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 |
4,442,726 |
A→C |
27.6% |
intergenic (‑89/+49) |
nicP‑II ← / ← nicT |
porin‑like protein/metabolite transport protein NicT |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_002947_CJ‑RC | 4,442,726 | 0 | A | C | 27.6%
| 26.9
/ 2.5
| 32 | intergenic (‑89/+49) | nicP‑II/nicT | porin‑like protein/metabolite transport protein NicT |
| Reads supporting (aligned to +/- strand): ref base A (8/12); new base C (6/3); total (14/18) |
| Fisher's exact test for biased strand distribution p-value = 2.45e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
AACCGCCGGCCAGGCGTGCAGACGAAGAAAAACGCGGCGCAGTGAAACCTTGCATAGGGCTACTCCTGGATTTGGGCAACAGCAACCCGGCGCGGCGGCACTGCATGGCCACCGGCGTGCGGGTTGCATCGAGAGAGGTC‑GGCAGGCGGGCCCCGGCCCGCCTGCCCTGCCGTTGCGTGAAGCGCTGGGCCGCTAGCGGTTGACCAGCTTGGCCGGCAAGGCGATGACCAGGAAGCAGCTGAGGATCAGGCAGCCGGCAAACACCCACAGCGCAGCGTGCGAGGTGCCGG > NC_002947_CJ‑RC/4442583‑4442872
|
aaCCGCCGGCCAGGCGTGCAGACGAAGAAAAACGCGGCGCAGTGAAACCTTGCATAGGGCTACTCCTGGATTTGGGCAACAGCAACCCGGCGCGGCGGCACTGCATGGCCACCGGCGTGCGGGTTGCATCGAGAGAGGTC‑GGCACGCgg > 3:147595/1‑149 (MQ=255)
aCCGCCGGCCAGGCGTGCAGACGAAGAAAAACGCGGCGCAGTGAAACCTTGCATAGGGCTACTCCTGGATTTGGGCAACAGCAACCCGGCGCGGCGGCACTGCATGGCCACCGGCGTGCGGGTTGCATCGAGAGAGGTC‑GGCAGGCggg < 7:306858/149‑1 (MQ=255)
ccgccgGCCAGGCGTGCAGACGAAGAAAAACGCGGCGCAGTGAAACCTTGCATAGGGCTACTCCTGGATTTGGGCAACAGCAACCCGGCGCGGCGGCACTGCATGGCCACCGGCGTGCGGGTTGCATCGAGAGAGGTC‑GGCCGGCgggg > 5:260986/1‑148 (MQ=255)
cAGGCGTGCAGACGAAGAAAAACGCGGCGCAGTGAAACCTTGCATAGGGCTACTCCTGGATTTGGGCAACAGCAACCCGGCGCGGCGGCACTGCATGGCCACCGGCGTGCGGGTTGCATCGAGAGAGGTC‑GGCAGGCGGGCCCCGGccc > 8:2865/1‑149 (MQ=255)
gACGAAGAAAAACGCGGCGCAGTGAAACCTTGCATAGGGCTACTCCTGGATTTGGGCAACAGCAACCCGGCGCGGCGGCACTGCATGGCCACCGGCGTGCGGGTTGCATCGAGAGAGGTC‑GGCAGGCGGGCCCCCGCCCCcctggcctg > 7:145475/1‑149 (MQ=255)
gaagaaAAACGCGGCGCAGTGAAACCTTGCATAGGGCTACTCCTGGATTTGGGCAACAGCAACCCGGCGCGGCGGCACTGCATGGCCACCGGCGTGCGGGTTGCATCGAGAGAGGTCGGGCCGGGGCGCccccgcccccccgccccccg > 5:49139/1‑145 (MQ=255)
cgcgGCGCAGTGAAACCTTGCATAGGGCTACTCCTGGATTTGGGCAACAGCAACCCGGCGCGGCGGCACTGCATGGCCACCGGCGTGCGGGTTGCATCGAGAGAGGTC‑GGCAGGCGGGCCCCGGCCCGCCTGCCCTGCCGTTGCGTGaa < 2:94184/149‑1 (MQ=255)
gcAGTGAAACCTTGCATAGGGCTACTCCTGGATTTGGGCAACAGCAACCCGGCGCGGCGGCACTGCATGGCCACCGGCGTGCGGGTTGCATCGAGAGAGGTC‑GGCCGGCGGGCCCCCGCCCCCCTGCCCAGCCGTTGCGTGAAgcgcag > 6:401683/1‑147 (MQ=255)
