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 F50 I3 R1
|
143 |
109.6 |
3434427 |
98.5% |
3382910 |
150.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
1,097,492 |
+G |
intergenic (+663/+73) |
ycdU → / ← serX |
putative inner membrane protein/tRNA‑Ser |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 1,097,488 | 1 | . | G | 91.7%
| 57.7
/ 2.0
| 24 | intergenic (+659/+77) | ycdU/serX | putative inner membrane protein/tRNA‑Ser |
| Reads supporting (aligned to +/- strand): ref base . (2/0); new base G (10/12); total (12/12) |
| Fisher's exact test for biased strand distribution p-value = 4.78e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.61e-01 |
ATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTGACTCGCTTCGCTCGCCCTGCGGGCAGCCCGCTCACTGCGTTCACGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTC‑GGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACA‑CTTTCCAGGCGTGCTCCT > NC_000913/1097338‑1097630
|
ataCGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTGACTCGCTTCGCTCGCCCTGCGGGCAGCCCGCTCACTGCGTTCACGGTCTGTCCAACTGGCTGTCGCCAGTTGTGGAACCCCGGTc < 1:198026/151‑1 (MQ=14)
cACTGCGTTCACGGTCTGGCCAACTGGGTGGCGCCCGTTGTTGGGGCCCGGTCGGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTc < 2:683042/150‑1 (MQ=11)
cGTTCACGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTC‑GGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGGGGGGGGGGtttacactcc > 1:370080/1‑143 (MQ=0)
cGTTCACGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTC‑GGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAgggggggggttactcgc > 1:557447/1‑140 (MQ=2)
cACGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAGCCCCGGTCGGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGTTCGAAcccccc > 2:898722/1‑149 (MQ=255)
aCGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAGCCCCGGTCGGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGa < 1:1662716/150‑1 (MQ=255)
ggTCTGTCCAACTGGCTGTCGCCAGTTGTCGAGCCCCGGTCGGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGGGGGGGGGGGGGTTGAAaccccccaa > 2:1158272/1‑146 (MQ=1)
gTCCAACTGGCTGTCGCCAGTTGTCGAGCCCCGGTCGGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGTTTGAACCCCCCATACgct > 2:214536/1‑147 (MQ=11)
gTCCAACTGGCTGTCGCCAGTTGTCGAGCCCCGGTCGGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTg < 1:566261/150‑1 (MQ=255)
gTCGCCAGTTGTCGAGCCCCGGTCGGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATacaca < 2:638150/149‑1 (MQ=255)
tCGCCAGTTGTCGAGCCCCGGTCGGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACA‑Ct < 2:1194821/150‑1 (MQ=255)
cGCCAGTTGTCGAGCCCCGGTCGGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACA‑Cttt < 2:687674/151‑1 (MQ=255)
cGCCAGTTGTCGAGCCCCGGTCGGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGGGGGGGGGGGGGTCTAACCCCCCGCACCTTGCCGTATACACA‑Cttt > 1:183758/1‑151 (MQ=14)
ccAGTTGTCGAGCCCCGGTCGGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGGGGGGGGGGGTCGAAACCCCCATACGTTGCCGTATACACA‑Cctt > 1:1119297/1‑149 (MQ=14)
ccAGTTGTCGAGCCCCGGTCGGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACA‑CTTTcc < 2:96335/151‑1 (MQ=255)
ccAGTTGTCGAGCCCCGGTCGGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACA‑CTTTc < 1:202410/150‑1 (MQ=255)
cAGTTGTCGAGCCCCGGTCGGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACA‑CTTTCCa < 1:1630340/151‑1 (MQ=255)
gTTGTCGAGCCCCGGTCGGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGGTTGTACCCCCCATACCCTTCCCTATACCCACCTTTccgg > 1:547417/1‑149 (MQ=11)
ttGTCGAGCCCCGGTCGGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGGGGGGGGGGTTCGGAACCCCCCTACGGTGTCGTATAAACA‑Cttttccgg > 1:1079625/1‑145 (MQ=14)
gTCGAGCCCCGGTCGGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACA‑CTTTCCAGGCg < 2:1294028/150‑1 (MQ=255)
gagccccGGTCGGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGGGGGGGGGGTTTGAACCCCCCATCCCTTGTCGTTTACACC‑Cttt > 1:497951/4‑140 (MQ=14)
gagccccGGTCGGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGGGGGGGGGGGTCGAAACCCCCATACGTTGCCGTATAAACA‑CTTTTCCGGCggg > 2:1047552/4‑147 (MQ=14)
agccccGGTCGGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGGGGGGGGGGGTCTAACCCCCCCAAAGCTGGCGTATACAAA‑Atttttcggcggg > 1:1598423/3‑139 (MQ=11)
ccccGGTCGGGGGTTTCTAATCCCCCGGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACA‑CTTTCCAGGCGTGCTcc < 2:370108/150‑1 (MQ=255)
ccccGGTCGGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACA‑CTTTCCAGGCGTGCTCCt < 1:1688435/151‑1 (MQ=255)
|
ATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTGACTCGCTTCGCTCGCCCTGCGGGCAGCCCGCTCACTGCGTTCACGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTC‑GGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACA‑CTTTCCAGGCGTGCTCCT > NC_000913/1097338‑1097630
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
