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 F4 I88 R1
|
217 |
30.5 |
1742422 |
95.9% |
1670982 |
87.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
469,392 |
T→C |
L324P (CTC→CCC) |
amtB → |
ammonium transporter AmtB |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 469,392 | 0 | T | C | 100.0%
| 60.4
/ NA
| 18 | L324P (CTC→CCC) | amtB | ammonium transporter AmtB |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (9/9); total (9/9) |
ACGCCAGCCTGCGGCTACATTGGGGTTGGCGGCGCGTTGATTATCGGCGTGGTAGCTGGTCTGGCGGGCTTGTGGGGCGTTACCATGCTCAAACGCTTGCTGCGGGTGGATGATCCCTGCGATGTCTTCGGTGTGCACGGCGTTTGTGGCATTGTCGGCTGTATCATGA > NZ_CP009273/469304‑469472
|
aCGCCAGCCTGCGGCTACATTGGGGTTGGCGGCGCGTTGATTATCGGCGTGGTAGCTGGTCTGGCGGGCTTGTGGGGCGTTACCATGCCCa > 1:651231/1‑91 (MQ=255)
cTACATTGGGGTTGGCGGCGCGTTGATTATCGGCGTGGTAGCTGGTCTGGCGGGCTTGTGGGGCGTTACCATGCCCAAACGCTTGCTGCgg < 2:651231/91‑1 (MQ=255)
tACATTGGGGTTGGCGGCGCGTTGATTATCGGCGTGGTAGCTGGTCTGGCGGGCTTGTGGGGCGTTACCATGCCCAAACGCTTGCTGCggg > 1:176965/1‑91 (MQ=255)
ggggTTGGCGGCGCGTTGATTATCGGCGTGGTAGCTGGTCTGGCGGGCTTGTGGGGCGTTACCATGCCCAAACGCTTGCTGCGGGTGgatg < 2:617920/91‑1 (MQ=255)
ggggTTGGCGGCGCGTTGATTATCGGCGTGGTAGCTGGTCTGGCGGGCTTGTGGGGCGTTACCATGCCCAAACGCTTGCTGCGGGTGgatg < 2:361321/91‑1 (MQ=255)
ggTTGGCGGCGCGTTGATTATCGGCGTGATAGCTGGTCTGGCGGGCTTGTGGGGCGTTACCATGCCCAAACGCTTGCTGCGGGTGgatgat > 1:276531/1‑91 (MQ=255)
ggcggcGCGTTGATTATCGGCGTGGTAGCTGGTCTGGCGGGCTTGTGGGGCGTTTCCATGCCCAAACGCTTGCTGCGGGGGGGTGATTCCt > 2:441785/1‑91 (MQ=255)
gcggcgCGTTGATTATCGGCGTGGTAGCTGGTCTGGCGGGCTTGTGGGGCGTTACCATGCCCAAACGCTTGCTGCGGGTGGATGATCCCTg > 2:737537/1‑91 (MQ=255)
ggcgCGTTGATTATCGGCGTGGTAGCTGGTCTGGCGGGCTTGTGGGGCGTTACCATGCCCAAACGCTTGCTGCGGGTGGATGATCCCTGCg < 1:401832/91‑1 (MQ=255)
ggcgCGTTGATTATCGGCGTGGTAGCTGGTCTGGCGGGCTTGTGGGGCGTTACCATGCCCAAACGCTTGCTGCGGGTGGATGATCCCTGCg < 1:182890/91‑1 (MQ=255)
tGATTATCGGCGTGGTAGCTGGTCTGGCGGGCTTGTGGGGCGTTACCATGCCCAAACGCTTGCTGCGGGTGGATGATCCCTGCGATGTCtt < 2:101100/91‑1 (MQ=255)
gTGGTAGCTGGTCTGGCGGGCTTGTGGGGCGTTACCATGCCCAAACGCTTGCTGCGGGTGGATGATCCCTGCGATGTCTTCGGTGTGCACg > 1:121306/1‑91 (MQ=255)
tGGCGGGCTTGTGGGGCGTTACCATGCCCAAACGCTTGCTGCGGGTGGATGATCCCTGCGATGTCTTCGGTGTGCACGGCGTTTGTGGCAt > 2:173040/1‑91 (MQ=255)
gCGGGCTTGTGGGGCGTTACCATGCCCAAACGCTTGCTGCGGGTGGATGATCCCTGCGATGTCTTCGGTGTGCACGGCGTTTGTGGCATTg < 2:106364/91‑1 (MQ=255)
