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 I0 R1
|
248 |
61.6 |
2601574 |
98.7% |
2567753 |
146.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
NC_002947_CJ‑RC |
2,282,770 |
T→G |
20.7% |
intergenic (‑162/+67) |
PP_2010 ← / ← PP_2011 |
cytochrome b561/hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_002947_CJ‑RC | 2,282,770 | 0 | T | G | 20.7%
| 30.9
/ 6.1
| 21 | intergenic (‑162/+67) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base T (8/8); new base G (2/2); total (10/11) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.70e-01 |
TCAGGTCTGAATGGCGCTCTTGCTGGCGCTCAGGAGTCATTTTAATGGCTACCGGAAACAGATCTTTGCGCCAGGTCTGTGAAAAATGTGTTGCCAGCCACCGGCCTCTTCGCTGGCACGCCCGCTCCCACAGTCCAACTGCACAGTCTTGGAAGCCTGTGCAGTTGGACTGTGGGAGCGGGCGTGCCCGCGAAGGGGCCGGAGCAGGCGACATCAGTTACCGGGCAGATAGGGCCAGTCATCACCCACCAGAAACACCCGTTCTGCCTCCTGCCAGGCACCATCGGCATCAGG > NC_002947_CJ‑RC/2282624‑2282917
|
tcaGGTCTGAATGGCGCTCTTGCTGGCGCTCAGGAGTCATTTTAATGGCTACCGGAAACAGATCTTTGCGCCAGGTCTGTGAAAAATGTGTTGCCAGCCACCGGCCTCTTCGCTGGCACGCCCGCTCCCACAGTCCAACTGCACAGTCt < 8:253176/149‑1 (MQ=255)
ggTCTGAATGGCGCTCTTGCTGGCGCGCAGGAGTCATTTTAATGGCTACCGGAAACAGATCTTTGCGCCAGGGCTGTGAAAAATGTGTTGCCAGCCTCCGGCCCCTTCGCGGGCACGCCCGCTCCCACAGTCCAACTGCACAGGCttcc < 6:171215/149‑3 (MQ=37)
gTCTGAATGGCGCTCTTGCTGGCGCTCAGGAGTCATTTTAATGGCTACCGGAAACAGATCTTTGCGCCAGGTCTGTGAAAAATGTGTTGCCAGCCACCGGCCTCTTCGCTGGCACCCCCGCTACCACAGTCCAACAGCACAGTCTTgg > 6:113135/1‑148 (MQ=255)
tCTGAATGGCGCTCTTGCTGGCGCTCAGGAGTCATTTTAATGGCTACCGGAAACAGATCTTTGCGCCAGGTCTGTGAAAAATGTGTTGCCAGCCACCGGCCTCTTCGCTGGCACGCCCGCTCCCACAGTCCAACTGCACAGTCTTGGaa < 5:176318/149‑1 (MQ=255)
tGGCGCTCTTGCTGGCGCTCAGGAGTCATTTTAATGGCTACCGGAAACAGATCTTTGCGCCAGGTCTGTGAAAAATGTGTTGCCAGCCACCGGCCTCTTCGCTGGCACGCCCGCTCCCACAGTCCAACTGCACAGTCTTGGAAGCCtgt < 7:290750/149‑1 (MQ=255)
cgcTCTTGCTGGCGCTCAGGAGTCATTTTAATGGCTACCGGAAACAGATCTTTGCGCCAGGTCTGTGAAAAATGTGTTGCCAGCCTCCGGCCCCTTCGCGGGCACGCCCGCTCCCACAGTCCAACTGCACAGGCTTCCAAGACTGTGCa < 7:315764/149‑1 (MQ=25)
gcTCTTGCTGGCGCTCAGGAGTCATTTTAATGGCTACCGGAAACAGATCTTTGCGCCAGGTCTGTGAAAAATGTGTTGCCAGCCACCGGCCTCTTCGCTGGCACGCCCGCTCCCACACTCCAACTGCCCAGGCGTGGAATCCGGTGGAg > 6:145477/1‑149 (MQ=255)
cTGGCGCTCAGGAGTCATTTTAATGGCTACCGGAAACAGATCTTTGCGCCAGGTCTGTGAAAAATGTGTTGCCAGCCACCGGCCTCTTCGCTGGCACGCCCGCTCCCACAGTCCAACTGCACAGTCTTGGAAGCCTGTGCAGTTGGACt < 6:108118/149‑1 (MQ=255)
aGGAGTCATTTTATTGGCTACCGGAAACAGATGTTTGCGCCTGGTCTGTGAAAAATTTGTTGCCAGCCTCCGGCCTCTTCGCTGGCACGCCCGCTCCCACACCCCAACTGCACAGTCTTGGAAGCCTGTTCAGTTGGAATGTGGTAGCg < 4:161431/149‑1 (MQ=255)
