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 F13 I0 R1
|
203 |
85.6 |
3649704 |
98.8% |
3605907 |
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 |
25.7% |
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 | 25.7%
| 47.0
/ 8.1
| 34 | intergenic (+17/‑89) | PP_4263/hemN | cytochrome biogenesis protein/oxygen‑independent coproporphyrinogen III dehydrogenase |
| Reads supporting (aligned to +/- strand): ref base G (12/13); new base C (5/4); total (17/17) |
| 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 |
GGCTGGCTGCCGAACGGATGAACGCCCTGTTGCGGCGACGCAGCGTGCGAGTGGCAGGCGGTGTGCTGGTGATGCTATTCGGTATCTGGACCCTGCCGGGCCCACACCAGCACTGGCTGATGGGCCA‑TTGACGGGGGCTGCAAAGCAGCCCCAATGCCCTTGATACAAATCAACACAGTTTCCTACAGACGGCCATAGACTCCGGTGCACTGCTGCTCTTTCCGGGGACTACCCTCATGCTCGACGACCTCCGTTGGGATACCGACCTGATCCGCCGCTACGATCTCGCCGGGC > NC_002947_CJ‑RC/4850168‑4850461
|
ggctggctGCCGAACGGATGAACGCCCTGTTGCGGCGACGCAGCGTGCGAGTGGCAGGCGGTGTGCTGGTGATGCTATTCGGTATCTGGACCCTGCCGGGCCCACACCAGCACTGGCTGATGGGCCA‑TTGACGGGGGCTGCAAagcagc < 5:281025/149‑1 (MQ=255)
gctggctgCCGAACGGATGAACGCCCTGTTGCGGCGACGCAGCGTGCGAGTGGCAGGCGGTGTGCTGGTGATGCTATTCGGTATCTGGACCCTGCCGGGCCCACACCAGCACTGGCTGATGGGCCA‑TTGACGGGGGCTGCAAAGCAGcc < 2:142105/149‑1 (MQ=255)
ggctgCCGAACGGATGAACGCCCTGTTGCGGCGACGCAGCGTGCGAGTGGCAGGCGGTGTGCTGGTGATGCTATTCGGTATCTGGACCCTGCCGGGCCCACACCAGCACTGGCTGATGGGCCA‑TTGACGGGGGGGGGGAAGCCGccccc > 1:176181/1‑148 (MQ=255)
tgCCGAACGGATGAACGCCCTGTTGCGGCGACGCAGCGTGCGAGTGGCAGGCGGTGTGCTGGTGATGCTATTCGGTATCTGGACCCTGCCGGGCCCACACCAGCACTGGCTGATGGGCCA‑TTGACGGGGGGGGGAAAACACcccccaa > 3:369292/1‑145 (MQ=255)
aaCGGATGAACGCCCTGTTGCGGCGACGCAGCGTGCGAGTGGCAGGCGGTGTGCTGGTGATGCTATTCGGTATCTGGACCCTGCCGGGCCCACACCAGCACTGGCTGATGGGCCA‑TTGACGGGGGGTGCAAAGCACCCCCCAAGcccct > 8:9190/1‑147 (MQ=255)
aCGGATTACCGCCGTGTTGCGGCGACGCTGGGTGCGTGTGGCTGGGGGTGTGCTGTTTATTCTATTCGTTTTCTGGACCCTGCCGGGCCCACACCAGCAGTGGCTTTTGGGCCT‑TTGCGGGGGGCTGAAAAGCAGCCCCAATGCCCtt < 2:333425/148‑1 (MQ=255)