gCGGGCTTGTGGGGCGTTACCATGCCCAAACGCTTGCTGCGGGTGGATGATCCCTGCGATGTCTTCGGTGTGCACGGCGTTTGTGGCATTg < 2:704680/91‑1 (MQ=255)
ttGTGGGGCGTTACCATGCCCAAACGCTTGCTGCGGGTGGATGATCCCTGCGATGTCTTCGGTGTGCACGGCGTTTGTGGCATTGTCGGCt < 2:293575/91‑1 (MQ=255)
tgGGGCGTTACCATGCCCAAACGCTTGCTGCGGGTGGATGATCCCTGCGATGTCTTCGGTGTGCACGGCGTTTGTGGCATTGTCGGCTGTa > 2:358651/1‑91 (MQ=255)
gTTACCATGCCCAAACGCTTGCTGCGGGTGGATGATCCCTGCGATGTCTTCGGTGTGCACGGCGTTTGTGGCATTGTCGGCTGTATCATGa > 1:183197/1‑91 (MQ=255)
|
ACGCCAGCCTGCGGCTACATTGGGGTTGGCGGCGCGTTGATTATCGGCGTGGTAGCTGGTCTGGCGGGCTTGTGGGGCGTTACCATGCTCAAACGCTTGCTGCGGGTGGATGATCCCTGCGATGTCTTCGGTGTGCACGGCGTTTGTGGCATTGTCGGCTGTATCATGA > NZ_CP009273/469304‑469472
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GGTCGGCGTGACGCCAGCCTGCGGCTACATTGGGGTTGGCGGCGCGTTGATTATCGGCGTGGTAGCTGGTCTGGCGGGCTTGTGGGGCGTTACCATGCTCAAACGCTTGCTGCGGGTGGATGATCCCTGCGATGTCTTCGGTGTGCACGGCGTTTGTGGCATTGTCGGCTGTATCATGACCGGGATT > NZ_CP009273/469294‑469480
|
GGTCGGCGTGACGCCAGCCTGCGGCTACATTGGGGTTGGCGGCGCGTTGATTATCGGCGTGGTAGCTGGTCTGGCGGGCTTGTGGGGCGTTACCATGCCCA > SRR3722118.665307/1‑101 (MQ=60)
AGCCTGCGGCTACATTGGGGTTGGCGGCGCGTTGATTATCGGCGTGGTAGCTGGTCTGGCGGGCTTGTGGGGCGTTACCATGCCCAAACGCTTGCTGCGGG > SRR3722118.180443/1‑101 (MQ=60)
GCTACATTGGGGTTGGCGGCGCGTTGATTATCGGCGTGATAGCTGGTCTGGCGGGCTTGTGGGGCGTTACCATGCCCAAACGCTTGCTGCGGGTGGATGAT > SRR3722118.282207/1‑101 (MQ=60)
GGCGCGTTGATTATCGGCGTGGTAGCTGGTCTGGCGGGCTTGTGGGGCGTTACCATGCCCAAACGCTTGCTGCGGGTGGATGATCCCTGCGATGTCTTCGG < SRR3722118.186499/101‑1 (MQ=60)
GGCGCGTTGATTATCGGCGTGGTAGCTGGTCTGGCGGGCTTGTGGGGCGTTACCATGCCCAAACGCTTGCTGCGGGTGGATGATCCCTGCGATGTCTTCGG < SRR3722118.410267/101‑1 (MQ=60)
GATTATCGGCGTGGTAGCTGGTCTGGCGGGCTTGTGGGGCGTTACCATGCCCAAACGCTTGCTGCGGGTGGATGATCCCTGCGATGTCTTCGGTGTGCACG > SRR3722118.123575/1‑101 (MQ=60)
CTTGTGGGGCGTTACCATGCCCAAACGCTTGCTGCGGGTGGATGATCCCTGCGATGTCTTCGGTGTGCACGGCGTTTGTGGCATTGTCGGCTGTATCATGA > SRR3722118.186809/1‑101 (MQ=60)
GCGTTACCATGCCCAAACGCTTGCTGCGGGTGGATGATCCCTGCGATGTCTTCGGTGTGCACGGCGTTTGTGGCATTGTCGGCTGTATCATGACCGGGATT > SRR3722118.472943/1‑101 (MQ=60)
|
GGTCGGCGTGACGCCAGCCTGCGGCTACATTGGGGTTGGCGGCGCGTTGATTATCGGCGTGGTAGCTGGTCTGGCGGGCTTGTGGGGCGTTACCATGCTCAAACGCTTGCTGCGGGTGGATGATCCCTGCGATGTCTTCGGTGTGCACGGCGTTTGTGGCATTGTCGGCTGTATCATGACCGGGATT > NZ_CP009273/469294‑469480
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
