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 I211 R1
|
223 |
18.0 |
1007644 |
96.3% |
970361 |
85.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,678,723 |
A→C |
G48G (GGT→GGG) |
glyA ← |
serine hydroxymethyltransferase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,678,723 | 0 | A | C | 100.0%
| 49.0
/ NA
| 16 | G48G (GGT→GGG) | glyA | serine hydroxymethyltransferase |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base C (7/9); total (7/9) |
AGTTGTTCAACGATATCAACATACTCGCAACCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGAACCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGATGTGCTCTTCCTGACGTACTT > NZ_CP009273/2678637‑2678799
|
aGTTGTTCAACGATATCAACATACTCGCAACCGCCGTAGTAGCGTTTGCCCGAATAACCTTCAGCATATTTGTTGGTCAGCTGAGAcccc > 2:471867/1‑90 (MQ=255)
atatCAACATACTCGCAACCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGACCCCTGCGCCTGCAtt > 2:214396/1‑90 (MQ=255)
aCATACCCCCAACCGCCGTAGTAGCGTTTGCCCGAATAACCTTCAGCATATTTGTTGGTCAGCTGAGACCCCTGCGCCTGCATTAcgcgc < 1:471867/90‑1 (MQ=255)
aTACTCGCAACCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCgg > 1:189256/1‑90 (MQ=255)
aCTCGCAACCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGc > 2:389676/1‑90 (MQ=255)
gTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGa > 1:189815/1‑90 (MQ=255)
gATAACCTTCAGCATATTTGTTGGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGa < 1:101445/90‑1 (MQ=255)
aTAACCTTCAGCATATTTGTTGGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGAt < 1:438686/90‑1 (MQ=255)
tAACCTTCAGCATATTTGTTGGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGAtg < 2:487896/90‑1 (MQ=255)
cAGCATATTTGTTGGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCgg < 2:5440/49‑1 (MQ=255)
cAGCATATTTGTTGGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCgg > 1:5440/1‑49 (MQ=255)
tttGTTGGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGATGTGCTCTTCCTGACg < 2:189815/90‑1 (MQ=255)
tttGTTGGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGATGTGCTCTTCCTGACg < 1:46774/90‑1 (MQ=255)
ttgttgGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGATGTGCTCTTCCTGACGt < 1:476445/90‑1 (MQ=255)
tgGTCAGCTGAGACCCCTGCGCCTGCATTAcgcgc > 1:48612/1‑35 (MQ=38)
tgGTCAGCTGAGACCCCTGCGCCTGCATTAcgcgc < 2:48612/35‑1 (MQ=38)
tgGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGATGTGCTCTTCCTGACGTACtt > 2:364983/1‑90 (MQ=255)
|
AGTTGTTCAACGATATCAACATACTCGCAACCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGAACCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGATGTGCTCTTCCTGACGTACTT > NZ_CP009273/2678637‑2678799
|
| 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
TCGCCAGTTGTTCAACGATATCAACATACTCGCAACCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGAACCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGATGTGCTCTTCCTGACGTACTTTTTCCTGCTCCATAGCCTGCCAC > NZ_CP009273/2678632‑2678822
|
ccgccttttttcaaacaatacaaccatcccccCAACCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGACCCCTGCGC < SRR3722094.1345/68‑1 (MQ=60)
CGATATCAACATACTCGCAACCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGG > SRR3722094.191844/1‑100 (MQ=60)
ACATACCCCCAACCGCCGTAGTAGCGTTTGCCCGAATAACCTTCAGCATATTTGTTGGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGT < SRR3722094.480203/100‑1 (MQ=60)
atccccccacCCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAG < SRR3722094.51648/90‑1 (MQ=60)
CCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGA > SRR3722094.192405/1‑100 (MQ=60)
GGATAACCTTCAGCATATTTGTTGGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGctgtctcttatacacatctgacgctgccgac > SRR3722094.5526/1‑69 (MQ=60)
GATAACCTTCAGCATATTTGTTGGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGATGTGCTCTTC < SRR3722094.102901/100‑1 (MQ=60)
ATAACCTTCAGCATATTTGTTGGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGATGTGCTCTTCC < SRR3722094.446361/100‑1 (MQ=60)
GCATATTTGTTGGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTctgtctcttatacacatctgacgctgccgacgaccatcttagtgt > SRR3722094.49296/1‑55 (MQ=60)
TTTGTTGGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGATGTGCTCTTCCTGACGTACTTTTTCC < SRR3722094.47438/100‑1 (MQ=60)
TTGTTGGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGATGTGCTCTTCCTGACGTACTTTTTCCT < SRR3722094.484862/100‑1 (MQ=60)
GCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGATGTGCTCTTCCTGACGTACTTTTTCCTGCTCCATAGC > SRR3722094.10416/1‑100 (MQ=60)
GCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGATGTGCTCTTCCTGACGTACTTTTTCCTGCTCCATAGC > SRR3722094.388263/1‑100 (MQ=60)
CCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGATGTGCTCTTCCTGACGTACTTTTTCCTGCTCCATAGCCTGCCAC < SRR3722094.304259/100‑1 (MQ=60)
CCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGATGTGCTCTTCCTGACGTACTTTTTCCTGCTCCATAGCCTGCCAC < SRR3722094.4823/100‑1 (MQ=60)
|
TCGCCAGTTGTTCAACGATATCAACATACTCGCAACCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGAACCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGATGTGCTCTTCCTGACGTACTTTTTCCTGCTCCATAGCCTGCCAC > NZ_CP009273/2678632‑2678822
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
