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 F48 I1 R1
|
58 |
71.3 |
3054194 |
98.3% |
3002272 |
146.3 |
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 | 91.7%
| 16.1
/ ‑4.0
| 12 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| Reads supporting (aligned to +/- strand): ref base . (0/0); major base G (4/7); minor base C (0/1); total (4/8) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.79e-01 |
| * | NC_002947_CJ‑RC | 5,558,423 | 2 | . | C | 100.0%
| 37.0
/ NA
| 12 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base C (4/8); total (4/8) |
| * | NC_002947_CJ‑RC | 5,558,423 | 3 | . | C | 100.0%
| 37.5
/ NA
| 12 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base C (4/8); total (4/8) |
CGCTGTCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCG‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCG > NC_002947_CJ‑RC/5558276‑5558550
|||
cGCTGTCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAgcg < 1:62747/148‑1 (MQ=255)
cGCTGTCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAgcg < 7:152876/148‑1 (MQ=255)
tCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAgcggccc < 4:183108/147‑5 (MQ=255)
ccggTCGGCCGGGGCCGCGATTTGGCGGGCGCACATGAGCAACTCTTTTTGTCATGTGCCGCCGACAGCATAGCAACCCCGCTCTGGGGGGGGCGCGGCCTTGTGGCGCCAACGGCCCCCATCGCGGCCCCGGCAATTTCCGCGTGTAt < 4:78488/147‑1 (MQ=255)
gCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTgg < 6:97802/149‑1 (MQ=255)
ttAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCGGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCGGCCCCGGCAATTTcc > 1:225798/1‑121 (MQ=37)
ggcGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACACCAAACCAACACCACTCAGGTGTGGGAGCGGCCTTGGGTCGCGAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATg < 4:161612/147‑1 (MQ=255)
gTCGGGCGTACATCAGCAACTCCTTTTGTATTGTGGCCCCGACAGAAAAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCTAACGGGCCGCATCGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATg < 7:193036/149‑1 (MQ=25)
ttacaaaCTCCTTTTGTCATGTGGCGCCGACAGAATACCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCTAACGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTcgc < 6:4905/144‑1 (MQ=37)
tGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGGGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTcgc < 2:207549/149‑1 (MQ=38)
tGAGCAACCCCTTTTGTCATGGGGCCCCGACAGCATACCAACCCCGCTCCGGGGGGGGCGCGGCCTTGTGCCGCTAACGGCCCGCATAGCGCCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTcgc < 5:21865/149‑1 (MQ=255)
aGCGGCCTGGTGGCGCCAACGGGCCCCATCGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGgc < 8:111171/149‑1 (MQ=38)
gtgtCGCGAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTg > 6:101648/1‑149 (MQ=255)
tCGCGAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCCGCCCGTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAAATGGCCCCGGCTGGCGCGCCGCTGAgc > 3:352752/1‑149 (MQ=255)
gcgAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgccg > 5:333898/1‑149 (MQ=255)
|||
CGCTGTCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCG‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCG > NC_002947_CJ‑RC/5558276‑5558550
|
| 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
