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 I206 R1
|
206 |
23.7 |
1314362 |
96.8% |
1272302 |
86.2 |
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%
| 31.1
/ NA
| 11 | A188A (GCG→GCC) | ybaT | APC family permease |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base C (4/7); total (4/7) |
ATCCTCGTCGGCATTAAAATGATGATCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCG‑CCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATAACTTTCCTTGCCTATGCGGGCTTTGGCATGATGGCGAACGCGGCG > NZ_CP009273/508506‑508679
|
aTCCTCGTCGGCATTAAAATGATGATCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTgcg > 1:87219/1‑90 (MQ=255)
gCATTAAAATGATGATCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCG‑cccccccagc > 1:413399/1‑86 (MQ=255)
gatgatCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGt < 1:453138/90‑1 (MQ=255)
gatgatCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGt > 2:331138/1‑90 (MQ=255)
gatgatCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGt < 2:654215/90‑1 (MQ=255)
tCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGttcttc < 1:331138/90‑1 (MQ=255)
tCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGttcttc < 2:159307/90‑1 (MQ=255)
tGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTcc < 1:507162/90‑1 (MQ=255)
ttattGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATa < 2:104705/90‑1 (MQ=255)
ttGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATAAc > 1:656775/1‑89 (MQ=255)
ttGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATAAc < 2:656775/89‑1 (MQ=255)
gcgcATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATAACTTTCCTTGCCTATGCGGGCTTTGGCat > 1:573285/1‑90 (MQ=255)
ctGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATAACTTTCCTTGCCTATGCGGGCTTTGGCATGATGGCGAACgcggcg > 2:633105/1‑90 (MQ=255)
|
ATCCTCGTCGGCATTAAAATGATGATCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCG‑CCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATAACTTTCCTTGCCTATGCGGGCTTTGGCATGATGGCGAACGCGGCG > NZ_CP009273/508506‑508679
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ 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: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
ATCCTCGTCGGCATTAAAATGATGATCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCG‑CCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATAACTTTCCTTGCCTATGCGGGCTTTGGCATGATGGCGAACGCGGCGGATAAAGTGAAAGATCCG > NZ_CP009273/508506‑508697
|
ATCCTCGTCGGCATTAAAATGATGATCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGC > SRR3722088.417966/1‑100 (MQ=60)
GATGATCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTG < SRR3722088.458418/100‑1 (MQ=60)
TCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTG < SRR3722088.334571/100‑1 (MQ=60)
TGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGA < SRR3722088.513270/100‑1 (MQ=60)
TTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATAACT > SRR3722088.664907/1‑100 (MQ=60)
GCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATAACTTTCCTTGCCTATGCGGGCTTTGGCAT > SRR3722088.580316/1‑100 (MQ=60)
GCTGCAACCGGCGCATATTTCCGTCTCTGCG‑CCCCCCcctgtctcttatacacatctccgagcccacgagaccgtactagatctcgtatgccgtcttctg > SRR3722088.261323/1‑37 (MQ=60)
CCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATAACTTTCCTTGCCTATGCGGGCTTTGGCATGATGGCGAACGCGGCGGATAAAGTGAAAGATCCG > SRR3722088.564548/1‑100 (MQ=60)
|
ATCCTCGTCGGCATTAAAATGATGATCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCG‑CCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATAACTTTCCTTGCCTATGCGGGCTTTGGCATGATGGCGAACGCGGCGGATAAAGTGAAAGATCCG > NZ_CP009273/508506‑508697
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
