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 |
|
A1 F42 I1 R1
|
60 |
69.9 |
3000528 |
98.3% |
2949519 |
146.4 |
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%
| 20.3
/ NA
| 8 | 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 (3/5); total (3/5) |
| * | NC_002947_CJ‑RC | 5,684,230 | 2 | . | G | 100.0%
| 21.6
/ NA
| 8 | 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 (3/5); total (3/5) |
| * | NC_002947_CJ‑RC | 5,684,230 | 3 | . | G | 87.5%
| 17.2
/ ‑2.2
| 8 | intergenic (‑133/+71) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein |
| Reads supporting (aligned to +/- strand): ref base . (0/1); new base G (3/4); total (3/5) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.25e-01 |
| * | NC_002947_CJ‑RC | 5,684,230 | 4 | . | G | 87.5%
| 17.9
/ ‑2.2
| 8 | intergenic (‑133/+71) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein |
| Reads supporting (aligned to +/- strand): ref base . (0/1); new base G (3/4); total (3/5) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.65e-01 |
ACCGTAATACATGCAAACACAGACCTCCTGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGC‑GGCCCCAGGCTTTCATTGCCACTGCATGAACCGC‑‑‑‑G‑‑CTGCTGCGCAGCCCTATCGCGACACAAGGCCGCTCCCACTCCAGACCACCAGGCCCTGCGCCTCACATCCTAACCAAGGTCAGGTTGCAGATCCGCGTCACGCACCAGCCTTTC > NC_002947_CJ‑RC/5684086‑5684345
||||
aCCGTAATACATGCAAACACAGACCTCCTGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGC‑GGCCCCAGGCTTTCATTGCCACTGCATGAACcgccgg < 3:157350/148‑4 (MQ=255)
ccGTAATACATGCAAACACAGACCTCCTGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGGCATTTTTGGCGAAAGGGGGGCGAAGCGGGCCCCCGGGTTGAATTG‑CACAGGATGAACcgcccggg > 6:333397/1‑144 (MQ=255)
ccGTAATACATGCAAACACAGACCTCCTGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGC‑GGCCCCAGGCTTTCATTGCCACTGCATGAACcgccgggg < 6:102901/149‑6 (MQ=255)
cacaGACCTCCTGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGC‑GGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGG‑‑CTGCTGCGCAGCCCTa < 5:299787/149‑1 (MQ=37)
tggTGGGCTGGGTTCCTGTTGTGTTGCTGATGGCTTCGTTCTTTGTGGGTGCGGCGTTGTGGCGCGAATGGGGCGCGAAGC‑GGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGG‑‑CTGCTGCGCAGCCCTATCGCGACACAAgg < 5:194855/148‑1 (MQ=25)
agggtgccTGGGTTCCTTATGAGATGCAGATGGCTGCGTGCATTGTGGCTCCGGCCTTGAGCCGCGAAAGGGGCTCGAAGC‑GTCCCAAGGCTTTCATTGCCACTGCATGAACCGCCG‑‑GCCCTGCTCCGCAGGCCTATCGCGACACAAg < 6:107036/141‑1 (MQ=255)
aGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGC‑GGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGG‑‑CTGCTGCGCAGCCCTATCGCGACACAAgg < 5:138462/149‑1 (MQ=25)
gcgAAAGGGGCGCGAAGC‑GGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGG‑‑GTGCTGCGCAGCCCAATAGCGCCCCCAAGCCGCGCCCCCACCAGCCCACCACGCCCAGCCCCGCACAACCAAACCAAAGGGACGTTGCaca > 6:68255/1‑146 (MQ=255)
gAAGC‑GGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGG‑‑GGGGTGCGCAGCCCAATCGCGCCACAAGGCCCCACCCCCACCCGACCCCCCCGCCCTGGGCCGCACAACAAAACCAAGGGCAGGTTGGAGATACCCGGCACGcc > 8:118613/1‑147 (MQ=255)
ccccAGGCTTTCATTGCCACTGCATGAACCGCCGGGG‑‑GAGCTGCGCAGCCCTTTAGCGACACAAGGCCGCTCCCCCTCCAGACCACCAGGCCCGGCGGCGCACATACTAACCAAGGGCAGGGTTCAGATACGCGGGGCGCAcccggcgt > 2:217933/1‑143 (MQ=255)
aTTGCCACTGCATGAACCGCCGGGG‑‑CTGCTGCGCAGCCCTATCGCGACACAAGGCCGCTCCCTCTCCAGACCACCAGGCCCTGCGCCTCACATCCTAACCAAGGTCAGGTTGCAGATCCGCGTCTCGCACCAGCCTTTc < 5:340136/139‑1 (MQ=38)
||||
ACCGTAATACATGCAAACACAGACCTCCTGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGC‑GGCCCCAGGCTTTCATTGCCACTGCATGAACCGC‑‑‑‑G‑‑CTGCTGCGCAGCCCTATCGCGACACAAGGCCGCTCCCACTCCAGACCACCAGGCCCTGCGCCTCACATCCTAACCAAGGTCAGGTTGCAGATCCGCGTCACGCACCAGCCTTTC > NC_002947_CJ‑RC/5684086‑5684345
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