cGGATGAACGCCCTGTTGCGGCGACGCTGGGTGCGTGTGGCTGGCGGTGTGCTGGTTATGCTATTGGGTATCTGGACCCTGCCGGGCCCACACCAGCAGTGGCTTTTGGGCCA‑TTGACGGGGGCTGCAAAGCAGCCCCAATGCCCTTGa < 6:121460/149‑1 (MQ=255)
ggATGAACGCCCTGTTCCGGCGACGCAGCGTGCGAGAGGCAGGCGCTGTGCTGGTGATGCTATTCGGTATCTCGACCCTGCCGGGCCCACACCAGCACTGGCTGATGGGCCA‑TTGACGGGGGCTGCCTACCACCCCCCATACCCATGa > 6:82729/1‑148 (MQ=255)
tttGAACGCTCGGTTGGGGCGAGGCAGCGTGCGTGTGGCTGGGGGGGTGGTGGTGAGTGTTTTCGGTTTCTGGCCCGTGGGGGGCCCACACCAGCTCTGGCTGAGGGGCCT‑TTGACGGGGGGTGAAATGCAGCCCCAATGCCCTTGATa < 8:247714/147‑1 (MQ=255)
aCGCCCTTTTGCGGCTACGCTGGGTGGGTGGGGCTGGGGGTGTGCTGGTGTTTATATTGGTTTTCTGGACCCTGCCGGGCCCACACCAGCAGTGGCTTATGGGCCA‑TTGACGGGGGCTGCAAAGCTGCCCCAATGCCCTTGATACAAAt < 8:323076/149‑1 (MQ=255)
aCGCCCTGTTGCGGCGACGCAGCGTGCGAGTGGCAGGCGGTGTGCTGGTGATGCTATTCGGTATCTGGACCCTGCCGGGCCCACACCAGCACTGGCTGATGGGCCA‑TTGACGGGGGCTGGAAAACCGCCCCAATTCCCTTGATAaaaa > 6:383571/1‑148 (MQ=255)
gCCCTGTTGCGGCGACGCAGCGTGCGAGTGGCAGGCGGTGTGCTGGTGATGCTATTCGGTATCTGGACCCTGCCGGGCCCACACCAGCACTGGCTGATGGGCCA‑TTGACGGGGGCTGCAAAGCAGCCCCAATGCCCGTGATACaaaaa > 2:388756/1‑146 (MQ=255)
ccgtGTTGCGGCGACGCTGGGTGGTAGTGGCAGGCGGTGTGCTGGTTATGATATTCGTTATCTGCACCCTGCCGGGCCAACACCAGCAGTGGCTTATGGGCCT‑TTGACGGGGGCTGAAAAGCAGCCCCAATGCCCTTGATACAAATCaa < 8:437910/146‑1 (MQ=255)
cccTGTTGCGGCGACGCAGCGTGCGAGTGGCAGGCGGTGTGCTGGTGATGCTATTCGGTATCTGGACCCTGCCGGGCCCACACCAGCACTGGCTGATGGGCCA‑TTGACGGGGGGTGGAAAGCCCCCCCCATGCCCGTGATACAAATaaa > 7:147001/1‑149 (MQ=255)
ccTGTTGCGGCGACGCAGCGTGCGAGTGGCAGGCGGTGTGCTGGTGATGCTATTCGGTATCTGGACCCTGCCGGGCCCACACCAGCACTGGCTGATGGGCCA‑TTGACGGGGGCTGCAAAGCAGCCCCAAAGCCCGTGATAAAAATaaa > 8:245795/1‑148 (MQ=255)
tGCGGCGACGCTGCGTGCGTGGGGCTGGGGGTGTGCTGGTGATGCTATGCGTTATCTGCACCCTGCCGGGCCCACACCAGCAGTGGCTGTGGGGCCA‑TGGACGGGGGCTGCAAAGCACCCCCAATGCCCTTGATACAAATCAACACAg < 5:231725/148‑1 (MQ=255)
ggcgACGCTGGGTGGGTGTGGCTGGGGGTGTGTTGGTTATGATTTTGTTTTTCTGCCCCCTGCGGGGCCCACACCTGCTGTGGGTGTGGGGCCT‑TTGCGGGGGGCTTAAACCCACCCCCAATGCCCTTGATACAAATCAACACAGTTTc < 2:233265/149‑1 (MQ=255)
