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 F24 I1 R1
|
58 |
74.9 |
3151412 |
98.7% |
3110443 |
147.7 |
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 | 78.6%
| 52.5
/ 15.3
| 30 | 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 . (4/2); new base G (5/17); total (11/19) |
| Fisher's exact test for biased strand distribution p-value = 6.38e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.35e-01 |
| * | NC_002947_CJ‑RC | 1,070,246 | 2 | . | A | 80.0%
| 59.5
/ 16.3
| 30 | 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 . (4/2); new base A (7/17); total (11/19) |
| Fisher's exact test for biased strand distribution p-value = 1.56e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.49e-01 |
GCCGCCGATTCGCATCTCGGTAATGCTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑TGT‑‑GAT‑‑‑CGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCAAGCACGCACAGTGGTGTACAGCAAC > NC_002947_CJ‑RC/1070104‑1070384
||
gccgccGATTCGCATCTCGGTAATGCTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑TGT‑‑Gagatc < 8:222105/149‑5 (MQ=255)
aTTCGCATCTCGGTAATGCTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑TGTGAGAT‑‑‑CGAGcgcc < 5:277636/149‑1 (MQ=255)
cATCTCGGTAATGCTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCAGTGT‑‑GAT‑‑‑AGCGCGCcgcgcg > 8:30640/1‑149 (MQ=255)
tctcGGTAATGCTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑TGTGAGAT‑‑‑CGAGCGCCGCgcggg > 6:202257/1‑149 (MQ=255)
tctcGGTAATGCTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑TGT‑‑GATATACGAGCGCCGCgcgg > 2:104954/1‑149 (MQ=255)
ggTAATGCTGATGCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑TGTGAGAT‑‑‑CGAGCGCCGCgcgggcgg < 4:140490/148‑1 (MQ=255)
ggTAATGCTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTGAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑TGTGAGAT‑‑‑CGAGCGCCGCgcgggcgg < 2:155319/148‑1 (MQ=255)
aTGCTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑TGTGAGAT‑‑‑CGAGCGCCGCGCGGGCGGCGCt < 8:88827/148‑1 (MQ=255)
cGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑TGTTAGTT‑‑‑AGAGCGCCGCGCGGGCGGCGCGCGCTCacaccc > 2:268852/1‑147 (MQ=255)
cGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑TGTGAGAT‑‑‑CGAGCGCCGCGCGGGCGGCGCGCGCTCTCACAg > 8:321456/1‑149 (MQ=39)
ggCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑TGTGAGAT‑‑‑AGAGCGCCGCGCGGGCGGGGCTCGATCTCACAgg > 7:109382/1‑149 (MQ=255)
gctgtgcgggGGGTGGCTTTCAAGCTGAAGAAGGCCCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGAACGGGGTATGCCGTAAGGTTTTCGGCGCC‑‑TGTGAGAC‑‑‑CGCGCCCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGc < 4:367052/149‑1 (MQ=25)
ctgtgGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑TGTGAGAT‑‑‑CGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTaaa < 2:72697/148‑1 (MQ=255)
gtgggtggCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCAGTGA‑‑GAT‑‑‑AGAGGCCCGCGCGGGCGGCGGGGGATCTCCCCGGCGGTGAAACCCGaaatg > 8:180706/1‑146 (MQ=255)
tgggtggCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑TGTGAGAT‑‑‑CGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGc < 8:69801/148‑1 (MQ=255)
tttCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑AGTTAGAT‑‑‑AGAGCGCCGCGCGGGGGGGGCGAGGTGGAACAGGGGGTTGAAGCCGAAAAGCATGCgggag > 6:5282/1‑145 (MQ=255)
ggCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGTGCC‑‑TGTGAGAT‑‑‑CGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGt > 6:183237/1‑149 (MQ=255)
ggCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑TGTGAGAT‑‑‑CGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGt > 2:264597/1‑149 (MQ=255)
ggCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTTTGA‑‑GAT‑‑‑CGAGCGCCGCGGGGGCGGCGCTCGATCTGACAGGCGATGAAAGCCTAAAGGCATGCGTAAGGCGGCCCGGACGCGTTGCCCTTCCCTGcccc > 6:160226/1‑149 (MQ=255)
aTCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑TGTGAGAT‑‑‑CGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCaa < 2:47306/148‑1 (MQ=255)
gTTTGTTCGTTTGGGGTATGCCGTTAGGGTTTCGGGGCC‑‑TGTGAGAT‑‑‑CGAGCGCCGCGCGGGCGGGGCTCGATCTCACAGGCGATGTAAGCCTAAAGGCATGCGTCTGGCGTCCCTGACGCGTTCCCCTTCCATGCCCCTCAAtgctgc < 8:184521/149‑1 (MQ=37)
gTTCTTATGGGGTAGGCGTTTTGGTTTGCGGCGCG‑‑TGT‑‑TATAC‑CGCGCGCCGCGCGGGGGGGGCGCGATCTAACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTc < 3:209106/148‑1 (MQ=255)
gTAAGGGGTATGCCTTTAGGTTTTCGGGGCC‑‑TGTGAGAT‑‑‑CGAGGCCCGGGCGGTCGGGGCTGGATGTCAAAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGcc < 7:52601/148‑1 (MQ=255)
tacggggTATGCCGTTAGGTTTTCGGCGCC‑‑TGTGAGAG‑‑‑CGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCaa < 2:103060/146‑1 (MQ=38)
tAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑TGTGAGAT‑‑‑CGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCaa < 6:213456/149‑1 (MQ=255)
aGGTTTTCGGCGCC‑‑TGTGAGAG‑‑‑CGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCCGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCAAGCACGCACAgtggtg < 2:299788/148‑1 (MQ=38)
ggTTTTCGGCGCC‑‑TGTGAGAT‑‑‑CGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCAAGCACGCACAGTGgtgt < 3:249556/148‑1 (MQ=255)
ggTTTTCGGCGCC‑‑TGTGAGAT‑‑‑CGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCAAGCACGCACAGTGGTGTa < 5:347496/149‑1 (MQ=255)
ggCGCC‑‑TGTGAGAT‑‑‑CGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCAAGCACGCACAGTGGTGTACAGCaa < 3:45358/148‑1 (MQ=255)
ggCGCC‑‑TGTGAGAT‑‑‑CGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCAAGCACGCACAGTGGTGTACAGCAac < 8:73133/149‑1 (MQ=255)
||
GCCGCCGATTCGCATCTCGGTAATGCTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑TGT‑‑GAT‑‑‑CGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCAAGCACGCACAGTGGTGTACAGCAAC > NC_002947_CJ‑RC/1070104‑1070384
|
| 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
