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 I195 R1
|
222 |
27.1 |
1551108 |
96.0% |
1489063 |
86.0 |
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%
| 37.4
/ NA
| 12 | G48G (GGT→GGG) | glyA | serine hydroxymethyltransferase |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base C (6/6); total (6/6) |
AGTTGTTCAACGATATCAACATACTCGCAACCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGAACCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGATGTGCTCTTCCTGACGTACTT > NZ_CP009273/2678637‑2678799
|
aGTTGTTCAACGATATCAACATACTCGCAACCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGAcccc > 2:93292/1‑90 (MQ=255)
tttgtaCAACAATATCACCATCCTCCCAACCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGACCCCt < 1:427209/89‑1 (MQ=255)
aaaCGATATAAACATCCCCGAAACCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGACCCCTGCGCCt < 2:179516/89‑1 (MQ=255)
gATATCAACATACTCGCAACCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGACCCCTGCGCCTGCAt > 1:168285/1‑90 (MQ=255)
tacaaaCATCCCCCCACCCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGACCCCTGCGCCTGCATTa < 1:663482/86‑1 (MQ=255)
aCATCCCCGCACCCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGACCCCTGCGCCTGCATTAcgcgc < 1:396831/90‑1 (MQ=255)
ccgTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGttt > 2:721271/1‑90 (MQ=255)
ggATAACCTTCAGCATATTTGTTGGTAAGCTGAGACCCCTGCGCCGGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCg > 1:188924/1‑90 (MQ=255)
atTTGTTGGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGATGTGc > 1:296702/1‑80 (MQ=255)
atTTGTTGGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGATGTGc < 2:296702/80‑1 (MQ=255)
atTTGTTGGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGATGTGCTCTTCCTGAc > 1:473731/1‑90 (MQ=255)
tttGTTGGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGATGTGCTCTTCCTGACg < 1:721271/90‑1 (MQ=255)
tgGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGATGTGCTCTTCCTGACGTACtt > 2:224262/1‑90 (MQ=255)
|
AGTTGTTCAACGATATCAACATACTCGCAACCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGAACCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGATGTGCTCTTCCTGACGTACTT > NZ_CP009273/2678637‑2678799
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 24 ≤ 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
CGATCGATCGCCAGTTGTTCAACGATATCAACATACTCGCAACCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGAACCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGATGTGCTCTTCCTGACGTACTTTTTCCTGCTCCATAGC > NZ_CP009273/2678625‑2678815
|
gcaccgcccccgttttgttcaaaaataccaacacccccccacCCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGACC < SRR3722073.631011/58‑1 (MQ=60)
cgtccgaccgcctgttttcaaacaataacaacatcctcccacCCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGACC < SRR3722073.466567/58‑1 (MQ=60)
agatcgatcgcctgttttccaacaataaaAACATCCTCGCACCCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGACC < SRR3722073.759908/71‑1 (MQ=60)
ttttttaaacaATATCAACATCCCCGCACCCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGACCCCTGCGCCTGCAT < SRR3722073.508521/89‑1 (MQ=60)
TTTGTACAACAATATCACCATCCTCCCAACCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGACCCCTGCGCCTGCAT < SRR3722073.436347/100‑1 (MQ=60)
GTTGTTCAACGATATCAACATACTCGCAACCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGACCCCTGCGCCTGCAT > SRR3722073.171601/1‑100 (MQ=60)
tacaaacatccccccacCCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCT < SRR3722073.677083/83‑1 (MQ=60)
aataaacacactccCAACCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCT < SRR3722073.111551/86‑1 (MQ=60)
caccgagatctacacactgcatatcgtcggcagcgtcagatgtgtataagagacagGGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGT < SRR3722073.410273/44‑1 (MQ=60)
ACATCCCCGCACCCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGT < SRR3722073.405281/100‑1 (MQ=60)
GCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTAAGCTGAGACCCCTGCGCCGGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCG > SRR3722073.192660/1‑100 (MQ=60)
CCTTCAGCATATTTGTTGGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGATGTGCTCTTCCTGAC > SRR3722073.302984/1‑100 (MQ=60)
CCTTCAGCATATTTGTTGGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGATGTGCTCTTCCTGAC > SRR3722073.483818/1‑100 (MQ=60)
TTTGTTGGTCAGCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGATGTGCTCTTCCTGACGTACTTTTTCC < SRR3722073.735841/100‑1 (MQ=60)
GCTGAGACCCCTGCGCCTGCATTGCGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGATGTGCTCTTCCTGACGTACTTTTTCCTGCTCCATAGC > SRR3722073.253330/1‑100 (MQ=60)
GCTGAGACCCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGATGTGCTCTTCCTGACGTACTTTTTCCTGCTCCATAGC > SRR3722073.255006/1‑100 (MQ=60)
|
CGATCGATCGCCAGTTGTTCAACGATATCAACATACTCGCAACCGCCGTAGTAGCGTTTGCCCGGATAACCTTCAGCATATTTGTTGGTCAGCTGAGAACCCTGCGCCTGCATTACGCGCGGGCTGGTGTAGTTTTCGGAGGCGATCAGTTCGATGTGCTCTTCCTGACGTACTTTTTCCTGCTCCATAGC > NZ_CP009273/2678625‑2678815
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
