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 F49 I1 R1
|
57 |
62.9 |
2678826 |
98.4% |
2635964 |
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 | 81.8%
| 22.2
/ ‑3.6
| 12 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| Reads supporting (aligned to +/- strand): ref base . (0/1); major base G (4/5); minor base C (0/2); total (4/8) |
| Fisher's exact test for biased strand distribution p-value = 4.91e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
| * | NC_002947_CJ‑RC | 5,558,423 | 2 | . | C | 91.7%
| 34.8
/ ‑2.9
| 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%
| 34.8
/ ‑2.9
| 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 |
CGCTGTCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCAT‑‑‑AGCG‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCGC > NC_002947_CJ‑RC/5558276‑5558551
|||
cGCTGTCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCAT‑‑‑Agcg < 8:246280/148‑1 (MQ=255)
aCTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCAT‑‑‑Agcggccccgg < 8:194100/148‑8 (MQ=255)
ggAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCAT‑‑‑AGCGGCCCCGGCAATTTc > 3:317590/1‑147 (MQ=255)
ggtggcccTGGGCTGCTTTTAGTGGGGGGGACATGAGCAACTCTTTTTGTCTTGTGTCGCCTACAGAATAGCAACACCGCTCTGGTGTGGGAGCGGCCTTGTGTGGCTAATGGGCCGAAT‑‑‑AGCGGCCCCGGCAATTTCCGCGTGTATGc < 8:194478/143‑1 (MQ=255)
aGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCAT‑‑‑AGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTgggg < 8:156420/149‑1 (MQ=255)
ttAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCAT‑‑‑AGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGgctgc < 8:101132/148‑1 (MQ=255)
ttAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGGCGCCGACAGCATAGCAACCCCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCAT‑‑‑AGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGgctgc < 8:73537/148‑1 (MQ=38)
gCGGACATTACCAACTCCTTTTTTCATGTGTCCCCGACAGCATAGCAACACCGCGCCGGTGTGGGCGCGGCCTTGTGGCCCTAACGGGCCGCAA‑‑‑CGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGcc < 8:143427/149‑1 (MQ=255)
gtaGCAACACCTTTTGTCTTGTGCCGCCGACAGCAAACCAACACCGCGCTGGTGTGGGAGCGGCCTTGGGTCGCTAAAGGGCCGAAT‑‑‑AGCGCCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTcgc < 7:54015/147‑1 (MQ=255)
ttttGTCCTGGGGCCCCCACAGCATCCCAACCCCCCTCCGGTGGGGGCGCGGCCTTGGGCCGCTAACGGCCCCCAT‑‑‑CGCGCCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTTGCGACACAAGGcc < 3:100238/149‑1 (MQ=255)
tttgttttgtGTCGCCTATAGAATTTAAACCCGGTTCTGGTGTGGGTGCGGCTTTGTGTCGCTAATGGGCCGAATTGGGGCC‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAgg < 4:272339/146‑1 (MQ=16)
tCGCGAAAGGGCCGCAT‑‑‑AGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGCCCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgc > 6:178541/1‑149 (MQ=38)
gcgAAAGGGCCGCAT‑‑‑AGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgccg > 1:120226/1‑149 (MQ=255)
cgAAAGGGCCGCAT‑‑‑AGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgccgc > 8:24912/1‑149 (MQ=255)
|||
CGCTGTCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCAT‑‑‑AGCG‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCGC > NC_002947_CJ‑RC/5558276‑5558551
|
| 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
