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 F64 I1 R1
|
60 |
70.4 |
2989830 |
98.5% |
2944982 |
146.7 |
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%
| 47.9
/ NA
| 16 | 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 (8/8); total (8/8) |
| * | NC_002947_CJ‑RC | 5,558,423 | 2 | . | C | 100.0%
| 49.8
/ NA
| 16 | 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 (8/8); total (8/8) |
| * | NC_002947_CJ‑RC | 5,558,423 | 3 | . | C | 100.0%
| 49.9
/ NA
| 16 | 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 (8/8); total (8/8) |
AGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCG‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGC‑GCGCAGCTGAGCCGCCAGATC > NC_002947_CJ‑RC/5558290‑5558557
|||
aGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCCTAGCGGCCCCGGCAATTTcc > 3:274969/1‑149 (MQ=38)
tCGGCCTGGGCAGCGATTAGCCGGGCGTACATGAGAAACTCCTTTTGTCATGTGTCGCCGAAAGCATAGCAACACCGCTCTGGTGTGGGAGCGGCCTTGTGTCGCTAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGcaa < 8:277580/149‑1 (MQ=37)
ggCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCTAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTg < 6:184030/149‑1 (MQ=38)
gCATCGATTAGTGGGGGGTAATTGTGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACGGCTCTGGTGTGGGAGCGGCCTTGTGTCGCTAATGGGCCGCATTGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTgg < 2:226509/149‑1 (MQ=25)
ttAGTCGGCGGTACATGAGCAACTCCTTTTGTCATGTGCCGCCGACAGCATAGAAACACCGCCCTGGTGTGGGTGCGGCCTTGTGTCGCGAAAGGCCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGgctgc < 8:306394/148‑1 (MQ=25)
tGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTcgc < 2:32977/149‑1 (MQ=255)
tCGCCTACAGATTAGAAACACCGCTCTGGTGTGGGTGCGGCTTTGTGTCGCTAATGGGCCGAATTGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACGTGGGGCTGCTATGAAGCCCTTTCGCGAAACAAGGCCCACAAAGGAcc < 8:100196/148‑1 (MQ=255)
gAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCt > 7:378987/1‑87 (MQ=21)
gAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCt < 8:378987/87‑1 (MQ=21)
cTTGTGTCGCGAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGGCCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGC‑GCGCAg > 3:95967/1‑149 (MQ=38)
ttGTGTCGCGAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCATCAGGCCCGGAACTGGCCCAGGCTGGC‑GCGCAg > 2:240586/1‑148 (MQ=38)
tgtCGCGAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGC‑GCGCAGCt > 6:326668/1‑147 (MQ=255)
gcgAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGC‑GCGCAGCTGAgccg > 5:139831/1‑149 (MQ=255)
aGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGC‑GCGCAGCTGAgccgc > 6:53954/1‑145 (MQ=255)
ggCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGGCTCAGCTGCG‑CGCCAgcct < 2:207048/149‑4 (MQ=255)
ggCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGC‑GCGCAGCTGAGCCGCCAGat > 2:293646/1‑148 (MQ=255)
|||
AGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCG‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGC‑GCGCAGCTGAGCCGCCAGATC > NC_002947_CJ‑RC/5558290‑5558557
|
| 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
