaTGGGCTTTGGTGAAACCCGCGACGAACCGTTCGTCAGCATGGAAGGCAAACGCGTGGTGGTCCTTGGc < 1:3774926/70‑1 (MQ=255)
aaTGGGCTTTGGTGAAACCCGCGACGAACCGTTCGTCAGCATGGAAGGCAAACGCGTGGTGGTCCTTGGc < 1:3717020/70‑1 (MQ=255)
tGGGCTTTGGTGAAACCCGCGACGAACCGTTCGTCAGCATGGAAGGCa < 1:1657424/48‑1 (MQ=255)
tGGGCTTTGGTGAAACCCGCGACGAACCGTTCGTCAGCATGGAAGGCa < 1:372532/48‑1 (MQ=255)
tGGGCTTTGGTGAAACCCGCGACGAACCGTTCGTCAGCATGGAAGGCAAACGCGTGGTGGTCCt > 1:71409/1‑64 (MQ=255)
ggCTTTGGTGAAACCCGCGACGAACCGTTCGTCAGCATGGAAGGCa < 1:4549553/46‑1 (MQ=255)
gCTTTGGTGAAACCCGCGACGAACCGTTCGTCAGCATGGAAGGCAAACGCGTGGTGGTCCTTGGCGGTGGc > 1:999905/1‑71 (MQ=255)
gCTTTGGTGAAACCCGCGACGAACCGTTCGTCAGCATGGAAGGCAAACGCGTGGTGGTCCTTGGCGGTGGc < 1:4529076/71‑1 (MQ=255)
tttGGTGAAACCCGCGACGAACCGTTCGTCAGCATGGAAGGCAAACGCGTGGTGGTCCTTGGCGGt < 1:3191985/66‑1 (MQ=255)
tttGGTGAAACCCGCGACGAACCGTTCGTCAGCATGGAAGGCAAACGCGTGGTGGTCCTTGGCGGTGGCGa > 1:3844414/1‑71 (MQ=255)
tGGTGAAACCCGCGACGAACCGTTCGTCAGCACGGAAGGCAAACGCGTGGTGGTCCTTGGCGGTGGCGa < 1:1709769/69‑1 (MQ=255)
ggTGAAACCCGCGACGAACCGTTCGTCAGCACGGAAGGCAAACGCGTGGTGGTCCTTGGCGGTGGc < 1:4164237/66‑1 (MQ=255)
aaaCCCGCGACGAACCGTTCGTCAGCATGGAAGGCAAACGCGTGGTGGTCCTTGGCGGTGGCGACACTGc > 1:970443/1‑70 (MQ=255)
ccGCGACGAACCGTTCGTCAGCATGGAAGGCAAACGCGTGGTGGTCCTTGGCGGTGGCGACACTGCGa > 1:3680530/1‑68 (MQ=255)
ccGCGACGAACCGTTCGTCAGCATGGAAGGCAAACGCGTGGTGGTCCTTGGCGGTGGCGACACTGCGa > 1:1553173/1‑68 (MQ=255)
ccGCGACGAACCGTTCGTCAGCATGGAAGGCAAACGCGTGGTGGTCCTTGGCGGTGGCGACACTGCGATg < 1:2836347/70‑1 (MQ=255)
cgcgACGAACCGTTCGTCAGCACGGAAGGCAAACGCGTGGTGGTCCTTGGCGGTGGCGACACTGCGATGGa > 1:196306/1‑71 (MQ=255)
gcgACGAACCGTTCGTCATCATGGAAGGCAAACGCGTGGTGGTCCTTGGCGGTGGCGACACTGCGATGGAc > 1:393283/1‑71 (MQ=255)
gcgACGAACCGTTCGTCAGCATGGAAGGCAAACGCGTGGTGGTCCTTGGCGGTGGCGACACTGCGATGGAc > 1:3832757/1‑71 (MQ=255)
cgacgaACCGTTCGTCAGCACGGAAGGCAAACGCgtggt > 1:3853501/1‑39 (MQ=255)
cgacgaACCGTTCGTCAGCACGGAAGGCAAACGCGTGGTGGTCCTTGGCGGTGGCGACACTGCGATGGAc > 1:2194718/1‑70 (MQ=255)
acgaACCGTTCGTCAGCATGGAAGGCAAACGCGTGGTGGTCCTTGGCGGTGGCGACACTGCGATGGACtgc < 1:3787093/71‑1 (MQ=255)
