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 |
|
A3 F14 I0 R1
|
206 |
76.7 |
3255580 |
98.8% |
3216513 |
146.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
NC_002947_CJ‑RC |
2,793,755 |
A→C |
25.4% |
intergenic (+64/+63) |
PP_2445 → / ← PP_2446 |
membrane protein/hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_002947_CJ‑RC | 2,793,755 | 0 | A | C | 25.4%
| 33.2
/ 2.6
| 23 | intergenic (+64/+63) | PP_2445/PP_2446 | membrane protein/hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base A (7/10); new base C (4/2); total (11/12) |
| Fisher's exact test for biased strand distribution p-value = 3.71e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CATGGCGTTCTCGACGGCTATCGAGGTCCTCAACATCCTGGCCCGTCGAGCGCGTTTGAAGCGTGAGGCGGCTGAAGGTTGATGTAAAAAGGGGCGCCTCGCGCCCCTCTTGCGGACAAGCCCGCTGCACAGGTATTCGCGTGGCACTGGCAACGCGAATACCTGTGCAGCGGGCTTGTCAGTCAGTGGGCTTCGGGAAATCCTGAGGTTAGCTCACCCCGGCATGCCGCCGGGGCCGTCTTACTGGCTGTGGCTTGGCGGGTGCCTGCGGTGGCAGGTGGTGTGCATGAC > NC_002947_CJ‑RC/2793610‑2793900
|
cATGGCGTTCTCGACGGCTATCGAGGTCCTCAACATCCTGGCCCGTCGAGCGCGTTTGAAGCGTGAGGCGGCTGAAGGTTGATGTAAAAAGGGGCGCCTCGCGCCCCTCTTGCGGACAAGCCCGCTGCACAGGTATTCGCGTGGCACTg < 1:341499/149‑1 (MQ=255)
tGGCGTTCTCGACGGCTATCGAGGTCCTCAACATCCTGGCCCGTCGAGCGCGTTTGAAGCGTGAGGCGGCTGAAGGTTGATGTAAAAAGGGGCGCCTCGCGCCCCTCTTGCGGACAAGCCCGCTGCACAGGTATTCGCGTGGCACTGGc < 2:268939/149‑1 (MQ=255)
cGACGGCTATCGAGGTCCTCAACATCCTGGCCCGTCGAGCGCGTTTGAAGCGTGAGGCGGCTGAAGGTTGATGTAAAAAGGGGCGCCTCGCGCCCCTCTTGCGGACAAGCCCGCTGCACAGGTATTCGCGTGGCACTGGCAACGCGAAt < 1:275608/149‑1 (MQ=255)
ggCTATCGAGGTCCTCAACATCCTGGCCCGTCGAGCGCGTTTGAAGCGTGCGGCGGCTGACGGTTGATGTAAAAAGGGGCGCCTCGCGCCCCTCTTGCGGACAAGCCCGCTGCACAGGTATTCGCGTGGCACTGGCAACGCGAATACCt < 3:33955/149‑1 (MQ=255)
ggCTATCGAGGTCCTCAACATCCTGGCCCGTCGAGCGCGTTTGAAGCGTGAGGCGGCTGAAGGTTGATGTAAAAAGGGGCGCCTCGCGCCCCTCTTGCGGACAAGCCCGCTGCACAGGTAATAGCGGGGGCCTGGGCACCCGAATaa > 2:298451/1‑146 (MQ=255)
ggCTATCGAGGTCCTCAACATCCTGGCCCGTCGAGCGCGTTTGAAGCATGAGGCGGCTGAAGGTTGATGTAAAAAGGGGCGCCTCGCGCCCCTCTTGCGGACAAGCCCGCTGCACAGGTATTCGCGTTGCCAGTGCCACGCGAATACCt < 2:218684/149‑1 (MQ=37)
tCGAGGTCCTCAACATCCTGGCCCGTCGAGCGCGTTTGAAGCGTGAGGCGGCTGAAGGTTGATGTAAAAAGGGGCGCCTCGCGCCCCTCTTGCGGACAAGCCCGCTGCACAGGTATTCGCGTGGCACTGGCAACGCGAATACCTGTGCa < 3:383073/149‑1 (MQ=255)
caGGCCCACACCATCCCGCCCCGCCCAGCGCGTTTCACGCGTGAGGCGGCTGAAGGATTATGTAAAACGGGGCCCCGCGCGCCCCTCTTGCGGACAAGCCCGCTGCACAGGTATTCGCGTGGCACTGGCAACGCGAATACCTGTGCAg < 5:222716/147‑1 (MQ=25)
gTCCTCAACATCCTGGCCCGTCGAGCGCGTTTGAAGCGTGAGGCGGCTGAAGGTTGATGTAAAAAGGGGCGCCTCGCGCCCCTCTTGCGGACAAGCCCGCTGCACAGGTATTAGCGTGGCACTGGCCACGCGAATACCTGTGCAGCggg > 2:6688/1‑149 (MQ=255)
aCATCCTGGCCCGTCGAGCGCGTTTGAAGCGTGAGGCGGCTGAAGGTTGATGTAAAAAGGGGCGCCTCGCGCCCCTCTTGCGGACAAGCCCGCAGCACCCGTATTAGCGGGGCCCAGGGCACCCGCAAACCGGTGGAGCgggggtgg > 7:324030/1‑142 (MQ=255)
