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 |
|
A4 F13 I0 R1
|
140 |
52.5 |
2164708 |
98.8% |
2138731 |
146.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
NC_002947_CJ‑RC |
4,850,315 |
G→C |
29.5% |
intergenic (+17/‑89) |
PP_4263 → / → hemN |
cytochrome biogenesis protein/oxygen‑independent coproporphyrinogen III dehydrogenase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_002947_CJ‑RC | 4,850,315 | 0 | G | C | 29.5%
| 12.4
/ 2.7
| 20 | intergenic (+17/‑89) | PP_4263/hemN | cytochrome biogenesis protein/oxygen‑independent coproporphyrinogen III dehydrogenase |
| Reads supporting (aligned to +/- strand): ref base G (2/12); new base C (3/3); total (5/15) |
| Fisher's exact test for biased strand distribution p-value = 1.31e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GCCCTGTTGCGGCGACGCAGCGTGCGAGTGGCAGGCGGTGTGCTGGTGATGCTATTCGGTATCTGGACCCTGCCGGGCCCACACCAGCACTGGCTGATGGGCCATTG‑ACGGGGGCTGCAAAGCA‑GCCCCAATGCCCTTGATACAAATCAACACAGTTTCCTACAGACGGCCATAGACTCCGGTGCACTGCTGCTCTTTCCGGGGACTACCCTCATGCTCGACGACCTCCGTTGGGATACCGA > NC_002947_CJ‑RC/4850191‑4850432
|
gCCCTTTTGGGGCGCCGCTGGGTGGGCGTGGCAGGGGGTGGGCTGGTTTTGCTATTCGGTATCTGCCCCCTGCCGGCCCCACACCACCAGTGGCTGATGGGCCATTG‑ACGGGGGCTGAAACGCA‑GCCCCAATGCCCTTGATACAAAt < 8:57232/147‑1 (MQ=255)
tGCGGCGACGCAGCGTGCGAGTGGCAGGCGGTGTGCTGGTGATGCTATTCGGTATCTGGACCCTGCCGGGCCCACACCAGCACTGGCTGATGGGCCATTG‑ACGGGGGCGGGAAAGCACCCCCCAATGCCGTT‑TTACAAATAAAcaca > 7:268544/1‑147 (MQ=255)
ggcgACGCAGCGTGCGAGTGGCAGGCGGTGTGCTGGTGATGCTATTCGGTATCTGGACCCTGCCGGGCCCACACCAGCACTGGCTGATGGGCCATTG‑ACGGGGGCTGCGAAGCA‑GCCCCAAAGGCCATGAAACAAAACAACACAGt > 6:267063/1‑146 (MQ=255)
gcgACGCAGCGTGCGAGTGGCAGGCGGTGTGCTGGTGATGCTATTCGGTATCTGGACCCTGCCGGGCCCACACCAGCACTGGCTGATGGGCCATTG‑ACGGGGGCTGCAAAGCA‑GCCCCAATGCCCTTGATACAAATCAACACAGttt < 2:154082/147‑1 (MQ=255)
gcgACGCAGCGTGCGAGTGGCAGGCGCTGTGCTGGTGATGCTATTCGGTATCTGGAAACTGCCGGGCCCACACCAGCACTGGCTGATGGGCCATTG‑ACGGTGTCTGCAAAACC‑GCCCCAAAGCCCATGATACAAATCAACACAAttt > 2:162396/1‑147 (MQ=255)
cGAGTGGCAGGCGGTGTGCTGGTGATGCTATTCGGTATCTGGACCCTGCCGGGCCCACACCAGCACTGGCTGATGGGCCATTG‑ACGGGGGCTGCAAAACA‑CCCCCAAAACCCATGATAAAAATAAACAAAATTTACTAAAGACTGc > 6:44318/1‑146 (MQ=255)
gtgCGGGTTTTGCTATTCGGTATCTGGACCCTGCCGGGCCCACACCAGCACTGGCTGAGGGGCCATTG‑ACGGGGGCTGCAAAGCA‑GCCCCAATGCCCTTGATACAAATCAACACAGTTTCCTACAGACGGCCATAGACTCCGGTGCa < 2:225194/147‑1 (MQ=255)
cgttacgtGGACGCTGCGGGGCCCACACAAGCAGTGGTTGTGGGGCCTTTG‑AGGGTTGGGGCAATCCA‑GCCCCAATGCCCTTTATACAAATCAACACAGTTTCCTACAGACGGCCATAGACTCCGGTGCACTGCTGCTCTTTCCgg < 8:180373/139‑1 (MQ=255)
