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 F20 I1 R1
|
61 |
89.3 |
4078092 |
98.3% |
4008764 |
146.1 |
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 | 91.7%
| 26.4
/ ‑2.5
| 12 | 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 (4/7); 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 = 4.76e-01 |
| * | NC_002947_CJ‑RC | 5,558,423 | 2 | . | C | 91.7%
| 32.4
/ ‑2.4
| 12 | 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 (4/7); 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 = 1.00e+00 |
| * | NC_002947_CJ‑RC | 5,558,423 | 3 | . | C | 91.7%
| 32.4
/ ‑2.4
| 12 | 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 (4/7); 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 = 9.85e-01 |
AGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATA‑‑‑GCG‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCGC > NC_002947_CJ‑RC/5558290‑5558551
|||
cgtaaaTTCTGGTGGGCGTGGGCTGGGATTAGGCGGGCGTACATGAGCAACTCCTTTTGTCTTGTGTCGCCGACTGAATAGCAACACCGCTCTGGTGTGGGAGCGGCCTTGTGTCGCTAATGGGCCGCATA‑‑‑GCGGCCCCGGCAATTTcc < 4:166954/146‑1 (MQ=21)
gCAGCGTTTAGTCGGGCGGAAATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATACCAACCCCGCTCTGGTGTGGGAGCGGCCTTGGGTCGCTAACGGGCCGCATC‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTgg < 2:212428/149‑1 (MQ=255)
gctaTTTGTCGGGCGTACATGAGCAACTCCTTTTGTCATGTGTCGCCTACAGCATAGAAACACCGCTCAGGTTTGGGAGCGGCCTTGTGTCGCTAATGGGCCGCATA‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGc < 6:448841/132‑1 (MQ=25)
gCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATA‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGc > 5:448841/1‑135 (MQ=38)
ttAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATA‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGgctgc < 5:250305/148‑1 (MQ=255)
cGGGCGCAAATGAGCAACTCCTTTTGTCATGGGGCGCCGACAGCAAAGCAACACCGCTCTGGTGTGGGAGCGGCCTTGTGTCGCTAAAGGGCCGCATAGGGGCC‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCa < 1:46126/149‑1 (MQ=37)
ggCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATA‑‑‑GCGGCCCCGGCAATTTAcgc > 1:340509/1‑116 (MQ=25)
ccGGACATGAGCAACTCCTTTTGTCATGTGTCCCCGACAGCATACCACCACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCTAAAGGGCCGCATT‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGcc < 2:185302/148‑1 (MQ=37)
taGCAACTCCTTTTGTCATGTGGCGCCGACAGCATAGCAACCCCGCTCTGGTGTGGGAGCGGCCTTGGGGCGCTAACGGGCCGCATA‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTcgc < 7:255328/147‑1 (MQ=255)
ggAGCGGCCTTGTGTGGCTAATGGGCCGCATC‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTg < 8:333098/149‑1 (MQ=38)
ccTTGTGTCGCGAAAGGGCCGCATA‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCa > 6:266787/1‑149 (MQ=255)
cgAAAGGGCCGCATA‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgccgc > 1:269932/1‑149 (MQ=255)
|||
AGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATA‑‑‑GCG‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCGC > NC_002947_CJ‑RC/5558290‑5558551
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
