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 F2 I230 R1
|
226 |
18.8 |
1048726 |
96.7% |
1014118 |
86.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
4,104,266 |
G→C |
G45G (GGC→GGG) |
fpr ← |
ferredoxin‑‑NADP(+) reductase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,104,266 | 0 | G | C | 93.3%
| 89.6
/ 0.1
| 30 | G45G (GGC→GGG) | fpr | ferredoxin‑‑NADP(+) reductase |
| Reads supporting (aligned to +/- strand): ref base G (1/1); new base C (15/13); total (16/14) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.88e-01 |
ATCGGGGACGGTGACCAGGTAAAACTCCAGATCGGGATTATCGGGCGAGTTTACATAGGAGTAGGCGCGCTGGACGCGTTCGCCGTCGATTTCAAGGCCAAGCTTGGTAAATTGCCCGGCGGTAAACGGAAGCACGGGGGCGTGAACGGTGAGACTAAACAGGGCGT > NZ_CP009273/4104185‑4104351
|
aTCGGGGACGGTGACCAGGTAAAACTCCAGATCGGGATTATCGGGCGAGTTTACATAGGAGTAGGCGCGCTGGACGCGTTCCCCGTCGAt < 1:314655/90‑1 (MQ=255)
gTGACCAGGTAAAACTCCAGATCGGGATTATCGGGCGAGTTTACATAGGAGTAGGCGCGCTGGACGCGTTCCCCGTCGATTTCAAGGCCa < 2:8932/90‑1 (MQ=255)
aGGTAAAACTCCAGATCGGGATTATCGGGCGAGTTTACATAGGAGTAGGCGCGCTGGACGCGTTCCCCGTCGATTTCAAGGCCAAGCTTg > 1:265227/1‑90 (MQ=255)
ccAGATCGGGATTATCGGGCGAGTTTACATAGGAGTAGGCGCGCTGGACGCGTTCCCCGTCGATTTCAAGGCCAAGCTTGGTAAATTGcc > 1:6037/1‑90 (MQ=255)
cAGATCGGGATTATCGGGCGAGTTTACATAGGAGTAGGCGCGCTGGACGCGTTCCCCGTCGATTTCAAGGCCAAGCTTGGTAAATTGccc < 2:403136/90‑1 (MQ=255)
cAGATCGGGATTATCGGGCGAGTTTACATAGGAGTAGGCGCGCTGGACGCGTTCCCCGTCGATTTCAAGGCCAAGCTTGGTAAATTGccc < 1:56637/90‑1 (MQ=255)
gCGAGTTTACATAGGAGTAGGCGCGCTGGACGCGTTCCCCGTCGATTTCAAGGCCAAGCTTGGTAAATTGccc < 2:519474/73‑1 (MQ=255)
gCGAGTTTACATAGGAGTAGGCGCGCTGGACGCGTTCCCCGTCGATTTCAAGGCCAAGCTTGGTAAATTGccc > 1:519474/1‑73 (MQ=255)
gCGAGTTTACATAGGAGTAGGCGCGCTGGACGCGTTCCCCGTCGATTTCAAGGCCAAGCTTGGTAAATTGCCCGGCGGTAAACGGAAGCa > 1:151080/1‑90 (MQ=255)
aGTTTACATAGGAGTAGGCGCGCTGGACGCGTTCCCCGTCGATTTCAAGGCCAAGCTTGGTAAATTGCCCGGCGGTAAACGGAAGCACgg < 1:282821/90‑1 (MQ=255)
tACATAGGAGTAGGCGCGCTGGACGCGTTCCCCGTCGATTTCAAGGCCAAGCTTGGTAAATTGCCCGGCGGTAAACGGAAGCACGGGGGc > 1:298011/1‑90 (MQ=255)
ggAGTAGGCGCGCTGGACGCGTTCCCCGTCGATTTCAAGGCCAAGCTTGGTAAATTGCCCGGCGGTAAACGGAAGCACGGGGGCGTGAAc > 2:350406/1‑90 (MQ=255)
ggAGTAGGCGCGCTGGACGCGTTCCCCGTCGATTTCAAGGCCAAGCTTGGTAAATTGCCCGGCGGTAAACGGAAGCACGGGGGCGTGAAc > 1:201801/1‑90 (MQ=255)
ggAGAAGGCGCGCTGGACGCGTTCCCCGTCGATTTCAAGGCCAAGCTTGGTAAATTGCCCGGCGGTAAACGGAAGCACGGGGGCGTGAAc > 1:309899/1‑90 (MQ=255)
gAGTAGGCGCGCTGGACGCGTTCCCCGTCGATTTCAAGGCCAAGCTTGGTAAATTGCCCGGCGGTAAACGGAAGCACGGGGGCGTGAACg > 2:52200/1‑90 (MQ=255)