tGAAACCTTGCATAGGGCTACTCCTGGATTTGGGCAACAGCAACCCGGCGCGGCGGCACTGCATGGCCACCGGCGTGCGGGTTGCATCGAGAGAGGTC‑GGCCGGCGGGCCCCGGCCCGCCTGCCCTGCCGTTGCGTGAAGCGCTGGGcc > 8:132411/1‑149 (MQ=255)
aCCTTGCATAGGGCTACTCCTGGATTTGGGCAACAGCAACCCGGCGCGGCGGCATTGCATGGCCACCGGCGTGCGGGTTGAATCGAGAGAGGTC‑GGCAGGCGGGCCCCGGCCCGCCTGCCCTGCCGTTGCGTGAAGCGCTGGGCCGCTa < 8:64038/149‑1 (MQ=255)
ccTTGCATAGGGCTACTCCTGGATTTGGGCAACAGCAACCCGGCGCGGCGGCACTGCATGGCCACCGGCGTGCGGGTTGCATCGAGAGAGGTCGGGCCGCCGGGCCCC‑GCCCCCCCGCCCCGCCGGTTGGGGGAGCGCGGGGCCGcgat > 3:136239/1‑146 (MQ=255)
ttGCATAGGGCTACTCCTGGATTTGGGCAACAGCAACCCGGCGCGGCGGCACTGCATGGCCACCGGCGTGCGGGTTGCATCGAGAGAGGTC‑GGCAGGCGGGCCCCGGCCCGcc > 5:103702/1‑113 (MQ=255)
ttGCATAGGGCTACTCCTGGATTTGGGCAACAGCAACCCGGCGCGGCGGCACTGCATGGCCACCGGCGTGCGGGTTGCATCGAGAGAGGTC‑GGCAGGCGGGCCCCGGCCCGcc < 6:103702/113‑1 (MQ=255)
cATAGGGCTACTCCTGGATTTGGGCAACAGCAACCCGGCGCGGCGGCACTGCATGGCCACGGGGGTGGGGGTTGCATCTAGAGAGGTC‑GGCAGGCGGGCCCCGGCCCGCCTGCCCTGCCGTTGCGTGAAGCGCTGGGCCGCTAGCGGtt < 8:460209/149‑1 (MQ=255)
ttcgggCTACTCCTGTATTTGGGCAACCGCAACCGGGCGCGGCGGCACTGCTTGGCCACGGGGGGGGGGGTTGAATCGAGAGTGGGC‑GGCCGGCGGGCCCCGGCCCGCCTGCCCTGCCGTTGCGTGAAGCGCTGGGCCGCTAGCGGTTg < 4:110464/146‑1 (MQ=255)
aTAGGGCTACTCCTGGATTTGGGCAACAGCAACCCGGCGCGGCGGCACTGCATGGCCACCGGCGTGCGGGTTGCATCGAGAGAGGTC‑GGCCGGCGGGGCCCCGCCCCCCAGCCCAGCCGGTGGGGGTAGCGCGGGGGCCCGAGCGGGTg > 3:205325/1‑149 (MQ=255)
cTACTCCTGGATTTGGGCAACAGCAACCCGGCGCGGCGGCACTGCATGGCCACCGGCGTGCGGGTTGCATCGAGAGAGGTC‑GGCAGGCGGGCCCCGGCCCGCCTGCCCTGCCGTTGCGTGAAGCGCTGGGCCGCTAGCGGTTGACCAGc < 6:87964/149‑1 (MQ=255)
tttGGGCAAAAGAAACCCGGCCCGGCGGCCATGCATGGCCACCGGCGTGCGGGTTGCATCGAGAGAGGTC‑GGCAGGCGGGCCCCCCCCCCCCGGCCCGGCCCTTGGGGGAAACGCGGGGGCCCGTGGGGTTGACCACCATGGGCggg > 4:56960/1‑146 (MQ=255)
caccAACCCGGCGCGGCGGCACTGCAGGGCCACGGGCGGGGGGGTTGATTCGACCGAGGGC‑GGCAGGGGGGCCCCGGCCCGCCTGCCCTGCCGTTGCGTGAAGCGCTGGGCCGCTAGCGGTTGACCAGCTTGGCCGGCAAGGCGATGAc < 1:22367/146‑1 (MQ=255)
cAGCAACCCGGCGCGGCGGCACTGCATGGCCACCGGCGTGCGGGTTGCATCGAGAGAGGTC‑GGCAGGCGGGCCCCGGCCCGCCTGCCCTGCCGTTGCGTGAAGCGCTGGGCCGCTAGCGGTTGACCAGCTTGGCCGGCAAGGCGATGAc < 2:148027/149‑1 (MQ=255)
ccGGCGCGGCGGCACTGCATGGCCACCGGCGTGCGGGTTGCATCGAGAGAGGTC‑GGCACGCCGGCCCCCGCCCCCCAGCCCAGCCCTTGGGTGAAGCCCTGGGCCGCTACCCGTTGACAAGCTTGGCCCGCAAGGCCATGAACACGAag > 8:16358/1‑149 (MQ=255)
