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 F17 I1 R1
|
56 |
89.2 |
4010200 |
98.4% |
3946036 |
146.5 |
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 | 94.1%
| 43.9
/ ‑6.2
| 18 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| Reads supporting (aligned to +/- strand): ref base . (1/0); major base G (5/11); minor base C (0/1); total (6/12) |
| 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 | 94.1%
| 52.4
/ ‑2.9
| 18 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| Reads supporting (aligned to +/- strand): ref base . (1/0); major base C (4/12); minor base G (1/0); total (6/12) |
| Fisher's exact test for biased strand distribution p-value = 2.94e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.93e-01 |
| * | NC_002947_CJ‑RC | 5,558,423 | 3 | . | C | 94.4%
| 56.0
/ ‑2.5
| 18 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| Reads supporting (aligned to +/- strand): ref base . (1/0); new base C (5/12); total (6/12) |
| Fisher's exact test for biased strand distribution p-value = 3.33e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATA‑‑‑GCG‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCGC > NC_002947_CJ‑RC/5558281‑5558551
|||
tCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATA‑‑‑gcggccc < 3:60411/147‑5 (MQ=255)
tCACTGTGCAGGAAATTCAGCTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATA‑‑‑gcggcccc < 5:472/148‑6 (MQ=255)
aaatCAGGTCGGCCTGGGCAGCCATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATA‑‑‑GCGGCCCCGGCAATTTCCGCgt < 6:468901/146‑1 (MQ=38)
ggCAGCTATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCTTGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGTGCGGCCTTGTGTCGCTAATGGGCCGCATA‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTg < 5:139191/149‑1 (MQ=37)
ttAGGCGGGCGCACATTACCAAATCTTTTTGACTTGTGTCGCCGACAGAATACAAACACCGCTCTGGTGGGGGCGCGGCCTTGGGACGCTAACGGCCCCAATA‑‑‑GCGCCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGgctgc < 2:363005/148‑1 (MQ=255)
ggggCGGACTTGAGAAACTCCTTTTGTCTTGTGTCGCCTACAGCATAGCAACACCGCTCCGGTGTGGGAGCGGCCTTGTGTCGCGAATGGGCCGAATA‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCa < 2:350399/148‑1 (MQ=37)
ggCGGAAATGAGCAACTCCTTTTGTCTTGTGTCGCCTACAGAATAGCAACACCGCTCTGGTGTGGGAGCGGCCTTGTGTCGCTAAAGGGCCGCATA‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGc < 2:216978/149‑1 (MQ=37)
gcgcaaaTGAGCAACTCCTTTTGTCTTGTGTCGCCGACAGCTTAGCAACCCCGCTCTGGTGGGGGAGCGGCCTTGTGTCGCGAACGGGCCGCATA‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGcc < 2:358531/143‑1 (MQ=37)
aTGACCAACTCCTTTTGTCTTGTGTCGCCGACAGAATAGCAACACCGCTCTGGTGTGGGTGGGGCCTTGTGTCGCTAATGGGCCGCATT‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTcg < 4:342063/149‑1 (MQ=255)
gCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGTTGTGGGAGCGGCCTTGTGTCGCTAATGGGCCGCATA‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGa < 2:7215/148‑1 (MQ=38)
gCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATA‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGa < 6:157704/148‑1 (MQ=255)
cAACTCCTTTTGACATGTGTCGCCGACAGCATAGCAACACCGCACAGGTGTGGGAGCGGCCATGTGTCGCCAAATGGCCCCATACCCGCC‑‑‑CCGCCAATTTACGCGTGATTTCAACAAAACTGTGGCAGCTATTCACCCCATTcctgac > 8:154814/1‑143 (MQ=255)
ctttttGTATTGTGTCCCCGAAAGAATACCAACACCGCTCTGGTGGGGTTGGGGCTTTGTGTCGCTAATGGGCCGAATT‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAg < 2:448931/146‑1 (MQ=255)
tttGTATTGTGTCGCCTACAGAATAGAAACCCCGCTCTGGTGTGGGTGGGGCGTTGTGTCGCTAATGGGCCGATTA‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGcc < 6:187966/148‑1 (MQ=21)
aGCGGCCTTGTGTCGCTAAAGGACCGCATA‑‑‑GCGGCCCCGGAAATTTCCGGGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGGGAAACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGgc < 2:430405/149‑1 (MQ=255)
ccTTGTGTCGCGAAAGGGCCGCATA‑‑‑GCGGGCCCGGCAATTTGCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGGCACAAGGCCCACAAAGGACCGCGCCCGCTTCAGGCCCGGGACAGGCCCAGGCTGgcgcg > 4:231768/1‑147 (MQ=37)
cTTGTGTCGCGAAAGGGCCGCATA‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAg > 3:331775/1‑149 (MQ=255)
cTTGTGTCGCGAAAGGGCCGCATA‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAg > 1:395080/1‑149 (MQ=255)
tCGCGAAAGGGCCGCATA‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgc > 4:126241/1‑149 (MQ=255)
cgAAAGGGCCGCATA‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTAAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgccgc > 3:373771/1‑149 (MQ=39)
|||
TCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATA‑‑‑GCG‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCGC > NC_002947_CJ‑RC/5558281‑5558551
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
