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 F37 I1 R1
|
57 |
76.9 |
3276914 |
98.4% |
3224483 |
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 | 80.0%
| 18.4
/ 1.3
| 10 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| Reads supporting (aligned to +/- strand): ref base . (0/2); new base G (1/7); total (1/9) |
| 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 | 2 | . | C | 77.8%
| 15.6
/ 0.9
| 10 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| Reads supporting (aligned to +/- strand): ref base . (0/2); new base C (1/6); total (1/9) |
| 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 | 80.0%
| 23.0
/ 0.9
| 10 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| Reads supporting (aligned to +/- strand): ref base . (0/2); new base C (1/7); total (1/9) |
| 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‑‑‑CCGGCAA‑TTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCG > NC_002947_CJ‑RC/5558276‑5558550
|||
cGCTGTCACTGTGCAGGATATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCTTGTGTCGCCGACAGCTTAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCAT‑‑‑Agcg < 3:20953/148‑1 (MQ=255)
cGCTGTCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCAT‑‑‑Agcg < 4:184870/148‑1 (MQ=255)
tGTCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCAT‑‑‑Agcggccc > 7:51051/1‑145 (MQ=255)
atttCAGGTCGGCCTGGGCAGCTTTTAGTCGGGCGGAAATGAGAAACTCTTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTGTGGTGTGGGAGCGGCCTTGTGTCGCTAATGGGCCGCAT‑‑‑AGCGGCCCCGGCAA‑TTTCCGCgt < 4:244265/147‑1 (MQ=25)
ttCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTCGTGTCGCGAAAGGGCCGCAT‑‑‑Agcg < 3:151642/128‑1 (MQ=255)
ttCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTCGTGTCGCGAAAGGGCCGCAT‑‑‑Agcg > 4:151642/1‑128 (MQ=255)
aGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCAT‑‑‑AGCGGTCCCGGCAA‑TTTCCGCGTGTAt < 5:122437/148‑1 (MQ=255)
ggcGGCCTGGGCTGCGATTAGTCGGGCGGACATGAGAAACTCCTTTTGTCATGTGTCGCCGACAGCATACCAACACCGCTCAGGTGTGGGTGCGGCCTTGTGTCGCTAAAGGGCCGAAT‑‑‑AGCGGCCCCGGCAA‑TTTCCGCGTGTAt < 6:298367/144‑1 (MQ=37)
tGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCAT‑‑‑AGCGGCCCCGGCAA‑TTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTcgc < 2:58106/149‑1 (MQ=255)
aGCAACTCTTTTTGTCTTGTGTCGCCGACTGCATAGCAACACCGCTCTGGTGTGGGAGCGGCGTTGTGTCGCGAATGGGCCGAAT‑‑‑AGCGGCCCCGGCAA‑TTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTcgcg < 8:51051/148‑1 (MQ=255)
gCAACTCCTTTTGTCTTGTGGCGCCGACAGCATAGCAACCCCGCTCTGGTGTGGGAGCGGCCTTGTGTCGCTAACGGGCCGCAT‑‑‑AGCGGCCCCGGCAA‑TTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGac < 4:195773/149‑1 (MQ=37)
catcATAGCAACCCCGCTCCGGGGTGGTAGGGGCTGTGTGTTGCTAATGGGCCGCTTCGGGGCC‑‑‑CCGGCAA‑TTTCCGCGTGTATGCAACACACCTGGGGCTGCTATGCAGCCCTTTCGCTACACAAGGCCCACAAAGGACCGCGCAGGc < 8:107889/146‑1 (MQ=255)
ccGCTCTGGTGTGGGTGGGGCCTTGTGTCGCTAATGGGGCTAATTG‑GGCC‑‑‑CCGGGAATTTTCCGCGTGTATGAAACAAACCTGGGGGTGCTTTGCAGCCCTTTCGCTAAACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGaa < 8:43981/149‑1 (MQ=255)
tgtCGCGAACGGGCCGCAT‑‑‑AGCGGCCCCGGCAA‑TTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGa < 2:247533/149‑1 (MQ=38)
gcgAAAGGGCCGCAT‑‑‑AGCGGCCCCGGCAA‑TTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACCAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgccg > 8:101679/1‑149 (MQ=255)
|||
CGCTGTCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCAT‑‑‑AGCG‑‑‑CCGGCAA‑TTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCG > NC_002947_CJ‑RC/5558276‑5558550
|
| 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
