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 |
|
A4 F25 I1 R1
|
60 |
73.8 |
3348830 |
98.7% |
3305295 |
145.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_002947_CJ‑RC |
1,070,248 |
+GA |
intergenic (+48/+94) |
aroP‑I → / ← PP_0928 |
aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_002947_CJ‑RC | 1,070,246 | 1 | . | G | 75.0%
| 41.4
/ 15.1
| 26 | intergenic (+46/+96) | aroP‑I/PP_0928 | aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein |
| Reads supporting (aligned to +/- strand): ref base . (0/6); new base G (4/14); total (6/20) |
| Fisher's exact test for biased strand distribution p-value = 5.39e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
| * | NC_002947_CJ‑RC | 1,070,246 | 2 | . | A | 76.9%
| 48.4
/ 15.4
| 26 | intergenic (+46/+96) | aroP‑I/PP_0928 | aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein |
| Reads supporting (aligned to +/- strand): ref base . (0/6); new base A (6/14); total (6/20) |
| Fisher's exact test for biased strand distribution p-value = 2.80e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CCTGACGCCGCCGATTCGCATCTCGGTAATGCTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑T‑‑GT‑‑G‑‑ATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCAAGCACGCACAGTGGTGTACA > NC_002947_CJ‑RC/1070098‑1070379
||
ccTGACGCCGCCGATTCGCATCTCGGTAATGCTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑t‑‑gt < 8:97749/149‑1 (MQ=255)
ccTGACGCCGCCGATTCGCATCTCGGTAATGCTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑t‑‑gt < 2:198979/149‑1 (MQ=255)
ccTGACGCCGCCGATTCGCATCTCGGTAATGCTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑t‑‑gt < 8:325054/149‑1 (MQ=255)
aCGCCGCCGATTCGCATCTCGGTAATGCTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑T‑‑GT‑‑G‑‑aga < 2:4858/149‑3 (MQ=255)
gccgccGATTCGCATCTCGGTAATGCTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGTTATGGTTTGTTCGTAAGGGGTATGCGGTTAGGTTTTCGGCGCC‑‑T‑‑GT‑‑G‑‑agatc < 2:144653/149‑5 (MQ=255)
cTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑T‑‑GTGAG‑‑ATCGAGCGCCGCCCGCGCGGCGCTCGAt < 5:291164/149‑1 (MQ=38)
cTGATCCCGGCATGGATCGCTGTGCTGTGGGGGGCTTTCAAGCTTAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGTTATGCCGTTAGGTTTTCCGCGCC‑‑T‑‑GTGAG‑‑ATCGAGCGCCGCGCGGGCGGCGCTCGAt < 7:86579/149‑1 (MQ=38)
ccGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑T‑‑GTGAG‑‑ATCGAGCGCCGCGCGGGCGGCGCTCGATCTcaca < 6:183222/149‑1 (MQ=255)
gCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑T‑‑GTGAG‑‑ATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGc > 8:318524/1‑149 (MQ=255)
gtgggtggCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑T‑‑GTGAG‑‑ATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGCTGAAATCCAAAAgg > 6:334233/1‑148 (MQ=37)
ggCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑T‑‑GTTAG‑‑ATAGAGCGCCCCCCGGGCCGCCCTCCCAGAAAAAGGGCATGAAATCCAAAAGGCATGCGt > 6:324329/1‑149 (MQ=255)
ggCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑T‑‑GTGAG‑‑ATCGAGCGCCGCgcgg < 2:127078/87‑1 (MQ=38)
ggCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑T‑‑GTGAG‑‑ATCGAGCGCCGCgcgg > 1:127078/1‑87 (MQ=38)
ggCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑T‑‑GTGAG‑‑ATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGt > 6:225812/1‑149 (MQ=255)
cTCGCCCGGCCATGGGCGGTTGGGTTGTGTTCGTATGGGTCTTGCCGTTAGGTTTTCGGCGCG‑‑T‑‑GG‑‑GCCATCGTGGGCGGCGGGGGCGGCGCGCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTc < 4:78179/149‑1 (MQ=255)
gCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑T‑‑GTGAG‑‑ACCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTcccc < 5:111783/149‑1 (MQ=255)
gcaaaGGGCGGTTCGGGTTTGTTGGTAAGGGGTATGCGGTTTGGTTTTGGGCGCG‑‑T‑‑GTGAG‑‑ATCGAGCGCCGCGGGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTcc < 4:182822/145‑1 (MQ=37)
aTCGTGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCGGT‑‑GA‑‑G‑‑AGCGCGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAAt < 8:54994/149‑1 (MQ=38)
tCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑T‑‑GTGAG‑‑ATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAAtg < 2:61731/149‑1 (MQ=255)
gggTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑T‑‑GTGAG‑‑ATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAAtgct < 7:318524/149‑1 (MQ=255)
gggTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑T‑‑GTGAG‑‑ATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAAtgct < 3:117455/149‑1 (MQ=255)
gggTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑T‑‑GTGAG‑‑ATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAAtgct < 5:225812/149‑1 (MQ=255)
ggTTTGTTCGAAGGGGGTAGGCCGTTAGGTTTGCGGCGCG‑‑T‑‑GT‑‑GCCCCCGCGCCCCGCGGGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAAtgctg < 3:223831/149‑1 (MQ=255)
gTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑T‑‑GTTAG‑‑ATAGAGCGCCCCGCGGGCGGCGCTCGATCTAACAGGCGATGAAAGCCTAAAGGCATTCGTCTGGCGGCCCTGACGCGTTGCCCATACAAGCCCCACAAatctgc > 6:78789/1‑149 (MQ=37)
aaGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑T‑‑GTGAG‑‑ATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCaa < 8:238593/148‑1 (MQ=255)
aGGGGTTTGCCGTTAGGTTTTCGGCGCC‑‑T‑‑GTGAG‑‑ATCGCGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCAAGCCCCTCAATGCTGCCTCCGCCAAgc < 6:278192/149‑1 (MQ=38)
tATGCCGTTAGGTTTTCGGCGCC‑‑T‑‑GTGAG‑‑ATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCAAgcacgca < 4:258528/149‑1 (MQ=255)
ccGTTAGGTTTTCGGCGCC‑‑TGGGA‑‑G‑‑ATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCAAGCACGCACAgt < 8:241983/149‑1 (MQ=255)
ttttCGGCGCC‑‑T‑‑GTGAG‑‑ATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCAAGCACGCACAGTGGTGTACa < 5:78789/149‑1 (MQ=255)
||
CCTGACGCCGCCGATTCGCATCTCGGTAATGCTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑T‑‑GT‑‑G‑‑ATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCAAGCACGCACAGTGGTGTACA > NC_002947_CJ‑RC/1070098‑1070379
|
| 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
