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 |
|
A5 F26 I1 R1
|
57 |
84.6 |
3443374 |
98.5% |
3391723 |
147.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_002947_CJ‑RC |
5,558,423 |
+GCC |
intergenic (‑84/+87) |
PP_4887 ← / ← PP_4888 |
hypothetical protein/methyl‑accepting chemotaxis transducer |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_002947_CJ‑RC | 5,558,423 | 1 | . | G | 84.6%
| 26.2
/ ‑4.1
| 15 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| Reads supporting (aligned to +/- strand): ref base . (0/2); major base G (5/6); minor base C (0/2); total (5/10) |
| Fisher's exact test for biased strand distribution p-value = 4.87e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
| * | NC_002947_CJ‑RC | 5,558,423 | 2 | . | C | 86.7%
| 42.3
/ 0.5
| 15 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| Reads supporting (aligned to +/- strand): ref base . (0/2); new base C (5/8); total (5/10) |
| Fisher's exact test for biased strand distribution p-value = 5.24e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
| * | NC_002947_CJ‑RC | 5,558,423 | 3 | . | C | 86.7%
| 43.0
/ 0.5
| 15 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| Reads supporting (aligned to +/- strand): ref base . (0/2); new base C (5/8); total (5/10) |
| Fisher's exact test for biased strand distribution p-value = 5.24e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCAT‑‑‑A‑‑‑GCG‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCG > NC_002947_CJ‑RC/5558308‑5558550
|||
tGGGCCGCGATTTGGCGGGCGTACATGAGAAACTCATTTTGTCTTGTGTCGCCGACAGAATAGCAACACCGCTCTGGTGTGGGCGCGGCCTTGTGGCGCTAAAGGGCCGCAT‑‑‑A‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGCAACAAAc < 4:55666/148‑1 (MQ=255)
tGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCTAAAGGGCCGCAT‑‑‑A‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGCAACAAAc < 6:75522/148‑1 (MQ=38)
ctggcaTTAGGCGGGCGTACTTGTGCAAGTCGTTTTGTCTTGTGGCGCCGACTGCTTAGCAACACGGCTCAGGTGGGTGAGCTGGCTTGTGTCGGGAAAGGGCCTCATTGGG‑‑‑GCC‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTgg < 8:333239/143‑1 (MQ=255)
aGCTATTTGGCGGGCGGACATGACCAACTCCTTTTGTCATGTGTCGCCGACAGAATAGAAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCAT‑‑‑A‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTggg < 7:320768/148‑1 (MQ=37)
tAGGCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCAT‑‑‑A‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGgctgc < 2:363148/147‑1 (MQ=38)
gcGGGCGGACATTAGCAACTCCTTTTGTCTTGTGTCGCCGACAGCATAGCAACCCCGCTCAGGTGTGGGAGCGGCCTTTTGTCGCTAACGGGCCGCAT‑‑‑A‑‑‑GCGCCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTAt < 3:144403/146‑1 (MQ=255)
gggCGGACATGACCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACCCCGCTCTGGTGGGGGAGCGGCCTTGTGTCGCGAACGGGCCGCAT‑‑‑A‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTACTATGCa < 6:293429/148‑1 (MQ=37)
aTGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCAT‑‑‑AGGGGCC‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTc < 6:104500/148‑1 (MQ=38)
aaaCTCCTTTTGTCTTGTGTCGCCGACAGAATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTTTGTCGCTAAAGGGCCGAAT‑‑‑A‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGa < 2:122716/146‑1 (MQ=255)
ttGGGTCGCTAACGGCCCGCAT‑‑‑A‑‑‑GCGCCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACGCAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAg < 7:14986/148‑1 (MQ=255)
gtgtCGCGAAAGGGCCGCAT‑‑‑A‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGc > 4:147249/1‑147 (MQ=255)
gtCGCGAAAGGGCCGCAT‑‑‑A‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGCCCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGa > 5:196744/1‑148 (MQ=38)
tCGCGAAAGGGCCGCAT‑‑‑A‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAg > 4:114856/1‑148 (MQ=255)
gcgAAAGGGCCGCAT‑‑‑A‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgcc > 8:280642/1‑148 (MQ=255)
aGGGCCGCAT‑‑‑A‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgccg > 7:363396/1‑144 (MQ=255)
|||
TGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCAT‑‑‑A‑‑‑GCG‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCG > NC_002947_CJ‑RC/5558308‑5558550
|
| 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
