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 I227 R1
|
223 |
21.3 |
1167702 |
97.0% |
1132670 |
86.4 |
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 | 88.9%
| 51.7
/ 0.3
| 18 | I115N (ATC→AAC) | phnM | alpha‑D‑ribose 1‑methylphosphonate 5‑triphosphate diphosphatase |
| Reads supporting (aligned to +/- strand): ref base A (1/1); new base T (6/10); total (7/11) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.07e-01 |
GCAGTTCGCAGCGCAGATGCAGACGGTGCTCGGCGCGGTTGACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGATCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACGGCATCCAGTACGGTGGTGATGCCGCT > NZ_CP009273/4306618‑4306777
|
gCAGTTCGCAGCGCAGATGCAGACGGTGCTCGGCGCGGTTGACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAGAt < 2:253053/90‑1 (MQ=255)
cagATGCAGACGGTGCTCGGCGCGGTTGACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAg < 2:78067/75‑1 (MQ=255)
cagATGCAGACGGTGCTCGGCGCGGTTGACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAg > 1:78067/1‑75 (MQ=255)
cagATGCAGACGGTGCTCGGCGCGGTTGACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATc > 1:329657/1‑90 (MQ=255)
gCAGACGGTGCTCGGCGCGGTTGACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATcgccgc < 2:1297/90‑1 (MQ=255)
gTTGACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAAt > 1:121496/1‑90 (MQ=255)
cgTTTCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACGGCa < 2:511199/90‑1 (MQ=255)
cgTTTCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACGGCa > 1:380492/1‑90 (MQ=255)
gTTTCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACGGCAt < 2:426497/90‑1 (MQ=255)
ttCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACGGCATcc < 1:539762/90‑1 (MQ=255)
ttCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACGGCATcc < 1:416513/90‑1 (MQ=255)
ttCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACGGCATcc < 2:421329/90‑1 (MQ=255)
cGTCTCTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACGGCATCCAGTAc < 2:121496/90‑1 (MQ=255)
tctcTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACGGCATCCAGTACgg > 2:401423/1‑90 (MQ=255)
ctctTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACGGCATCCAGTACggt < 2:380492/90‑1 (MQ=255)
aTGGCGTTGATCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACgg > 1:342507/1‑70 (MQ=255)
aTGGCGTTGATCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACgg < 2:342507/70‑1 (MQ=255)
gCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACGGCATCCAGTACGGTGGTGATGCCg > 1:146855/1‑90 (MQ=255)
gttgttCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACGGCATCCAGTACGGTGGTGATGCCGCt < 2:33760/90‑1 (MQ=255)
gttgttCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACGGCATCCAGTACGGTGGTGATGCCGCt > 1:338241/1‑90 (MQ=255)
gttgttCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACGGCATCCAGTACGGTGGTGATGCCGCt > 2:7959/1‑90 (MQ=255)
|
GCAGTTCGCAGCGCAGATGCAGACGGTGCTCGGCGCGGTTGACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGATCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACGGCATCCAGTACGGTGGTGATGCCGCT > NZ_CP009273/4306618‑4306777
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ 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
CGTGGTGTGATGCGGCAGTTCGCAGCGCAGATGCAGACGGTGCTCGGCGCGGTTGACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGATCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACGGCATCCAGTACGGTGGTGATGCCGCT > NZ_CP009273/4306604‑4306777
|
CGTGGTGTGATGCGGCAGTTCGCAGCGCAGATGCAGACGGTGCTCGGCGCGGTTGACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCC < SRR3722111.567090/100‑1 (MQ=60)
ATGCGGCAGTTCGCAGCGCAGATGCAGACGGTGCTCGGCGCGGTTGACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGATCctgtctcttatacacatc > SRR3722111.98248/1‑82 (MQ=60)
GTTCGCAGCGCAGATGCAGACGGTGCTCGGCGCGGTTGACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCtgtc > SRR3722111.79011/1‑96 (MQ=60)
GTTCGCAGCGCAGATGCAGACGGTGCTCGGCGCGGTTGACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATC > SRR3722111.334077/1‑100 (MQ=60)
GCTCGGCGCGGTTGACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAAT > SRR3722111.123020/1‑100 (MQ=60)
GTTGACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACGGCA > SRR3722111.385953/1‑100 (MQ=60)
agcgtcagatgtgtataagagacaGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACGGCATCCAGT < SRR3722111.367568/76‑1 (MQ=60)
TTCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACGGCATCCAGTACGGTGG < SRR3722111.422653/100‑1 (MQ=60)
TTCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACGGCATCCAGTACGGTGG < SRR3722111.548251/100‑1 (MQ=60)
CGTCTCTTCGATGGCGTTGATCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACGGCATCCAGTACctgtctctta > SRR3722111.347087/1‑90 (MQ=60)
CTCTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACGGCATCCAGTACGGTGGTGATGCCG > SRR3722111.148705/1‑100 (MQ=60)
CTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACGGCATCCAGTACGGTGGTGATGCCGCT > SRR3722111.342768/1‑100 (MQ=60)
|
CGTGGTGTGATGCGGCAGTTCGCAGCGCAGATGCAGACGGTGCTCGGCGCGGTTGACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGATCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACGGCATCCAGTACGGTGGTGATGCCGCT > NZ_CP009273/4306604‑4306777
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