tCGAGCGCGTTTGAAGCGTGAGGCGGCTGAAGGTTGATGTAAAAAGGGGCGCCTCGCGCCCCTCTTGCGGACAAGCCCGCAGCACCGGTATTAGCGGGGCCCAGGCCACGCGAATACCTGTGCCGCGGGCTTGTGAGTCAGTgggggt > 8:310315/1‑145 (MQ=38)
gTGAGGCGGCTGAAGGTTGATGTAAAAAGGGGCGCCTCGCGCCCCTCTTGCGGACAAGCCCGCAGCACAGGTATTAGCGGGGCACTGGCAACGCGAATAACAGTGGAGCGGGCGCGTCAGTCAGTGGGGGTCGGGAAATACTGAGGtt > 6:129527/1‑148 (MQ=255)
ggggCGCCTCGCGCCCCTCTTGCGGACAACCCCGCTGCACTGGTATTCGCGTGGCACTGGCAACGCTAATACCTGTGCTGCGGGCTTGTCAGTCAGTGGGCTTCGGGAAATCCTGAGGTTAGCTCACCCCGGCATGCCGCCGGGGCCg < 6:111702/148‑1 (MQ=255)
cccgccCCCCTCTGGCGCACAACCCCGCGCCACCGGTATCCGCGGGCCCCGGCCAACGCTAAAACCTGTGCAGCGGGCTTGTCAGTCAGTGGGCTTCGGGAAATCCTGAGGTTAGCTCACCCCGGCATGCCGCCGGGGCCGTCTTACTg < 1:321771/147‑1 (MQ=255)
tttgggaacacGCCCGCTCCACCGTTTTTGGCGTGCAACTGCCACCGCTAAAACGTGTGCAGCGGGCTTGTCAGTCAGTGGGCTTCGGGAAATCCTGAGGTTAGCTCACCCCGGCATGCCGCCGGGGCCGTCTTACTGGCTGTGGCt < 8:405940/140‑1 (MQ=255)
aGCCCGCATCACAGGTATTAGCGTGGCACTGGCAACGCGAATACCTGTGCAGCGGGGTTGTGAGTCAGTGGGGGTCGGGAAATCCTGAGGTTAGCTCACCCCGGCATGCCGCCGGGGCCGTATTAATGGCTGTGGCTTGGCGGGTGcc > 6:164401/1‑148 (MQ=255)
gCCCGCTGCACAGGTATTAGCGTGGCCCTGGCAACGCGAATACCTGTGCAGCGGGCTTGTCAGTCAGTGGGCGTCGGGAAATCCTGAGGTTAGCTCACCCCGGCATGCCGCCGGGGCCGTCTTACTGGCTGTGGCTTGGCGGGTGCCt > 6:117342/1‑148 (MQ=255)
gCTGCACAGGTATTCGCGTGGCACTGGCAACGCGAATACCTGTGCAGCGGGCTTGTCAGTCAGTGGGCTTCGGGAAATCCTGAGGTTAGCTCACCCCGGCATGCCGCCGGGGCCGTCTTACTGGCTGTGGCTTGGCGGGTGCCTGCGGt > 1:139435/1‑149 (MQ=255)
caccgttATCCGCGGGCCACGGCCAACCCTAAAACCTGGGCAGCGGGCTTGTCAGTCAGTGGGCTTCGGGAAATCCTGAGGTTAGCTCACCCCGGCATGCCGCCGGGGCCGTCTTACTGGCTGTGGCTTGGCGGGTGCCTGCGATGGCa < 1:219832/143‑1 (MQ=255)
caGGTATTCGCGTGGCACTGGCAACGCGAATACCTGTGCAGCGGGCTTGTCAGTCAGTGGGCTTCGGGAAATCCTGAGGTTAGCTCACCCCGGCATGCCGCCGGGGCCGTCTTACTGGCTGTGGCTTGGCGGGTGCCTGCGGTGGCAg > 7:116996/1‑148 (MQ=255)
ggTATTCGCGTGGCACTGGCAACGCGAATACCTGTGCAGCGGGCTTGTCAGTCAGTGGGCTTCGGGAAATCCTGAGGTTAGCTCACCCCGGCATGCCGCCGGGGCCGTCTTACTGGCTGTGGCTTGGCGGGTGCCTGCGGTGGCAggt > 7:158875/1‑148 (MQ=255)
ttCGCGTGGCACTGGCAACGCGAATACCTGTGCAGCGGGCTTGTCAGTCAGTGGGCTTCGGGAAATCCTGAGGTTAGCTCACCCCGGCATGCCGCCGGGGCCGTCTTACTGGCTGTGGCTTGGCGGGTGCCGGCGGTGGCAGgtggtg > 5:101841/1‑148 (MQ=255)
gccACTGCCAACGCTAATACCTGTGCAGCGGGCTTGTCAGTCAGTGGGCTTCGGGAAATCCTGAGGTTAGCTCACCCCGGCATGCCGCCGGGGCCGTCTTACTGGCTGTGGCTTGGCGGGTGCCTGCGGTGGCAGGTGGTGTGCATGAc < 1:6688/147‑1 (MQ=255)
|
CATGGCGTTCTCGACGGCTATCGAGGTCCTCAACATCCTGGCCCGTCGAGCGCGTTTGAAGCGTGAGGCGGCTGAAGGTTGATGTAAAAAGGGGCGCCTCGCGCCCCTCTTGCGGACAAGCCCGCTGCACAGGTATTCGCGTGGCACTGGCAACGCGAATACCTGTGCAGCGGGCTTGTCAGTCAGTGGGCTTCGGGAAATCCTGAGGTTAGCTCACCCCGGCATGCCGCCGGGGCCGTCTTACTGGCTGTGGCTTGGCGGGTGCCTGCGGTGGCAGGTGGTGTGCATGAC > NC_002947_CJ‑RC/2793610‑2793900
|
| 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
