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 F14 I1 R1
|
58 |
76.7 |
3323998 |
98.6% |
3277462 |
146.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_002947_CJ‑RC |
1,499,498 |
1 bp→CG |
intergenic (+75/‑89) |
trpS → / → zapE |
tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_002947_CJ‑RC | 1,499,497 | 1 | . | C | 92.3%
| 35.9
/ ‑2.5
| 13 | intergenic (+74/‑90) | trpS/zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein |
| Reads supporting (aligned to +/- strand): ref base . (0/1); new base C (11/1); total (11/2) |
| Fisher's exact test for biased strand distribution p-value = 1.54e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.87e-01 |
| * | NC_002947_CJ‑RC | 1,499,498 | 0 | T | G | 100.0%
| 38.7
/ NA
| 13 | intergenic (+75/‑89) | trpS/zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base G (11/2); total (11/2) |
AGGCTGCCAAACGGTGGGAGCGGGCGTGCCCGCGAAACAGGCGCCGCGGTGCATGGCCA‑CGGCTTTGCCGGTGT‑T‑TCGGGCACG‑CCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCAAGCAGATCTGAAACGTCCCGACTTCTTCCATGA > NC_002947_CJ‑RC/1499423‑1499642
||
aGGCTGCCAAACGGTGGTTGCGGGCGTGCCCGCTAAACAGGCGCCGCGGTGCATGGAAC‑GGGCTTTGCGGGTGT‑TCGCGGGCACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTttgt < 2:249608/149‑1 (MQ=25)
ccGGCCGTCCCCGCCAACCCGGCCCCGCGGT‑CCCGGCCACCGGCTTGGCCGGTGTCC‑GCGGCCACGCCCGCTCACACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCAt < 2:410132/148‑1 (MQ=255)
gCGTGCCCGCGAAACAGGCGCCGCGGTGCATGGCAC‑CGGCTTTGCCGGTGT‑TCGCGGGCACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACt > 6:71427/1‑149 (MQ=37)
ccGCGAAACAGGCGCCGCGGTGCATGGCAC‑CGGCTTTGCCGGTGT‑TCGCGGGCACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCt > 8:422406/1‑147 (MQ=37)
cgcgAAACAGGCGCCGCGGTGCATGGCAC‑CGGCTTTGCCGGTGT‑TCGCGGGCACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCt > 2:91812/1‑146 (MQ=37)
cgcgAAACAGGCGCCGCGGTGCATGGCAC‑CGGCTTTGCCGGTGT‑TCGCGGGCACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCt > 8:102798/1‑146 (MQ=37)
cgcgAAACAGGCGCCGCGGTGCATGGCAC‑CGGCTTTGCCGGTGT‑TCGCGGGCACGCCCGCGCCCACAGACTGATTGCCATTAATCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTACCt > 3:55100/1‑146 (MQ=25)
aGGCGCCGCGGTGCATGGCAC‑CGGCTTTGCCGGTGT‑TCGCGGGCACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTa > 5:216177/1‑148 (MQ=37)
gccgcGGTGCATGGCAC‑CGGCTTTGCCGGTGT‑TCGCGGGCACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCAAg > 6:385519/1‑149 (MQ=37)
ggcaccGGCTTTGCCGGTGT‑TCGCGGGCACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGAAGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCAAGCAGATCTGAAAc > 5:326405/6‑149 (MQ=38)
accGGCTTTGCCGGTGT‑TCGCGGGCACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCAAGCAGATCTGAAACGTc > 1:301056/3‑149 (MQ=38)
cGGCTTTGCCGGTGT‑TCGCGGGCACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCAAGCAGATCTGAAACGTccc > 4:195331/1‑149 (MQ=39)
tttGCCGGTGT‑TCGCGGGCACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCAAGCAGATCTGAAACGTCCCGAct > 8:216857/1‑149 (MQ=39)
ttcgcGGGCACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCAAGCAGATCTGAAACGTCCCGACTTCTTCCATGa > 8:52671/5‑149 (MQ=255)
||
AGGCTGCCAAACGGTGGGAGCGGGCGTGCCCGCGAAACAGGCGCCGCGGTGCATGGCCA‑CGGCTTTGCCGGTGT‑T‑TCGGGCACG‑CCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCAAGCAGATCTGAAACGTCCCGACTTCTTCCATGA > NC_002947_CJ‑RC/1499423‑1499642
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
