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 F22 I1 R1
|
55 |
83.2 |
3548070 |
98.1% |
3480656 |
146.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_002947_CJ‑RC |
5,684,230 |
+CGGG |
intergenic (‑133/+71) |
PP_4986 ← / ← PP_4987 |
hemolysin III family channel protein/putative Chemotaxis protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_002947_CJ‑RC | 5,684,230 | 1 | . | C | 100.0%
| 24.5
/ NA
| 9 | intergenic (‑133/+71) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base C (4/5); total (4/5) |
| * | NC_002947_CJ‑RC | 5,684,230 | 2 | . | G | 77.8%
| 12.6
/ ‑1.1
| 9 | intergenic (‑133/+71) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein |
| Reads supporting (aligned to +/- strand): ref base . (0/0); major base G (3/4); minor base A (1/1); total (4/5) |
| 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 |
| * | NC_002947_CJ‑RC | 5,684,230 | 3 | . | G | 100.0%
| 25.0
/ NA
| 9 | intergenic (‑133/+71) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base G (4/5); total (4/5) |
| * | NC_002947_CJ‑RC | 5,684,230 | 4 | . | G | 100.0%
| 25.0
/ NA
| 9 | intergenic (‑133/+71) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base G (4/5); total (4/5) |
CACCGTAATACATGCAAACACAGACCTCCTGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGC‑‑‑‑GCTGCTGCGCAGCCCTATCGCGACACAAGGCCGCTCCCACTCCAGACCACCAGGCCCTGCGCCTCACATCCTAACCAAGGTCAGGTTGCAGATCCGCGTCACGCACCAGC > NC_002947_CJ‑RC/5684085‑5684340
||||
cACCGTAATACATGCAAACACAGACCTCCTGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACcgccgg < 7:172085/149‑4 (MQ=255)
aCCGTAATACATGCAAACACAGACCTCCTGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACcgccgg < 3:265304/148‑4 (MQ=255)
aaaCACAGACCTCCTGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCGCAGcc < 3:348875/149‑1 (MQ=38)
gACCTCCTGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCGCAGCCCTATcgc < 3:113184/149‑1 (MQ=37)
gACCTCCTGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCGCAGCCCTATcgc < 8:374608/149‑1 (MQ=37)
gcgAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCAGGGCTGCTGCGCAGCCCTATCGCGACACAAGGCCGCTCCCACTCCAGACCACCAGGccc < 3:188367/113‑1 (MQ=25)
gcgAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCAGGGCTGCTGCGCAGCCCTATCGCGACACAAGGCCGCTCCCACTCCAGACCACCAGGccc > 4:188367/1‑113 (MQ=25)
gAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCGCAGCCCTATAGCGACAAAAGGCCGCGCCCACAACAGACCACCAGGCCCAGCGCCTCACCTCCTAACCAAGGGCAGGTTTCAGATcc > 2:265712/1‑149 (MQ=25)
gAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGGGGGCGGCGCAGCCCGATAGCGCCACCACGCCGCGCCCCCACCCCACCACCCCGCCCCGGGGCGCACCTCCGAAACAAGGGGAGGTTGGAGCTACCCGGCACGccc > 8:81530/1‑147 (MQ=255)
gAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCAGCGCAGCCCAATAGCGACACAAAGCCGCACCCACAACAAACCACCCGGCCCAGCGCCACCCAACCAAACCAAAGAAAGTTTTAAGATAAGCGTCACGCAc > 4:288302/1‑149 (MQ=255)
cGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCGCAGCCCTATCGCGACACAAGGCCGCTCCCACTCCAGACCACCAGGCCCTGCGCCTCACATCCTAACCAAGGTCAGGTTGCAGATCCGCGTCACGCACCAGc < 7:247156/149‑1 (MQ=38)
||||
CACCGTAATACATGCAAACACAGACCTCCTGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGC‑‑‑‑GCTGCTGCGCAGCCCTATCGCGACACAAGGCCGCTCCCACTCCAGACCACCAGGCCCTGCGCCTCACATCCTAACCAAGGTCAGGTTGCAGATCCGCGTCACGCACCAGC > NC_002947_CJ‑RC/5684085‑5684340
|
| 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
