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 |
|
A3 F53 I1 R1
|
62 |
81.2 |
3465250 |
98.6% |
3416736 |
145.3 |
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 | 88.9%
| 22.0
/ ‑2.8
| 9 | 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 (7/1); total (7/2) |
| Fisher's exact test for biased strand distribution p-value = 2.22e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
| * | NC_002947_CJ‑RC | 1,499,498 | 0 | T | G | 88.9%
| 22.2
/ ‑5.8
| 9 | intergenic (+75/‑89) | trpS/zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein |
| Reads supporting (aligned to +/- strand): ref base T (0/0); major base G (7/1); minor base C (0/1); total (7/2) |
| Fisher's exact test for biased strand distribution p-value = 2.22e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CCAAACGGTGGGAGCGGGCGTGCCCGCGAAACAGGCGCCGCGGTGCATGGCCAC‑GGCTTTGCCGGTGTT‑TCGGG‑‑‑CACG‑CCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCAAGCAGATCTGAAACGTCCCGACTTCT > NC_002947_CJ‑RC/1499429‑1499635
||
caatccGGGGGGCGCGGGCGTGCCCGATAAACCGGCGCCGCTGTGC‑TGTGCACGGGCTGTGGCGGTGTG‑CGGGGGCCCCCC‑CCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCCACAGTGACGGCCCGTTTTttgttg < 2:133356/141‑1 (MQ=255)
cgcgAAACAGGCGCCGCGGTGCATGGCACC‑GGCTTTGCCGGTGTTCGCGGG‑‑‑CACGCCCGCTCCCCCAGACAGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTATTTGTTGACTCGCTAACGAATCATGACTCCCTTa > 5:235321/1‑148 (MQ=25)
aCAGGCGCCGCGGTGCATGGCACC‑GGCTTTGCCGGTGTTCGCGGG‑‑‑CACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGGTTTTTGTTGCCTCGCTACCGAATCATGACTCCCTTAGAACGc > 5:224595/1‑148 (MQ=37)
ggCGCCGCGGTGCATGGCACC‑GGCTTTGCCGGTGTTCGCGGG‑‑‑CACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTAt > 4:263264/1‑148 (MQ=37)
ccgcGGTGCATGGCACC‑GGCTTTGCCGGTGTTCGCGGG‑‑‑CACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGATATCAAg > 1:297577/1‑148 (MQ=37)
cacc‑GGCTTTGCCGGTGTTCGCGGG‑‑‑CACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCAAGCAGATCTGAAACg > 6:408661/4‑148 (MQ=38)
tGCCGGTGTTCGCGGG‑‑‑CACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCAAGCAGATCTGAAACGTccc < 5:141671/143‑1 (MQ=255)
tGCCGGTGTTCGCGGG‑‑‑CACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCAAGCAGATCTGAAACGTccc > 6:141671/1‑143 (MQ=255)
ccGGTGTTCGCGGG‑‑‑CACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATAGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCAAGCAGATCTGAAACGTCACGActtct > 3:125352/1‑148 (MQ=255)
||
CCAAACGGTGGGAGCGGGCGTGCCCGCGAAACAGGCGCCGCGGTGCATGGCCAC‑GGCTTTGCCGGTGTT‑TCGGG‑‑‑CACG‑CCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCAAGCAGATCTGAAACGTCCCGACTTCT > NC_002947_CJ‑RC/1499429‑1499635
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