gTGCGAGTGGCAGGCGGTGTGCTGGTGATGCTATTCGGTATCTGGACCCTGCCGGGCCCACACCAGCACTGGCTGATGGGCCA‑TTGACGGGGGGGGCAAAGCAGCCCCCAAGCCCGTGGTACAAAAAAACACAGGTTTCTAAAGAAGGc > 5:108459/1‑149 (MQ=255)
gCGGTGTGCTGGTTATGCTATTCTGTATCTGGACCCGGCCGGGCCCACACCTGCTCTGGAGGATGGGCCA‑TTGACGGGGGCTGCAACGCAGCCCCAATGCCCTTGATACAAATCAACACAGTTTCCTACAGACGGCCATAGACTCCGGt < 2:431236/149‑1 (MQ=255)
gTGATGCTATTCGGTATCTGGACCCTGCCGGGCCCACACCAGCACTGGCTGATGGGCCA‑TTGACGGGGGGGGGAAAGCAGCCCCCAAGCCCGTGTTAAAAATAAAAACACGTTAAAAAACACGGCCCAAAACTCCGGTGCAcgggtggg > 6:40528/1‑142 (MQ=255)
ttCGGTATCTGGACCCTGCCGGGCCCACACCAGCAGTGGCTGAGGGGCCA‑TTGACGGGGGCTGCAAAGCAGCCCCAATGCCCTTGATACAAATCAACACAGTTTCCTACAGACGGCCATAGACTCCGGTGCACTGCTGCTCTTTCCgg < 8:436344/148‑1 (MQ=255)
ttCGGTATCTGGACCCTGCCGGGCCCACACCAGCACTGGCTGATGGGCCA‑TTGACGGGGGCTGCAAAGCACCCCCAATGCCCTTGATACAAATCAACACAGTTTCCTAc < 8:320077/109‑1 (MQ=255)
ttCGGTATCTGGACCCTGCCGGGCCCACACCAGCACTGGCTGATGGGCCA‑TTGACGGGGGCTGCAAAGCACCCCCAATGCCCTTGATACAAATCAACACAGTTTCCTAc > 7:320077/1‑109 (MQ=255)
ggTATCTGGACCCTGCCGGGCCCACACCAGCACTGGCTGATGGGCCA‑TTGACGGGGGCGGCAAAGAAGCCCCCAAGCCCATGATAAAAAAAAAAACAGTTTACTAAAGACGGCCATAGACAACGGGGCACTGCGGCTCTTTGAgggggc > 8:156639/1‑147 (MQ=255)
cTGTACCCTGCCGGGCCCACACCATCTCTGGTTGTTGGGCCT‑TTGTGGGGGGCTGAAAACCAGCCCCAATGCCCTTGATACAAATCAACACAGTTTCCTACAGACGGCCATAGACTCCGGTGCACTGCTGCTCTTTCCGGGGACTAcc < 8:178170/148‑1 (MQ=255)
tGGACCCTGCCGGGCCCACACCAGCACTGGCTGATGGGCCA‑TTGACGGGGGGGGGAAAGAAGCCCCAAATCCCATGATAAAAAAAAAAACAAATTACTAAAGACGGCCAAAGACTACGGGGCACAGCGGGTCTTTGACGGGGCTAccca > 4:324619/1‑148 (MQ=255)
gccccACCCCAGCAGGGGGTG‑TGGGCCATTTGCGGGGGGCTCCAAAGCCCCCCCAATGCCCTTGATACAAATCAACACAGTTTCCTACAGACGGCCATAGACTCCGGTGCACTGCTGCTCTTTCCGGGGACTACCCTCATGCTcgacga < 6:301824/147‑1 (MQ=255)
acacCACCAGGGGCTTATGGCCCT‑TTGCGGGGGGCTCAAAACCAGCCCCAATGCCCTTGATACAAATCAACACAGTTTCCTACAGACGGCCATAGACTCCGGTGCACTGCTGCTCTTTCCGGGGACTACCCTCATGCTCGACGACCTcc < 7:9190/149‑1 (MQ=255)
