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 |
|
A2 F59 I1 R1
|
58 |
78.7 |
3339874 |
98.5% |
3289775 |
147.1 |
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 | 88.0%
| 71.0
/ 4.2
| 27 | 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 . (1/2); new base G (6/16); total (7/20) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
| * | NC_002947_CJ‑RC | 1,070,246 | 2 | . | A | 88.9%
| 69.1
/ 4.7
| 27 | 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 . (1/2); new base A (6/18); total (7/20) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.20e-01 |
CCTGACGCCGCCGATTCGCATCTCGGTAATGCTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑TGT‑‑G‑‑ATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCAAGCACGCACAGTGGTGTACAGCAAC > NC_002947_CJ‑RC/1070098‑1070384
||
ccTGACGCCGCCGATTCGCATCTCGGTAATGCTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑agt > 5:303633/1‑149 (MQ=255)
cTGACGCCGCCGATTCGCATCTCGGTAATGCTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑tgt > 6:182054/1‑148 (MQ=255)
cgccgATTCGCTTCTCGGTAATGCTGATCCCGTCATGGATCGCTGTGCTGTGGGGGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCGGTTAGGTTTTCGGCGCC‑‑TGT‑‑G‑‑agatcga < 2:110772/149‑7 (MQ=255)
tCGCATCTCGGTAATGCTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑TGTGAG‑‑ATCGAGcgccgc > 8:328428/1‑149 (MQ=255)
cGCATCTCGGTAATGCTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑TGTGAG‑‑ATCGAGcgccgc < 1:8732/148‑1 (MQ=255)
gCATCTCGGTAATGCTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGTGCC‑‑TGTGAG‑‑ATCGAGCGCcgcgc > 8:272898/1‑149 (MQ=255)
aTCTCGGTAATGCTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑TGTGAG‑‑ATCGAGCGCCGCgcgg < 4:156114/149‑1 (MQ=255)
ggTAATGCTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑TGTGAG‑‑ATCGAGCGCCGCgcggg < 5:40201/145‑1 (MQ=255)
aTGCTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑TGTGAG‑‑ATCGAGCGCCGCGCGGGCGGCGCt < 5:176015/148‑1 (MQ=255)
aTGCTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑TGTGAG‑‑ATCGAGCGCCGCGCGGGCGGCGCt < 7:328428/148‑1 (MQ=255)
aTGCTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑TGTGAG‑‑ATCGAGCGCCGCGCGGGCGGCGCTc < 4:214695/149‑1 (MQ=255)
aTGCTGAACCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑TGTGAG‑‑ATCGAGCGCCGCGCGGGCGGCGCTc < 7:163305/149‑1 (MQ=255)
cTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑TGTGAG‑‑ATCGAGCGCCGCGCGGGCGGCGCTCGa < 4:259789/148‑1 (MQ=255)
tGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑TGTGAG‑‑ATCAAGCGCCCCGCCGGCGGCGCGCGCtc > 8:286416/1‑149 (MQ=255)
tGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑TGTGAG‑‑ATAGAGCCCCGCCCGGGCGGGGcgcggtg > 8:302359/1‑146 (MQ=255)
aTCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑TGTGAG‑‑ATCGAGCGCCGCGCGGGCGGCGCTCGAtc < 5:182054/147‑1 (MQ=255)
gATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGTGCC‑‑TGTGAG‑‑ATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGa < 7:272898/149‑1 (MQ=255)
gATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑TGTGAG‑‑ATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATg < 8:92741/148‑1 (MQ=255)
gggtggCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTACGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑TGTCAG‑‑ATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCAt < 4:154425/149‑1 (MQ=255)
tCAAGGTGATGAAGGCTCGCCAGGCCAAGGGCTTATGGTGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑TGT‑‑GATATCGTGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTg < 6:303633/147‑1 (MQ=37)
aagGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTAAGGTTTTCGGCGCC‑‑TGTGAG‑‑ATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGAcgc < 5:93775/149‑1 (MQ=255)
gCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCAGTGA‑‑G‑‑ATAGAGCGCCGCGCGGGCGGCGCTCGATCTAACAGGCGATGAAAGCCAAAAGGCATTCGTCTGGCGGCCCGGACGCGtt > 6:370290/1‑149 (MQ=38)
tCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑TGTGAG‑‑ATCCAGCCCCGCGCGGGGGGCGCGCGATCGCACAAGCGATGAAAGCCGAAAGGGATTCGTGTGGCGGCCCAGGcgcggtgc > 4:80282/1‑145 (MQ=255)
cAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑TGTGAG‑‑ATCGAGCGCCGCCCGCGCGGCGCTCg < 7:136795/85‑1 (MQ=21)
cAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑TGTGAG‑‑ATCGAGCGCCGCCCGCGCGGCGCTCg > 8:136795/1‑85 (MQ=21)
gTTCGTACGGGGTAGGCCGTTAGGTTTTCGGCGCC‑‑TGTGAG‑‑ATCGCCCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTc < 7:340228/148‑1 (MQ=38)
cGTTTGGTTTTCGGCGCC‑‑TGTTAT‑‑ATCGAGCGCCGCGGGGGCGGCGCTCTATCTAAAAGGCTATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCAAGCACGCACAgtg < 1:28225/149‑1 (MQ=255)
tAGGTTTTCGGCGCC‑‑TGTGAG‑‑AGCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCAAGCACGCACAgtggt < 7:147579/148‑1 (MQ=255)
ggCGCC‑‑TGTGAG‑‑ATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCAAGCACGCACAGTGGTGTACAGCAac < 6:113250/149‑1 (MQ=255)
||
CCTGACGCCGCCGATTCGCATCTCGGTAATGCTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑TGT‑‑G‑‑ATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCAAGCACGCACAGTGGTGTACAGCAAC > NC_002947_CJ‑RC/1070098‑1070384
|
| 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
