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 F55 I1 R1
|
61 |
67.4 |
2858014 |
98.3% |
2809427 |
146.5 |
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 | 100.0%
| 22.8
/ NA
| 11 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base G (4/7); total (4/7) |
| * | NC_002947_CJ‑RC | 5,558,423 | 2 | . | C | 100.0%
| 33.2
/ NA
| 11 | 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 (4/7); total (4/7) |
| * | NC_002947_CJ‑RC | 5,558,423 | 3 | . | C | 100.0%
| 33.2
/ NA
| 11 | 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 (4/7); total (4/7) |
CGCTGTCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCG‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCGCCAGAT > NC_002947_CJ‑RC/5558276‑5558556
|||
cGCTGTCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAgcg < 1:2638/148‑1 (MQ=255)
cACTCTCCAGCAAATCCAGGGCGCCCGGGGCAGCGATTCGGCGGGCGGACATGCGCAACTCCTTTTGTCATGTGCCCCCGCCAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGCCGCGAACGGGCCGCATAgcggccccgg < 4:325148/149‑8 (MQ=255)
atttCAGGGCGGCCGGGGCAGCGATTCGTCGGGCGGACATGAGCAACTCCTTTTGTCTTGTGTCGCCGACAGCATAGCAACACCGCTCTGGTGTGGGAGCGGCCTTGTGTCGCGAATGGGCCGAATAGCGGCCCCGGCAATTTCCGCgt < 2:135599/147‑1 (MQ=37)
gggCGGACATGAGCAACTCTTTTTGTAATGTGTCGCCGACAGCATAGCAACACCGCTCTGGTGTGGGAGGGGCGTTGTGTCGCTAATGGGCCGAATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCa < 8:79686/148‑1 (MQ=255)
gggCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCACATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCa < 1:103129/148‑1 (MQ=38)
cGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCTAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGcc < 6:19400/148‑1 (MQ=38)
cATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATTGCAACACCGCTCTGGTGGGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTc < 8:298295/149‑1 (MQ=38)
aGCAACTCTTTTTGTATTGTGGCGCCGACACAATAGCAACACCGCTCTGGGGTGGCAGCGGCCTTGTGGCGCTAACGGGCCGAATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGa < 1:135879/149‑1 (MQ=255)
aaCACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCgtgt > 7:256060/1‑73 (MQ=17)
gctttGTGTCGCTAATGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGgcgcgc < 8:364940/146‑1 (MQ=38)
ccTTGTGTCGCGAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGgcgcg > 7:107556/1‑147 (MQ=255)
ggCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACaaa > 5:93670/1‑87 (MQ=37)
ggCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCGCCAGat > 2:155166/1‑148 (MQ=255)
|||
CGCTGTCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCG‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCGCCAGAT > NC_002947_CJ‑RC/5558276‑5558556
|
| 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