tttGCGCCAGGTCTGTGAAAAATGTGTTGCCAGCCACCGGCCTCATCCCAGGCACGCCCCCACCCCCCCGCCACCAGCCCCCTCAGGGCACCCCGGGCAGTGGGACGGTGGGACCGGGCCGGCCCGCCAAGGGGccggcgccggcgcc > 6:63107/1‑146 (MQ=255)
tttGCGCCAGGTCTGTGAAAAATGTGTTGCCAGCCACCGGCCTCATACCAGGCACCCCCCCACCCACACTCCCACAGCACACTCATGGAACCCCGTGGAGGGGGACGGTGGGCGCGGGCCGGGCCGCGCAGGGGccggcgccggcgcc > 6:67866/1‑146 (MQ=255)
tGCGCCAGTTCTGTGAAAAATGTGCTGCCAGCCACCGGCCTCTTCGCTGGCACGCCCGCTCCCACAGTCCAACTGCACAGTCTTGGAAGCCTGTGCAGTTGGACTGTGGGAGCGGGCGTGCCCGCGAAGGGGCCGGAGCAGGCGa < 6:316362/145‑1 (MQ=255)
cccccGCCCCCCCGGTCCAACTGCACTTTTTTGGACCCGTGTGTTGTTGTTGTGTGGGTGGGGGGGTGCCCGCGAAGGGGCCGGAGCAGGCGACATCAGTTACCGGGCAGATAGGGCCAGTCATCACCCACCAGAAACACCCGTTCTGc < 5:113135/147‑1 (MQ=255)
cGCCCGCTCCCCCTGTCCAAGTCCACTGCGTTGGACGCCTGTGTAGTTGGACTGGGGTTGGGGGCGTGCCCGCGAAGGGGCCGGAGCAGGCGACATCAGTTACCGGGCAGATAGGGCCAGTCATCACCCACCAGAAACACCCGTTCTGc < 7:85554/149‑1 (MQ=255)
ccACAGTCCAACTGCACAGTCTTGGAAGCCTGTGCAGTTGGACTGTGGGAGCGGGCGTGCCCGCGAAGGGGCCGGAGCAGGCGACATCAGTTACCGGGCAGATAGGGCCAGTCATCACCCACCAGAAACACCCGTTCTGCCTCCTGc > 6:19290/1‑147 (MQ=255)
cAACTGCACAGTCTTGGAAGCCTGTGCAGTTGGACTGTAGGAGCGGGCGTGCCCGCGAAGGGGCCGGAGCAGGCGACATCAGTTACCGGGCAGATAGGGCCAGTCATCACCCACCAGAAACACCCGTTCTGCCTCCTGCCAGGCACCAt > 6:156581/1‑149 (MQ=255)
aaCTGCACAGTCTTGGAAGCCTGTGCAGTTGGACTGTGGGAGCGGGCGTGCCCGCGAAGGGGCCGGAGCAGGCGACATCAGTTACCGGGCAGATAGGGCCAGTCATCACCCACCAGAAACACCCGTTCTGCCTCCTGCCAGGCACCATc > 8:29457/1‑149 (MQ=255)
aaCTGCACAGGCTTCCAAGACTGTGCAGTTGGACTGTGGGAGCGGGCGTGCCCGCGAAGGGGCCGGAGCAGGCGACATCAGTTACCGGGCAGATAGGGCCAGTCATCACCCACCAGAAACACCCGTTCTGCCTCCTGCCAGGCACCATc > 5:183251/1‑149 (MQ=255)
cacaGTCTTGGAAGCCTGTGCAGTTGGACTGTGGGAGCGGGCGTGCCCGCGAAGGGGCCGGAGCAGGCGACATCAGTTACCGGGCAGATAGGGCCAGTCATCACCCACCAGAAACACCCGTTCTGCCTCCTGCCAGGCACCATCGGCAt > 5:284024/1‑149 (MQ=255)
aGTCTTGGAAGCCTGTGCAGTTGGACTGTGGGAGCGGGCGTGCCCGCGAAGGGGCCGGAGCAGGCGACATCAGTTACCGGGCAGATAGGGCCAGTCATCACCCACCAGAAACACCCGTTCTGCCTCCTGCCAGGCACCATCGGCATCAg > 1:259500/1‑149 (MQ=255)
gTCTTGGAAGCCTGTGCAGTTGGACTGTGGGAGCGGGCGTGCCCGCGAAGGGGCCGGAGCAGGCGACATCAGTTACCGGGCAGATAGGGCCAGTCATCACCCACCAGAAACACCCGTTCTGCCTCCTGCCAGGCACCATCGGCATCAgg < 2:259500/149‑1 (MQ=255)
|
TCAGGTCTGAATGGCGCTCTTGCTGGCGCTCAGGAGTCATTTTAATGGCTACCGGAAACAGATCTTTGCGCCAGGTCTGTGAAAAATGTGTTGCCAGCCACCGGCCTCTTCGCTGGCACGCCCGCTCCCACAGTCCAACTGCACAGTCTTGGAAGCCTGTGCAGTTGGACTGTGGGAGCGGGCGTGCCCGCGAAGGGGCCGGAGCAGGCGACATCAGTTACCGGGCAGATAGGGCCAGTCATCACCCACCAGAAACACCCGTTCTGCCTCCTGCCAGGCACCATCGGCATCAGG > NC_002947_CJ‑RC/2282624‑2282917
|
| 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
