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 |
|
A2 F56 I1 R1
|
57 |
68.1 |
2900404 |
98.5% |
2856897 |
146.6 |
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 | 93.8%
| 47.6
/ ‑2.6
| 16 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| Reads supporting (aligned to +/- strand): ref base . (0/1); new base G (9/6); total (9/7) |
| Fisher's exact test for biased strand distribution p-value = 4.38e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.28e-01 |
| * | NC_002947_CJ‑RC | 5,558,423 | 2 | . | C | 93.8%
| 49.7
/ ‑2.8
| 16 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| Reads supporting (aligned to +/- strand): ref base . (0/1); new base C (9/6); total (9/7) |
| Fisher's exact test for biased strand distribution p-value = 4.38e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
| * | NC_002947_CJ‑RC | 5,558,423 | 3 | . | C | 93.8%
| 49.3
/ ‑2.8
| 16 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| Reads supporting (aligned to +/- strand): ref base . (0/1); new base C (9/6); total (9/7) |
| Fisher's exact test for biased strand distribution p-value = 4.38e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GCTGTCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCG‑‑‑CC‑‑‑GGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCGC > NC_002947_CJ‑RC/5558277‑5558551
|||
gCTGTCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAgcgg > 7:64/1‑147 (MQ=255)
aGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAgcggc > 6:358119/1‑134 (MQ=255)
aGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAgcggc < 5:358119/136‑3 (MQ=255)
gggcGGCCGGGGCAGCTATTAGTCGGGCGTAAATGAGCAACTCCTTTTGTCATGTGTCGCCTACAGAATAGCAACACCGCTCAGGTGTGGTAGCGGCCTTGTGTCGCTAAAGGGCCGAATAGCGGCCCC‑‑‑GGCAATTTCCGCGTGTATg < 8:64/145‑1 (MQ=255)
cTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCTAAAGGGCCGCATAGCGGCCCC‑‑‑GGCAATTTCCGCGTGTATGCAACAAAc < 6:146405/149‑1 (MQ=38)
gCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCTGGTGTGGTAGCGGCCTTGTGTCGCTAAAGGGCCGCATAGCGGCCCC‑‑‑GGCAATTTCCGCGTGTATGCAACAAACCTgg < 1:47371/149‑1 (MQ=255)
aGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCGGCCCC‑‑‑GGCAATTTCCGCGTGTATGCAACAAACCTgggg > 5:10645/1‑149 (MQ=255)
tggggggCGTACTTGCGAAACTCTTTTTGTCTTGGGGCGCCTACAGCATAGCAACACCGGTCTGGGGTGGGTGCGGCCTTGTGTCGCTATGGGGCCGAATAGCGGCCCC‑‑‑GGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTa < 4:327428/144‑1 (MQ=255)
cATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCGGCCCC‑‑‑GGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCATAGCAGccccagg < 6:10645/149‑5 (MQ=37)
ccTTGTGTCGCGAAAGGGCCGCATAGCGGCCCC‑‑‑GGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGgcgcg > 2:63123/1‑147 (MQ=255)
ttGTGTCGCGAAAGGGCCGCATAGCGGCCCC‑‑‑GGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAg > 7:302113/1‑148 (MQ=255)
gtgtCGCGAAAGGGCCGCATAGCGGCCCC‑‑‑GGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCt > 2:90522/1‑148 (MQ=255)
tgtCGCTAACGGGCCGCATAGCGGCCCC‑‑‑GGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCt < 8:213682/147‑1 (MQ=38)
tgtCGCGAAAGGGCCGCATAGCGGCCCC‑‑‑GGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCt > 1:30980/1‑147 (MQ=255)
tCGCGAAAGGGCCGCATAGCGGCCCC‑‑‑GGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgc > 4:287260/1‑149 (MQ=255)
gcgAAAGGGCCGCATAGCGGCCCC‑‑‑GGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgcc > 7:206950/1‑148 (MQ=255)
ctaatgggCCGAATAGCG‑‑‑CCCCGGGCATTTTCCGCGTGTATCCAACAAACGTGGGGCTGCTATGCAGCCCTTTCGCTACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgcc < 8:84749/142‑1 (MQ=255)
cgAAAGGGCCGCATAGCGGCCCC‑‑‑GGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCCGGCTGGCGCGCAGCTGcgccgc > 5:24259/1‑149 (MQ=38)
cgAAAGGGCCGCATAGCGGCCCC‑‑‑GGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgccgc > 6:152805/1‑149 (MQ=255)
|||
GCTGTCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCG‑‑‑CC‑‑‑GGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCGC > NC_002947_CJ‑RC/5558277‑5558551
|
| 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