cTGGCTGATGGGCCA‑TTGACGGGGGCTGCAAAGCAGCCCCAATGCCCTTGATACAAATCAACACAGTTTCCTACAGACGGCCATAGACTCCGGTGCACTGCTGCTCTTTCCGGGGACTACCCTCATGCTCGACGACCTCCGTTGGGATa < 8:147001/149‑1 (MQ=255)
caa‑TTGAGGGGGGCTGCAAAGAAGCCCCAATGCCCTTGATACAAATCAACACAGTTTCCTACAGACGGCCATAGACTCCGGTGCACTGCTGCTCTTTCCGGGGACTACCCTCATGCTCGACGACCTCCGTTGGGATACCGACCTGATcc < 5:383571/147‑1 (MQ=255)
ttttcGGGGGCTTCAATGCAGCCCCAATGCCCTTGATACAAATCAACACAGTTTCCTACAGTCGGCCATAGACTCCGGTGCACTGCTGCTCTTTCCGGGGACTACCCTCATGCTCGACGACCTCCGTTGGGATACCGACCTGATccgc < 6:325009/144‑1 (MQ=255)
tGCAAAGCAGCCCCAATGCCCTTGATACAAATCAACACAGTTTCCTACAGACGGCCATAGACTCCGGTGCACTGCTGCTCTTTCCGGGGACTACCCTCATGCTCGACGACCTCCGTTGGGATACCGACCTGATCCGCCGCTACGAtctc > 5:296248/1‑149 (MQ=255)
gCAAAGCAGCCCCAATGCCCTTGATACAAATCAACACAGTTTCCTACAGACGGCCATAGACTCCGGTGCACTGCTGCTCTTTCCGGGGACTACCCTCATGCTCGACGACCTCCGTTGGGATACCGACCTGATCCGCCGCTACGATCTCg > 3:253993/1‑149 (MQ=255)
gCAAAGCAGCCCCAATGCCCTTGATACAAATCAACACAGTTTCCTACAGACGGCCATAGACTCCGGTGCACTGCTGCTCTTTCCGGGGACTACCCTCATGCTCGACGACCTCCGTTGGGATACCGACCTGATCCGCCGCTACGATCTCg > 1:173592/1‑149 (MQ=255)
aaaGCAGCCCCAATGCCCTTGATACAAATCAACACAGTTTCCTACAGACGGCCATAGACTCCGGTGCACTGCTGCTCTTTCCGGGGACTACCCTCATGCTCGACGACCTCCGTTGGGATACCGACCTGATCCGCCGCTACGATCTCGcc > 5:285593/1‑149 (MQ=255)
accagcCCCAATGCCCTTGATACAAATCAACACAGTTTCCTACAGACGGCCATAGACTCCGGTGCACTGCTGCTCTTTCCGGGGACTACCCTCATGCTCGACGACCTCCGTTGGGATACCGACCTGATCCGCCGCTACGATCTCGCCgg < 3:45536/147‑1 (MQ=255)
cagcCCCAATGCCCTTGATACAAATCAACACAGTTTCCTACAGACGGCCATAGACTCCGGTGCACTGCTGCTCTTTCCGGGGACTACCCTCATGCTCGACGACCTCCGTTGGGATACCGACCTGATCCGCCGCTACGATCTCGCCGGGc > 3:299130/1‑149 (MQ=255)
|
GGCTGGCTGCCGAACGGATGAACGCCCTGTTGCGGCGACGCAGCGTGCGAGTGGCAGGCGGTGTGCTGGTGATGCTATTCGGTATCTGGACCCTGCCGGGCCCACACCAGCACTGGCTGATGGGCCA‑TTGACGGGGGCTGCAAAGCAGCCCCAATGCCCTTGATACAAATCAACACAGTTTCCTACAGACGGCCATAGACTCCGGTGCACTGCTGCTCTTTCCGGGGACTACCCTCATGCTCGACGACCTCCGTTGGGATACCGACCTGATCCGCCGCTACGATCTCGCCGGGC > NC_002947_CJ‑RC/4850168‑4850461
|
| 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
