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 |
508,601 |
(C)6→7 |
coding (570/1293 nt) |
ybaT → |
APC family permease |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 508,595 | 1 | . | C | 100.0%
| 41.6
/ NA
| 14 | A188A (GCG→GCC) | ybaT | APC family permease |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base C (9/5); total (9/5) |
CCTCGTCGGCATTAAAATGATGATCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCG‑CCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATAACTTTCCTTGCCTATGCGGGCTTTGGCATGATGGCGAACGCGG > NZ_CP009273/508508‑508677
|
ccTCGTCGGCATTAAAATGATGATCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCG‑cc < 2:89358/90‑1 (MQ=255)
gatgatCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGt < 1:568887/90‑1 (MQ=255)
gatCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGttct < 1:273703/90‑1 (MQ=255)
tGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTcc > 2:392132/1‑90 (MQ=255)
aTTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTa < 1:92777/90‑1 (MQ=255)
tGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTAtt > 2:3294/1‑90 (MQ=255)
tGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTAtt > 2:518432/1‑90 (MQ=255)
gCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTg > 1:333860/1‑90 (MQ=255)
gCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTg > 2:582033/1‑90 (MQ=255)
gCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATAACTTTCCTTGCCTATGCgg > 2:223634/1‑90 (MQ=255)
cTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATAACTTTCCTTGCCTATGCggg > 1:323722/1‑90 (MQ=255)
aaCCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATAACTTTCCTTGCCTATGCGGGCttt < 1:195937/90‑1 (MQ=255)
cgcATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATAACTTTCCTTGCCTATGCGGGCTTTGGCatg > 2:339897/1‑90 (MQ=255)
tctcTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATAACTTTCCTTGCCTATGCGGGCTTTGGCATGATGGCGAAcgcg < 2:83145/90‑1 (MQ=255)
ctctGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATAACTTTCCTTGCCTATGCGGGCTTTGGCATGATGGCGAACgcgg > 1:229205/1‑90 (MQ=255)
|
CCTCGTCGGCATTAAAATGATGATCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCG‑CCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATAACTTTCCTTGCCTATGCGGGCTTTGGCATGATGGCGAACGCGG > NZ_CP009273/508508‑508677
|
| 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
GATGATCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCG‑CCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATAACTTTCCTTGCCTATGCGGGCTTTGGCATGATGGCGAACGCGGCGGATAAAGTGAAAGATCC > NZ_CP009273/508526‑508696
|
GATGATCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTG < SRR3722111.577835/100‑1 (MQ=60)
GATCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTAT < SRR3722111.277079/100‑1 (MQ=60)
TCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTG > SRR3722111.338327/1‑100 (MQ=60)
ATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATAAC < SRR3722111.93918/100‑1 (MQ=60)
TGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATAACTTTCCTTGCCTATGCGGG > SRR3722111.328029/1‑100 (MQ=60)
AACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATAACTTTCCTTGCCTATGCGGGCTTTGGCATGATGG < SRR3722111.198377/100‑1 (MQ=60)
ATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATAACTTTCCTTGCCTATGCGGGCTTTGGCATGATGGCGAACGCGG > SRR3722111.231965/1‑100 (MQ=60)
CCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATAACTTTCCTTGCCTATGCGGGCTTTGGCATGATGGCGAACGCGGCGGATAAAGTGAAAGATCC > SRR3722111.360499/1‑100 (MQ=60)
|
GATGATCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCG‑CCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATAACTTTCCTTGCCTATGCGGGCTTTGGCATGATGGCGAACGCGGCGGATAAAGTGAAAGATCC > NZ_CP009273/508526‑508696
|
| 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: ‑ |
