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 F11 I1 R1
|
56 |
91.5 |
3907174 |
98.4% |
3844659 |
146.2 |
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 | 93.3%
| 40.4
/ ‑2.5
| 15 | 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 C (2/12); total (2/13) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.59e-01 |
| * | NC_002947_CJ‑RC | 5,684,230 | 2 | . | G | 93.3%
| 42.8
/ ‑2.7
| 15 | 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 (2/12); total (2/13) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.63e-01 |
| * | NC_002947_CJ‑RC | 5,684,230 | 3 | . | G | 93.3%
| 42.6
/ ‑2.7
| 15 | 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 (2/12); total (2/13) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.59e-01 |
| * | NC_002947_CJ‑RC | 5,684,230 | 4 | . | G | 93.3%
| 42.2
/ ‑2.7
| 15 | 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 (2/12); total (2/13) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.59e-01 |
CCGTAATACATGCAAACACAGACCTCCTGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCG‑C‑‑‑‑GCTGCTGCGCAGCCCTATCGCGACACAAGGCCGCTCCCACTCCAGACCACCAGGCCCTGCGCCTCACATCCTAACCAAGGTCAGGTTGCAGATCCGCGTCACGCACCAGCCTTTCCAATGCGACCAG > NC_002947_CJ‑RC/5684087‑5684357
||||
ccGTAATACATGCAAACACAGACCTCCTGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACcg‑ccgggg < 1:21365/149‑6 (MQ=255)
ccGAAATACATGCAAACACAGACCTCCTGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACcg‑ccgggg < 3:108843/149‑6 (MQ=255)
aTGCAAACACAGACCTCCTGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACcg‑ccggg < 8:264592/139‑5 (MQ=255)
aTGCAAACACAGACCTCCTGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACcg‑ccggg > 7:264592/1‑135 (MQ=255)
aaaCACAGACCTCCTGCGGTGGGCTGGGTTCCTGTTTTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCG‑CCGGGGCTGCTGCGCAGcc < 3:378014/149‑1 (MQ=37)
ctgtcgtcctGTGGTGGGCTGGGTTGGTGTTGTGATGCTGATGGCTTCGTTGTTTGTGGGTGCGGCCTTGTGTCGGGAATGGGGCGCGAAGCGGCCCCAGGCTTTGATTGCCAGTGCATGAACCG‑CCGGGGCTGCTGCGCAGCCCTATc < 4:461049/143‑1 (MQ=25)
caGACCTCCTGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCG‑CCGGGGCTGCTGCGCAGCCCTATc < 7:287262/149‑1 (MQ=37)
cctcctGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCG‑CCGGGGCTGCTGCGCAGCCCTATCGCGa < 2:461793/149‑1 (MQ=37)
cctcctGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCG‑CCGGGGCTGCTGCGCAGCCCTATCGCGa < 3:103157/149‑1 (MQ=37)
ggTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCG‑CCGGGGCTGCTGCGCAGCCCTATCGCGACACAAgg < 6:179183/148‑1 (MQ=25)
gTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGCGCGGCCTGGTGGCGCGAAAGGGGCGCGACGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCG‑CCGGGGCTGCTGCGCAGCCCTATCGCGACACAAGGc < 1:256887/148‑1 (MQ=37)
gttgtGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCC‑‑‑‑GGGGCTGCGCAGcagcc < 5:152921/116‑5 (MQ=25)
ttgtGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCG‑CCGGGGCTGCTGCGCAGCCCTATCGCGa < 1:427924/124‑1 (MQ=25)
aaaGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCG‑CCGGGGCTGCTGCGCAGCCCTATAGCGACACAAGGCCGCACCCACTCCAGACCCCCAGGCCCAGCGCCACACATCCAAACCAAGGTCAGGTTGGAGAACcg > 2:302588/1‑149 (MQ=25)
ccAGGCTTTCATTGCCACTGCATGAACCG‑CCGGGGCTGCTGCGCAGCCCAATAGCGGCACAAGGCCGCACCCACTCCAGACCACCACGCCCTGCGCCGCACAAACAAACCAACGTCAGGTTGCAGATACGCGGCACCCACCAGCCatt > 6:194348/1‑148 (MQ=255)
gCTTTCATTGCCACTGCATGAACCG‑CCGGGGCTGCTGCGCAGCCCTATCGCGACACAAGGCCGCTCCCACTCCAGACCACCAGGCCCTGCGCCTCACATCCTAACCAAGGTCAGGTTGCAGATCCGCGTCACGCACCAGCCTTTCCAAt < 1:484473/149‑1 (MQ=38)
cATTGCCACTGCATGAACCG‑CCGGGGCTGCTGCGCAGCCCTATCGCGACACAAGGCCGCTCCCACTCCAGACCACCAGGCCCTGCGCCTCACATCCTAACCAAGGTCAGGTTGCAGATCCGCGTCACGCACCAGCCTTTCCAATGCGa < 3:305583/148‑1 (MQ=38)
aTTGCCACTGCATGAACCG‑CCGGGGCTGCTGCGCAGCCCTATCGCGACACAAGGCCGCTCCCACTCCAGACCACCAGGCCCTGCGCCTCACATCCTAACCAAGGTCa < 7:368397/107‑1 (MQ=37)
gCCACTGCATGAACCG‑CCGGGGCTGCTGCGCAGCCCTATCGCGACACAAGGCCGCTCCCACTCCAGACCACCAGGCCCTGCGCCTCACATCCTAACCAAGGTCAGGTTGCAGATCCGCGTCACGCACCAGCCTTTCCAATGCGACCAg < 7:144243/148‑1 (MQ=38)
||||
CCGTAATACATGCAAACACAGACCTCCTGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCG‑C‑‑‑‑GCTGCTGCGCAGCCCTATCGCGACACAAGGCCGCTCCCACTCCAGACCACCAGGCCCTGCGCCTCACATCCTAACCAAGGTCAGGTTGCAGATCCGCGTCACGCACCAGCCTTTCCAATGCGACCAG > NC_002947_CJ‑RC/5684087‑5684357
|
| 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