tCTGCACCCGGCGGGCCCCACCCCACCAGGGGCTGAGGGGCATTTG‑CCGGGGGCTCAAAACCC‑CCCCCAATGCCCTTGATACAAATCAACACAGTTTCCTACAGACGGCCATAGACTCCGGTGCACTGCTGCTCTTTCCGGGGACt < 6:172077/146‑1 (MQ=255)
ccccGGCCGGGCCCACACCCCCAGGGGGTGAGGGGCCATTG‑CCGGGGGGTGAAACGCA‑CCCCCAATGCCCTTGATACAAATCAACACAGTTTCCTACAGACGGCCATAGACTCCGGTGCACTGCTGCTCTTTCCGGGGACTACCCTc < 7:130457/146‑1 (MQ=255)
aCCCTGCCGGGCCCACACCAGCAGGGGCTTTGGGCCCATGC‑ACGGGGGGTCCAACGCA‑GCCCCAATGCCCTTGATACAAATCAACACAGTTTCCTACAGACGGCCATAGACTCCGGTGCACTGCTGCTCTTTCCGGGGACTAc < 4:121063/143‑1 (MQ=255)
cTGCGGGGCCCACACCCGCAGTGGCT‑TTGGGCCCTTGTAGGGGGGCTGCAAACCA‑GCCCCAATGCCCTTGATACAAATCAACACAGTTTCCTACAGACGGCCATAGACTCCGGTGCACTGCTGCTCTTTCCGGGGACTACCCTCATg < 7:181569/147‑1 (MQ=255)
ggCCCACACCAGAACGGGCTGTTGGGCCATTG‑ACGGGGGCTGCAAAGCC‑GCCCCAATGCCCTTGATACAAATCAACACAGTTTCCTACAGACGGCCATAGACTCCGGTGCACTGCTGCTCTTTCCGGGGACTACCCTCATGCTcgac < 4:256281/147‑1 (MQ=255)
gcccaacacCAGCAGTGGCTGATGGGCCATTG‑ACGGGGGCTCCAACGCA‑CCCCCAATGCCCTTGATACAAATCAACACAGTTTCCTACAGACGGCCATAGACTCCGGTGCACTGCTGCTCTTTCCGGGGACTACCCTCATGCTcgac < 7:22731/142‑1 (MQ=255)
gctttGGCTTTTGGGCATTTG‑AGGGGGGCTTAAAAGAA‑GCCCCAATGCCCTTGATACAAATCAACACAGTTTCCTACAGACGGCCATAGACTCCGGTGCACTGCTGCTCTTTCCGGGGACTACCCTCATGCTCGACGACCTCCGTTg < 6:244253/143‑1 (MQ=255)
aCTGGCTGATGGGCCTTTG‑AGGGGGGCTGCAAAGCA‑GCCCCAATGCCCTTGATACAAATCAACACAGTTTCCTACAGACGGCCATAGACTCCGGTGCACTGCTGCTCTTTCCGGGGACTACCCTCATGCTCGACGACCTCCGTTg < 6:230580/145‑1 (MQ=255)
gCTGATGGGCCATTG‑ACGGGGGCTGCAAACCA‑GCCCCAATGCCCTTGATACAAATCAACACAGTTTCCTACAGACGGCCATAGACTCCGGTGCACTGCTGCTCTTTCCGGGGACTACCCTCATGCTCGACGACCTCCGTTGGGATAc < 6:47537/147‑1 (MQ=255)
cttttGGGCAATTG‑AGGGGGGCTGAAAAGAA‑GCCCCAATGCCCTTGATACAAATCAACACAGTTTCCTACAGACGGCCATAGACTCCGGTGCACTGCTGCTCTTTCCGGGGACTACCCTCATGCTCGACGACCTCCGTTGGGATAcc < 8:121712/143‑1 (MQ=255)
cTGATGGGCCATTG‑ACGGGGGCTGAAAAGCA‑GCCCCAATGCCCTTGATACAAATCAACACAGTTTCCTACAGACGGCCATAGACTCCGGTGCACTGCTGCTCTTTCCGGGGACTACCCTCATGCTCGACGACCTCCGTTGGGATAcc < 2:249895/147‑1 (MQ=255)
gATGGGCCATTG‑ACGGGGGCTGCAAAGCA‑CCCCCCAAGCCCGTGATAAAAAAAAAAACACGTTAATAAAGACCGCCATAGACACCCGTGGACAGGTGGGGTTTACGGGGGCTACACGCATGCTCGTCGCCCAGCGGTGGGGTTCCGa > 2:86982/1‑147 (MQ=255)
|
GCCCTGTTGCGGCGACGCAGCGTGCGAGTGGCAGGCGGTGTGCTGGTGATGCTATTCGGTATCTGGACCCTGCCGGGCCCACACCAGCACTGGCTGATGGGCCATTG‑ACGGGGGCTGCAAAGCA‑GCCCCAATGCCCTTGATACAAATCAACACAGTTTCCTACAGACGGCCATAGACTCCGGTGCACTGCTGCTCTTTCCGGGGACTACCCTCATGCTCGACGACCTCCGTTGGGATACCGA > NC_002947_CJ‑RC/4850191‑4850432
|
| 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