gTAGGCGCGCTGGACGCGTTCCCCGTCGATTTCAAGGCCAAGCTTGGTAAATTGCCCGGCGGTAAACGGAAGCACGGGGGCGTGAACGGt > 1:523360/1‑90 (MQ=255)
gTAGGCGCGCTGGACGCGTTCCCCGTCGATTTCAAGGCCAAGCTTGGTAAATTGCCCGGCGGTAAACGGAAGCACGGGGGCGTGAACGGt < 1:176322/90‑1 (MQ=255)
gTAGGCGCGCTGGACGCGTTCCCCGTCGATTTCAAGGCCAAGCTTGGTAAATTGCCCGGCGGTAAACGGAAGCACGGGGGCGTGAACGGt < 1:101456/90‑1 (MQ=255)
aGGCGCGCTGGACGCGTTCCCCGTCGATTTCAAGGCCAAGCTTGGTAAATTGCCCGGCGGTAAACGGAAGCACGGGGGCGTGAACGGTga > 2:63248/1‑90 (MQ=255)
aGGCGCGCTGGACGCGTTCCCCGTCGATTTCAAGGCCAAGCTTGGTAAATTGCCCGGCGGTAAACGGAAGCACGGGGGCGTGAACGGTga > 1:130377/1‑90 (MQ=255)
aGGCGCGCTGGACGCGTTCCCCGTCGATTTCAAGGCCAAGCTTGGTAAATTGCCCGGCGGTAAACGGAAGCACGGGGGCGTGAACGGTga < 2:309899/90‑1 (MQ=255)
aGGCGCGCTGGACGCGTTCCCCGTCGATTTCAAGGCCAAGCTTGGTAAATTGCCCGGCGGTAAACGGAAGCACGGGGGCGTGAACGGTga < 2:21858/90‑1 (MQ=255)
cgcgcTGGACGCGTTCCCCGTCGATTTCAAGGCCAGGCTTGGTAAATTGCCCGGCGGTAAACGGAAGCACGGGGGCGTGAACGGTGAGAc > 1:79510/1‑90 (MQ=255)
cgcgcTGGACGCGTTCCCCGTCGATTTCAAGGCCAAGCTTGGTAAATTGCCCGGCGGTAAACGGAAGCACGGGGGCGTGAACGGTGAGAc < 2:46856/90‑1 (MQ=255)
cgcTGGACGCGTTCCCCGTCGATTTCAAGGCCAAGCTTGGTAAATTGCCCGGCGGTAAACGGAAGCACGGGGGCGTGAACGGTGAGACTa > 2:472549/1‑90 (MQ=255)
gcTGGACGCGTTCGCCGTCGATTTCAAGGCCAAGCTTGGTAAATTGCCCGGCGGTAAACGGa < 2:498140/62‑1 (MQ=255)
gcTGGACGCGTTCGCCGTCGATTTCAAGGCCAAGCTTGGTAAATTGCCCGGCGGTAAACGGa > 1:498140/1‑62 (MQ=255)
aCGCGTTCCCCGTCGATTTCAAGGCCAAGCTTGGTAAATTGCCCGGCGGTAAACGGAAGCACGGGGGCGTGAACGGTGAGACTAAACAgg < 2:130377/90‑1 (MQ=255)
aCGCGTTCCCCGTCGATTTCAAGGCCAAGCTTGGTAAATTGCCCGGCGGTAAACGGAAGCACGGGGGCGTGAACGGTGAGACTAAACAgg < 1:97856/90‑1 (MQ=255)
gTTCCCCGTCGATTTCAAGGCCAAGCTTGGTAAATTGCCCGGCGGTAAACGGAAGCACGGGGGCGTGAACGGTGAGACTAAACAGGGCGt > 2:34551/1‑90 (MQ=255)
|
ATCGGGGACGGTGACCAGGTAAAACTCCAGATCGGGATTATCGGGCGAGTTTACATAGGAGTAGGCGCGCTGGACGCGTTCGCCGTCGATTTCAAGGCCAAGCTTGGTAAATTGCCCGGCGGTAAACGGAAGCACGGGGGCGTGAACGGTGAGACTAAACAGGGCGT > NZ_CP009273/4104185‑4104351
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
ATCGGGGACGGTGACCAGGTAAAACTCCAGATCGGGATTATCGGGCGAGTTTACATAGGAGTAGGCGCGCTGGACGCGTTCGCCGTCGATTTCAAGGCCAAGCTTGGTAAATTGCCCGGCGGTAAACGGAAGCACGGGGGCGTGAACGGTGAGACTAAACAGGGCGTCGGTCCAGT > NZ_CP009273/4104185‑4104360
|
ATCGGGGACGGTGACCAGGTAAAACTCCAGATCGGGATTATCGGGCGAGTTTACATAGGAGTAGGCGCGCTGGACGCGTTCCCCGTCGATTTCAAGGCCA < SRR3722114.318023/100‑1 (MQ=60)
GACGGTGACCAGGTAAAACTCCAGATCGGGATTATCGGGCGAGTTTACATAGGAGTAGGCGCGCTGGACGCGTTCCCCGTCGATTTCAAGGCCAAGCTTG > SRR3722114.267935/1‑100 (MQ=60)
