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 F59 I1 R1
|
58 |
78.7 |
3339874 |
98.5% |
3289775 |
147.1 |
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 | 90.0%
| 19.9
/ ‑5.7
| 11 | 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 (6/3); minor base C (0/1); total (6/5) |
| Fisher's exact test for biased strand distribution p-value = 4.00e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
| * | NC_002947_CJ‑RC | 5,558,423 | 2 | . | C | 90.9%
| 31.0
/ ‑2.8
| 11 | 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 (6/4); total (6/5) |
| Fisher's exact test for biased strand distribution p-value = 4.55e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.82e-01 |
| * | NC_002947_CJ‑RC | 5,558,423 | 3 | . | C | 90.9%
| 31.3
/ ‑2.8
| 11 | 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 (6/4); total (6/5) |
| Fisher's exact test for biased strand distribution p-value = 4.55e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GTCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCAT‑‑‑AGCG‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCGC > NC_002947_CJ‑RC/5558280‑5558551
|||
gTCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCAT‑‑‑Agcggccc < 1:409545/148‑5 (MQ=255)
gTCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCAT‑‑‑Agcggccc > 2:409545/1‑144 (MQ=255)
tCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCAT‑‑‑Agcggccccg < 4:378908/149‑7 (MQ=255)
ggaaGCTATTCGGCGGGCGTACATGAGAAACTCTTTTTGTCTTGTGGCGCCGACACAAAAGCACCCCCGCGCGGGGGTGGGCGCGGCCTTGGGGCGCTAACGGGCCGCAT‑‑‑CGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTg < 6:39738/146‑1 (MQ=255)
gATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCAT‑‑‑AGCGGCCCCGGCCATTTCCGCGTGTATGGAACAAACCTGGGgcgg > 1:164993/1‑147 (MQ=38)
cGGGCGTACATTAGCAACTCCTTTTGTCATGTGTCGCCGACAGAATAGCAACACCGCTCTGGTGTGGTAGCGGCCTTGTGTCGCTAAAGGGCCGAAT‑‑‑AGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCa < 4:52847/149‑1 (MQ=255)
cATGAGCAACTCGTTTTGTCTTGTGGCGCCGACAGCATAGCAACAGCGGTCAGGGGTGGGCGCGGCCTTGTGTCGCTAATGGGCCGAAT‑‑‑TGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTc < 6:126077/149‑1 (MQ=255)
acaaaCTCATTTTGTCTTGTGGCGCCTACAGAATACCAACCCCGCTCTGGGGTGGGCGCGGCTTTGTGTCGCTAATGGGCCGCAT‑‑‑AGCGCCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGa < 2:164993/146‑1 (MQ=255)
ttgtgTCGCCTACAGAATCCAAACCCCGCTCTGGTGTGGGCGGGGCTTTGTGGCGCTAATGGCCCGAATCGGGGCC‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCTACACAAGGCCCACAAAg < 8:77517/148‑1 (MQ=255)
ccTTGTGTCGCGAAAGGGCCGCAT‑‑‑AGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGCCCGCGCCGGCTTCAGGCCCGGACCTGGCCCAGGCTGgcgcg > 7:321309/1‑147 (MQ=37)
ttGTGTCGCGAAAGGGCCGCAT‑‑‑AGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGc > 8:337622/1‑149 (MQ=255)
gcgAAAGGGCCGCAT‑‑‑AGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgccg > 2:35088/1‑149 (MQ=255)
gcgAAAGGGCCGCAT‑‑‑AGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgccg > 8:183485/1‑149 (MQ=255)
aGGGCCGCAT‑‑‑AGCGGCCCCGGCAATTTCCGCGCGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgccgc > 6:149994/1‑145 (MQ=39)
|||
GTCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCAT‑‑‑AGCG‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCGC > NC_002947_CJ‑RC/5558280‑5558551
|
| 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