gaACCGTTCGTCAGCATGGAAGGCAAACGCGTGGTGGTCCTTGGc < 1:1917874/45‑1 (MQ=255)
gaACCGTTCGTCAGCATGGAAGGCAAACGCGTGGTGGTCCTTGGc < 1:82898/45‑1 (MQ=255)
gaACCGTTCGTCAGCACGGAAGGCAAACGCGTGGTGGTCCTTGGCGGTGGCGACACTGc < 1:4021197/59‑1 (MQ=255)
gaACCGTTCGTCAGCACGGAAGGCAAACGCGTGGTGGTCCTTGGCGGTGGCGACACTGc < 1:2640517/59‑1 (MQ=255)
gaACCGTTCGTCAGCACGGAAGGCAAACGCGTGGTGGTCCTTGGCGGTGGCGACACTGc < 1:2014167/59‑1 (MQ=255)
aCCGTTCGTCAGCATGGAAGGCAAACGCGTGGTGGTCCTTGGCGGTGGCGACACTGCGATGGACtgcgtgc > 1:4482060/1‑71 (MQ=255)
aCCGTTCGTCAGCATGGAAGGCAAACGCGTGGTGGTCCTTGGCGGTGGCGACACTGCGATGGACtgcgtgc > 1:3239664/1‑71 (MQ=255)
aCCGTTCGTCAGCACGGAAGGCAAACGCGTGGTGGTCCTTGGCGGTGGCGACACTGCGa > 1:606664/1‑59 (MQ=255)
ccGTTCGTCAGCATGGAAGGCAAACGCGTGGTGGTCCTTGGCGGTGGCGa > 1:2768365/1‑50 (MQ=255)
ccGTTCGTCAGCATGGAAGGCAAACGCGTGGTGGTCCTTGGCGGTGGCGACACTGCGATGGACtgcgtgcg > 1:1579626/1‑71 (MQ=255)
gTTCGTCAGCACGGAAGGCAAACGCGTGGTGGTCCTTGGCGGTGGCGACTCTGCGATGGACTGCGTGCGTa < 1:2907387/71‑1 (MQ=255)
gTTCGTCAGCACGGAAGGCAAACGCGTGGTGGTCCTTGGCGGTGGCGACACTGCGATGGACTGCGTGCGTa < 1:737639/71‑1 (MQ=255)
cGTCAGCATGGAAGGCAAACGCGTGGTGGTCCTTGGCGGTGGCGac < 1:2278435/46‑1 (MQ=255)
cGTCAGCATGGAAGGCAAACGCGTGGTGGTCCTTGGCGGTGGCGACACt > 1:1084726/1‑49 (MQ=255)
gTCAGCATGGAAGGCAAACGCGTGGTGGTCCTTGGCGGTGGCGACACTGCGATGGACtgcg < 1:4087412/61‑1 (MQ=255)
gTCAGCATGGAAGGCAAACGCGTGGTGGTCCTTGGCGGTGGCGACACTGCGATGGACtgcg < 1:284451/61‑1 (MQ=255)
tCAGCATGGAAGGCAAACGCGTGGTGGTCCTTGGc < 1:1669338/35‑1 (MQ=255)
tCAGCATGGAAGGCAAACGCGTGGTGGTCCTTGGCGGTGGCGACACTGCGATGGACtg < 1:665519/58‑1 (MQ=255)
cAGCATGGAAGGCAAACGCGTGGTGGTCCTTGGCGGTGGCGACACTGCGATGGACtg < 1:2864597/57‑1 (MQ=255)
cAGCACGGAAGGCAAACGCGTGGTGGTCCTTGGCGGTGGCGACACTGCGATg < 1:3396196/52‑1 (MQ=255)
aGCACGGAAGGCAAACGCGTGGTGGTCCTTGGCGGTGGCGACACTGCGATGGACTgcgtgcgt < 1:3801288/63‑1 (MQ=255)
|
CCGTTCCTCATCGCCAACACCAAACAGTTAATGGGCTTTGGTGAAACCCGCGACGAACCGTTCGTCAGCATGGAAGGCAAACGCGTGGTGGTCCTTGGCGGTGGCGACACTGCGATGGACTGCGTGCGTA > W3110S.gb/3359836‑3359965
|
| 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