AGGTAAAACTCCAGATCGGGATTATCGGGCGAGTTTACATAGGAGTAGGCGCGCTGGACGCGTTCCCCGTCGATTTCAAGGCCAAGCTTGGTAAATTGCC > SRR3722114.6099/1‑100 (MQ=60)
CAGATCGGGATTATCGGGCGAGTTTACATAGGAGTAGGCGCGCTGGACGCGTTCCCCGTCGATTTCAAGGCCAAGCTTGGTAAATTGCCCGGCGGTAAAC < SRR3722114.57195/100‑1 (MQ=60)
GGATTATCGGGCGAGTTTACATAGGAGTAGGCGCGCTGGACGCGTTCCCCGTCGATTTCAAGGCCAAGCTTGGTAAATTGCCCGGCGGTAAACctgtctc > SRR3722114.525988/1‑93 (MQ=60)
GGATTATCGGGCGAGTTTACATAGGAGTAGGCGCGCTGGACGCGTTCCCCGTCGATTTCAAGGCCAAGCTTGGTAAATTGCCCGGCGGTAAACGGAAGCA > SRR3722114.152609/1‑100 (MQ=60)
CGGGCGAGTTTACATAGGAGTAGGCGCGCTGGACGCGTTCCCCGTCGATTTCAAGGCCAAGCTTGGTAAATTGCCCGGCGGTAAACGGAAGCACGGGGGC > SRR3722114.301185/1‑100 (MQ=60)
AGTTTACATAGGAGTAGGCGCGCTGGACGCGTTCCCCGTCGATTTCAAGGCCAAGCTTGGTAAATTGCCCGGCGGTAAACGGAAGCACGGGGGCGTGAAC > SRR3722114.203764/1‑100 (MQ=60)
AGTTTACATAGGAGTAGGCGCGCTGGACGCGTTCCCCGTCGATTTCAAGGCCAAGCTTGGTAAATTGCCCGGCGGTAAACGGAAGCACGGGGGCGTGAAC < SRR3722114.285788/100‑1 (MQ=60)
AGTTTACATAGGAGAAGGCGCGCTGGACGCGTTCCCCGTCGATTTCAAGGCCAAGCTTGGTAAATTGCCCGGCGGTAAACGGAAGCACGGGGGCGTGAAC > SRR3722114.313202/1‑100 (MQ=60)
TTACATAGGAGTAGGCGCGCTGGACGCGTTCCCCGTCGATTTCAAGGCCAAGCTTGGTAAATTGCCCGGCGGTAAACGGAAGCACGGGGGCGTGAACGGT > SRR3722114.529909/1‑100 (MQ=60)
ACATAGGAGTAGGCGCGCTGGACGCGTTCCCCGTCGATTTCAAGGCCAAGCTTGGTAAATTGCCCGGCGGTAAACGGAAGCACGGGGGCGTGAACGGTGA > SRR3722114.131734/1‑100 (MQ=60)
TAGGAGTAGGCGCGCTGGACGCGTTCCCCGTCGATTTCAAGGCCAGGCTTGGTAAATTGCCCGGCGGTAAACGGAAGCACGGGGGCGTGAACGGTGAGAC > SRR3722114.80346/1‑100 (MQ=60)
GAGTAGGCGCGCTGGACGCGTTCGCCGTCGATTTCAAGGCCAAGCTTGGTAAATTGCCCGGCGGTAAACGGAAGCACGGGGGCtgtctcttatacacatc > SRR3722114.504382/1‑83 (MQ=60)
GTAGGCGCGCTGGACGCGTTCCCCGTCGATTTCAAGGCCAAGCTTGGTAAATTGCCCGGCGGTAAACGGAAGCACGGGGGCGTGAACGGTGAGACTAAAC < SRR3722114.178076/100‑1 (MQ=60)
GTAGGCGCGCTGGACGCGTTCCCCGTCGATTTCAAGGCCAAGCTTGGTAAATTGCCCGGCGGTAAACGGAAGCACGGGGGCGTGAACGGTGAGACTAAAC < SRR3722114.102519/100‑1 (MQ=60)
ACGCGTTCCCCGTCGATTTCAAGGCCAAGCTTGGTAAATTGCCCGGCGGTAAACGGAAGCACGGGGGCGTGAACGGTGAGACTAAACAGGGCGTCGGTCC < SRR3722114.98889/100‑1 (MQ=60)
CGTTCCCCGTCGATTTCAAGGCCAAGCTTGGTAAATTGCCCGGCGGTAAACGGAAGCACGGGGGCGTGAACGGTGAGACTAAACAGGGCGTCGGTCCAGT > SRR3722114.104497/1‑100 (MQ=60)
|
ATCGGGGACGGTGACCAGGTAAAACTCCAGATCGGGATTATCGGGCGAGTTTACATAGGAGTAGGCGCGCTGGACGCGTTCGCCGTCGATTTCAAGGCCAAGCTTGGTAAATTGCCCGGCGGTAAACGGAAGCACGGGGGCGTGAACGGTGAGACTAAACAGGGCGTCGGTCCAGT > NZ_CP009273/4104185‑4104360
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
