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 |
|
A3 F11 I1 R1
|
56 |
79.5 |
3383150 |
98.4% |
3329019 |
146.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_002947_CJ‑RC |
1,126,647 |
+C |
intergenic (‑101/+48) |
tdcG‑II ← / ← gcvP‑I |
L‑serine dehydratase/glycine dehydrogenase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_002947_CJ‑RC | 1,126,645 | 1 | . | C | 95.0%
| 64.2
/ ‑2.8
| 20 | intergenic (‑99/+50) | tdcG‑II/gcvP‑I | L‑serine dehydratase/glycine dehydrogenase |
| Reads supporting (aligned to +/- strand): ref base . (1/0); new base C (15/4); total (16/4) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.77e-01 |
GGGGCCGATGCCGATCTTGAACAGGTCGAAGACGCTCAGTGACATGTGGACCTCCTGCCAGGTTGTTGGGTGGACATTGAGCCCTGTAGGCGCGGGTTTACCCGCGAATGCGGAGGTATAGCCACCATCGCATTCGCGGGTAAA‑CC‑GCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGACCCGGCCGACCGGCGGCCAGTAC > NC_002947_CJ‑RC/1126502‑1126788
|
ggggCCGATGCCTATCTTGAACAGGTCGAAGACGCTCAGTGACATGTGGACCTCCTGCCAGGTTGTTGGGTGGACATTGAGCCCTGTAGGCGCGGGTTAACCCGCGAATGCGGAGGTATAGCCACCATCGCATTCGCGGGTAAA‑cccgc < 3:302458/149‑4 (MQ=255)
ggggCCGATGCCGATCTTGAACAGGTCGAAGACGCTCAGTGACATGTGGACCTCCTGCCAGGTTGTTGGGTGGACATTGAGCCCTGTAGGCGCGGGTTTACCCGCGAATGCGGAGGTATAGCCACCATCGCATTCGCGGGTAAA‑cccgc < 8:363760/149‑4 (MQ=255)
aTTGAGCCCTGTCGGCGCGGGTTACCCCCCCAATGCGGCGGAATACCCCCCATCCAATCCGCGGTTAAACCC‑GCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACgg < 2:117780/149‑1 (MQ=255)
attcgcgGGTAAACCCGCGAATGCGGAGGTATAGCCACCATCGCATTCGCGGGTAAA‑CCTGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCacac > 3:62488/4‑149 (MQ=39)
aCCCGCGAATGCGGAGGTATAGCCACCATCGCATTCGCGGGTAAACCC‑GCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTc > 7:228562/1‑149 (MQ=255)
cccGCGAATGCGGAGGTATAGCCACCATCGCATTCGCGGGTAAACCC‑GCTCCTACACAGAGCCCGCCACCCAAGCCGGGTGGCGGGGAGGGCTATCAGGCGTCCTGTTAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCg > 8:372645/1‑149 (MQ=255)
ccGCGAATGCGGAGGTATAGCCACCATCGCATTCGCGGGTAAACCC‑GCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGc > 4:319590/1‑149 (MQ=255)
ccGCGAATGCGGAGGTATAGCCACCATCGCATTCGCGGGTAAACCC‑GCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTAACAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGc > 7:387851/1‑149 (MQ=255)
cgcgAATGCGGAGGTATAGCCACCATCGCATTCGCGGGTAAACCC‑GCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGcc > 6:411851/1‑149 (MQ=255)
ggAGGTATAGCCACCATCGCATTCGCGGGTAAACCC‑GCTCCTACACAGAGCCCGCCCCCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGtt > 2:342867/1‑149 (MQ=255)
gAGGTATAGCCACCATCGCATTCGCGGGTAAACCC‑GCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTg > 1:333677/1‑149 (MQ=255)
gCCACCATCGCATTCGCGGGTAAACCC‑GCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGACCCg < 6:192031/149‑1 (MQ=255)
caTCGCATTCGCGGGTAAACCC‑GCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGACCCGGCCGa > 3:363519/1‑149 (MQ=255)
aTTCGCGGGTAAACCC‑GCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGACCCGGCCGACcggcg > 6:406841/1‑149 (MQ=255)
ttCGCGGGTAAACCC‑GCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGACCCGGCCGACcggcgg > 8:428902/1‑149 (MQ=255)
ttCGCGGGTAAACCC‑GCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGACCCGGCCGACcggcgg > 6:106525/1‑149 (MQ=255)
gcgGGTAAACCC‑GCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGACCCGGCCGACCggcggc > 4:38616/1‑147 (MQ=255)
gcgGGTAAACCC‑GCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGACCCGGCCGACCggcggc > 1:234415/1‑147 (MQ=255)
ggTAAACCC‑GCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGACCCGGCCGACCGGCGGCCAGTa > 3:409480/1‑149 (MQ=255)
gTAAACCC‑GCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGACCCGGCCGACCGGCGGCCAg < 4:184175/146‑1 (MQ=255)
gTAAACCC‑GCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGACCCGGCCGACCGGCGGCCAg > 3:184175/1‑146 (MQ=255)
gTAAACCC‑GCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGACCCGGCCGACCGGCGGCCAGTAc < 5:106525/149‑1 (MQ=255)
|
GGGGCCGATGCCGATCTTGAACAGGTCGAAGACGCTCAGTGACATGTGGACCTCCTGCCAGGTTGTTGGGTGGACATTGAGCCCTGTAGGCGCGGGTTTACCCGCGAATGCGGAGGTATAGCCACCATCGCATTCGCGGGTAAA‑CC‑GCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGACCCGGCCGACCGGCGGCCAGTAC > NC_002947_CJ‑RC/1126502‑1126788
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
