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 |
|
A6 F21 I0 R1
|
2169 |
63.0 |
3952800 |
76.2% |
3012033 |
62.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
832,094 |
C→T |
15.0% |
D184D (GAC→GAT) |
narG → |
nitrate reductase 1, alpha subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 832,094 | 0 | C | T | 15.0%
| 150.0
/ 14.1
| 60 | D184D (GAC→GAT) | narG | nitrate reductase 1, alpha subunit |
| Reads supporting (aligned to +/- strand): ref base C (24/27); new base T (2/7); total (26/34) |
| Fisher's exact test for biased strand distribution p-value = 2.76e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TTCCTGGCAGGAGGTGAACGAACTGATCGCCGCATCTAACGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCTTACGCATCGGGTGCACGCTATCTC > minE/832025‑832163
|
ttcCTGGCAGGAGGTGAACGAACTGATCTCCGCATCTAACGTTTACACCATCAAAAACTACGGCCCGGAcc > 1:2541407/1‑71 (MQ=255)
tcCTGGCAGGAGGTGAACGAACTGATCGCCGCATCTAACGTTTACACCATCAAAAACTACGGCCCGGACCg > 1:1909914/1‑71 (MQ=255)
ccTGGCAGGAGGTGAACGAACTGATCGCCGCATCTAACGTTTACACCATCAAAAACTACGGCCCGGACCgt > 1:677371/1‑71 (MQ=255)
cTGGCAGGAGGTGAACGAACTGATCGCCGCATCTAACGTTTACACCATCAAAAACTACGGCCCGGACCgtg < 1:2900557/71‑1 (MQ=255)
ggCAGGAGGTGAACGAACTGATCGCCGCATCTAACGTTTACACCATCAAAAACTACGGCCCGGACCGTGtt > 1:119835/1‑71 (MQ=255)
gCAGGAGGTGAACGAACTGATCGCCGCATCTAACGTTTACACCATCAAAAACTACGGCCCGGACCgtgt < 1:2940158/69‑1 (MQ=255)
gCAGGAGGTGAACGAACTGATCGCCGCATCTAACGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTg < 1:196690/71‑1 (MQ=255)
gaggTGAACGAACTGATCGCCGCATCTAACGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTgg < 1:2809470/71‑1 (MQ=255)
gTGAACGAACTGATCGCCGCATCTAACGTTTACACCATCAAAAACTACGGCCCTGACCGTGTTGCTGGt < 1:3855664/69‑1 (MQ=255)
gaacgaacTGATCGCCGCATCTAACGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTgg > 1:788178/1‑66 (MQ=255)
gaacgaacTGATCGCCGCATCTAACGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGttt < 1:351880/69‑1 (MQ=255)
aacgaacTGATCGCCGCATCTAACGTTTACACCATCAAAAACTACGGCCCGGACCgtg < 1:2537009/58‑1 (MQ=255)
tGATCGCCGCATCTAACGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAAtt > 1:1041434/1‑71 (MQ=255)
tCGCCGCATCTAACGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGttt < 1:2612761/58‑1 (MQ=255)
tgccgccGCTAACGTCTGGACCATCAAAACCTACGGCCCGGATCGCGTTGCCGGTTTCTCGCCGATCCCgg > 1:935703/2‑71 (MQ=255)
cgccgcATCTAACGTTTACACCATCAAAAACTACGGCCCGGAcc > 1:634622/1‑44 (MQ=255)
cgccgcATCTAACGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCg > 1:1298201/1‑70 (MQ=255)
cgccgcATCTAACGTTTACACCATCAAAAACTACGGCCCCGACCGTGTTGCTGGTTTCTCGCCAATTCCgg > 1:3104682/1‑71 (MQ=255)
gccgccGCTAACGTCTGGACCATCAAAACCTACGGCCCGGATCGCGTTGCCGGTTTCTCGCCGATCCCgg < 1:3031776/70‑1 (MQ=255)
gcATCTAACGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAAt < 1:2560064/71‑1 (MQ=255)
gcATCTAACGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAAt < 1:2572548/71‑1 (MQ=255)
cATCTAACGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATg > 1:3678561/1‑71 (MQ=255)
cgcTAACGTCTGGACCATCAAAACCTACGGCCCGGATCGCGTTGCCGGTTTCTCGCCGATCCCGGCGATGt < 1:636593/69‑1 (MQ=255)
cgcTAACGTCTGGACCATCAAAACCTACGGCCCGGATCGCGTTGCCGGTTTCTCGCCGATCCCGGCGATGt < 1:3671646/69‑1 (MQ=255)
cTAACGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTc > 1:3169106/1‑70 (MQ=255)
aCGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCg < 1:3300731/68‑1 (MQ=255)
ttACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGtt > 1:1988771/1‑70 (MQ=255)
tACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGttt < 1:866329/70‑1 (MQ=255)
tACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTc > 1:3519133/1‑71 (MQ=255)
gacCATCAAAACTTACGGCCCGGATCGCGTTGCCGGTTTCTCGCCGATCCCGGCGATGTCGATGGttt < 1:2066270/67‑1 (MQ=255)
gacCATCAAAACCTACGGCCCGGATCGCGTTGCCGGTTTCTCGCCGATCCCGGCGATGTCGATGGTTTCtt < 1:1990199/70‑1 (MQ=255)
cacCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCtt < 1:1292348/71‑1 (MQ=255)
acCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCt < 1:3504019/69‑1 (MQ=255)
acCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCTTa > 1:3564092/1‑71 (MQ=255)
ccATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCTTAc < 1:3482110/71‑1 (MQ=255)
cATCAAAACCTACGGCCCGGATCGCGTTGCCGGTTTCTCGCCGATCCCGGCGATGTCGATGGTTTCTTACg < 1:2068268/71‑1 (MQ=255)
aaaacCTACGGCCCGGATCGCGTTGCCGGTTTCTCGCCGATCCCGGCGATGTCGATGGTTTCTTACGccg < 1:757389/70‑3 (MQ=255)
aaaCTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCaa > 1:2730605/1‑47 (MQ=255)
aaaCTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCaa > 1:2802201/1‑47 (MQ=255)
aaaCTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCTTACGCATCgg < 1:3312136/71‑1 (MQ=255)
aaaCTACGGCCCGGACCGTGTTGCTGGTTTATCGCCAATTCCGGCaa > 1:942336/1‑47 (MQ=255)
aaCTACGGCCCGGACCGTGTTGCTGGTTTCTCGcc > 1:1054923/1‑35 (MQ=255)
aaCTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCTTACGCATCggg < 1:3059410/71‑1 (MQ=255)
aaCTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCTTACGCATCgg > 1:371405/1‑70 (MQ=255)
cTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCtt < 1:2516922/59‑1 (MQ=255)
aCGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCTTa > 1:204929/1‑58 (MQ=255)
cGGCCCGGATCGCGTTGCCGGTTTCTCGCCGATCCCGGCGATGTCGATGGtt > 1:1641533/1‑52 (MQ=255)
cGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCTTACGCATCGGGTGCa < 1:1010444/70‑1 (MQ=255)
ggCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGa > 1:2791558/1‑46 (MQ=255)
ggCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGa > 1:3263008/1‑46 (MQ=255)
gCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGtt < 1:2548387/50‑1 (MQ=255)
ccGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCTTACGCATCGGGTGCACGCTa > 1:436276/1‑71 (MQ=255)
ggACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCTTACGCATCGGGTGCACGCTAtc > 1:3637623/1‑71 (MQ=255)
ggACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCTTACGCATCGGGTGCACGCTAtc > 1:616363/1‑71 (MQ=255)
gACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTc < 1:2185862/38‑1 (MQ=255)
gACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATgg > 1:1314347/1‑43 (MQ=255)
gACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATg < 1:1062666/42‑1 (MQ=255)
gACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATg < 1:2907780/42‑1 (MQ=255)
gACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATg < 1:954096/42‑1 (MQ=255)
gACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCTTACGCATCGGGTGCACGCTAtct < 1:1066680/71‑1 (MQ=255)
gACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCTTACGCATCGGGTGCACGCTAtct < 1:1695461/71‑1 (MQ=255)
aCCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCTTACGCATCGGGTGCACGCTAtctc < 1:14805/71‑1 (MQ=255)
|
TTCCTGGCAGGAGGTGAACGAACTGATCGCCGCATCTAACGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCTTACGCATCGGGTGCACGCTATCTC > minE/832025‑832163
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