gggggcACTGCAGGGCCACGGGCGTGGGGTTTGCATCGAGTGTGGTC‑GGCTGGGGGGCCCGGGCCGGCCGGCCCTGCCGTTGCGTGAAGCGCTGGGCCGCTAGCGGTTGACCAGCTTGGCCGGCAAGGCGATGACCAGGAAGCAGCTGa < 4:147595/146‑1 (MQ=255)
ggcggcACTGCTTGGCCCCGGGGGTGGGGGTTGAATCGAGTGAGGGG‑GGCCGGGGGGCCCCGGCCGGCGTGCCCTGCCGTTGCGTGAAGCGCTGGGCCGCTAGCGGTTGACCAGCTTGGCCGGCAAGGCGATGACCAGGAAGCAGCTGa < 4:328768/149‑1 (MQ=255)
aCTGCATGGCCACCGGCGTGCGGGTTGCATCGAGAGAGGTC‑GGCAGGCGGGCCCCGGCCCGCCTGCCCTGCCGTTGCGTGAAGCGCTGGGCCGCTAGCGGTTGACCAGCTTGGCCGGCAAGGCGATGACCAGGAAGCAGCTGAGGATCa < 1:4930/149‑1 (MQ=255)
aCTGCATGGCCACCGGCGTGCGGGTTGCATCGAGAGAGGTC‑GGCAGGCGGGCCCCGGCCCGCCTGCCCTGCCGTTGCGTGAAGCGCTGGGCCGCTAGCGGTTGACCAGCTTGGCCGGCAAGGCGATGACCAGGAAGCAGCTGAGGATCa < 8:391369/149‑1 (MQ=255)
gCGTGCGGGTTCCATCGATAGAGGTC‑GGCAGGCGGGCCCCGGCCCGCCTGCCCTGCCGTTGCGTGAAGCGCTGGGCCGCTAGCGGTTGACCAGCTTGGCCGGCAAGGCGATGACCAGGAAGCAGCTGa < 7:256299/128‑1 (MQ=255)
aTCGAGAGAGGTC‑GGCAGGCGGGCCCCCGCCCGCCGGCCCTGCCGTTGCGTGAAGCGCTGGGCCGCGAGCGGTTGACCAGCGTGGCCGGCAAGGCGATGACCACGAAGCAGCGGAGGGACAGGCAGCCGGCCAACACCCAcagcgcagc > 8:207461/1‑149 (MQ=255)
gtgtgagGTC‑GGCTGGCGGGCCCGGGCCCGCCTGCCCTGCCGTTGCGTGAAGCGCTGGGCCGCTAGCGGTTGACCAGCTTGGCCGGCAAGGCGATGACCAGGAAGCAGCTGAGGATCAGGCAGCCGGCAAACACCCACAGCGCAGCGt < 2:237365/144‑1 (MQ=255)
ggCTGGCGGGCCCCGGCCCGCCTGCCCTGCCGTTGCGTGAAGCGCTGGGCCGCTAGCGGTTGACCAGCTTGGCCGGCAAGGCGATGACCAGGAAGCAGCTGAGGATCAGGCAGCCGGCAAACACCCACAGCGCAGCGTGCGAGGTGCCg < 6:260986/149‑1 (MQ=255)
ggCCGGGGGGCCCGGCCCCGCCGGCCCTGCCGTTGCGTGAAGCGCTGGGCCGCTAGCGGTTGACCAGCTTGGCCGGCAAGGCGATGACCAGGAAGCAGCTGAGGATCAGGCAGCCGGCAAACACCCACAGCGCAGCGTGCGAGGTGCCg < 5:145010/149‑1 (MQ=255)
gCAGGCGGGCCCCGGCCCGCCTGCCCTGCCGTTGCGTGAAGCGCTGGGCCGCTAGCGGTTGACCAGCTTGGCCGGCAAGGCGATGACCAGGAAGCAGCTGAGGATCAGGCAGCCGGCAAACACCCACAGCGCAGCGTGCGAGGTGCCgg < 6:312413/149‑1 (MQ=255)
gCAGGCGGGCCCCGGCCCGCCTGCCCTGCCGTTGCGTGAAGCGCTGGGCCGCTAGCGGTTGACCAGCTTGGCCGGCAAGGCGATGACCAGGAAGCAGCTGAGGATCAGGCAGCCGGCAAACACCCACAGCGCAGCGTGCGAGGTGCCgg > 2:372335/1‑149 (MQ=255)
|
AACCGCCGGCCAGGCGTGCAGACGAAGAAAAACGCGGCGCAGTGAAACCTTGCATAGGGCTACTCCTGGATTTGGGCAACAGCAACCCGGCGCGGCGGCACTGCATGGCCACCGGCGTGCGGGTTGCATCGAGAGAGGTC‑GGCAGGCGGGCCCCGGCCCGCCTGCCCTGCCGTTGCGTGAAGCGCTGGGCCGCTAGCGGTTGACCAGCTTGGCCGGCAAGGCGATGACCAGGAAGCAGCTGAGGATCAGGCAGCCGGCAAACACCCACAGCGCAGCGTGCGAGGTGCCGG > NC_002947_CJ‑RC/4442583‑4442872
|
| 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
