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 I229 R1
|
214 |
17.4 |
943020 |
97.5% |
919444 |
87.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
4,306,692 |
A→T |
I115N (ATC→AAC) |
phnM ← |
alpha‑D‑ribose 1‑methylphosphonate 5‑triphosphate diphosphatase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,306,692 | 0 | A | T | 100.0%
| 40.9
/ NA
| 12 | I115N (ATC→AAC) | phnM | alpha‑D‑ribose 1‑methylphosphonate 5‑triphosphate diphosphatase |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base T (5/7); total (5/7) |
GTGGTGTGATGCGGCAGTTCGCAGCGCAGATGCAGACGGTGCTCGGCGCGGTTGACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGATCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACGGCATCCAGTACGGTGGTGATGCCGC > NZ_CP009273/4306605‑4306776
|
gtggtgTGATGCGGCAGTTCGCAGCGCAGATGCAGACGGTGCTCGGCGCGGTTGACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGttc > 2:61751/1‑90 (MQ=255)
gtgtGATGCGGCAGTTCGCAGCGCAGATGCAGACGGTGCTCGGCGCGGTTGACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGttcatc < 1:376854/90‑1 (MQ=255)
cGGCAGTTCGCAGCGCAGATGCAGACGGTGCTCGGCGCGGTTGACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAg < 2:280980/90‑1 (MQ=255)
gCAGTTCGCAGCGCAGATGCAGACGGTGCTCGGCGCGGTTGACGCCGCGTTTCTGCGGCTCTTCGATGGCGTTGTTCATCTTCTCCAGAt > 2:3848/1‑90 (MQ=255)
cagcgcagATGCAGACGGTGCTCGGCGCGGTTGACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGc < 2:47061/90‑1 (MQ=255)
cagATGCAGACGGTGCTCGGCGCGGTTGACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATc > 2:161864/1‑90 (MQ=255)
aGACGGTGCTCGGCGCGGTTGACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGccgccg > 1:159364/1‑90 (MQ=255)
gTGCTCGGCGCGGTTGACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTcgcg > 1:394447/1‑90 (MQ=255)
tGCTCGGCGCGGTTGACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCgcgc < 1:392349/90‑1 (MQ=255)
gACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGc < 2:242011/90‑1 (MQ=255)
cgcgTTTCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACgg < 2:380730/90‑1 (MQ=255)
gCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACGGCa < 1:305564/69‑1 (MQ=255)
gCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACGGCa > 2:305564/1‑69 (MQ=255)
cGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACGGCATCCAGTACGGTGGTGATGCCGc < 1:275749/90‑1 (MQ=255)
|
GTGGTGTGATGCGGCAGTTCGCAGCGCAGATGCAGACGGTGCTCGGCGCGGTTGACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGATCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACGGCATCCAGTACGGTGGTGATGCCGC > NZ_CP009273/4306605‑4306776
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 31 ≤ 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
GTGTGATGCGGCAGTTCGCAGCGCAGATGCAGACGGTGCTCGGCGCGGTTGACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGATCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACGGCATCCAGTACGGTGGTGATGCCGCTCGCCACCATCAGC > NZ_CP009273/4306608‑4306790
|
GTGTGATGCGGCAGTTCGCAGCGCAGATGCAGACGGTGCTCGGCGCGGTTGACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAGAT < SRR3722113.380763/100‑1 (MQ=60)
GCGCAGATGCAGACGGTGCTCGGCGCGGTTGACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCG > SRR3722113.160677/1‑100 (MQ=60)
GATGCAGACGGTGCTCGGCGCGGTTGACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCG > SRR3722113.398580/1‑100 (MQ=60)
TGCTCGGCGCGGTTGACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAA < SRR3722113.396459/100‑1 (MQ=60)
ataagagacagCTCTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACGGCATCCAGTACGG < SRR3722113.308501/89‑1 (MQ=60)
CGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACGGCATCCAGTACGGTGGTGATGCCGCTCGCCACCAT < SRR3722113.278174/100‑1 (MQ=60)
GTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACGGCATCCAGTACGGTGGTGATGCCGCTCGCCACCATCAGC > SRR3722113.351431/1‑100 (MQ=60)
|
GTGTGATGCGGCAGTTCGCAGCGCAGATGCAGACGGTGCTCGGCGCGGTTGACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGATCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACGGCATCCAGTACGGTGGTGATGCCGCTCGCCACCATCAGC > NZ_CP009273/4306608‑4306790
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
