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 F1 I1 R1
|
150 |
26.0 |
2053212 |
90.0% |
1847890 |
107.8 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
AM260479 |
1,231,142 |
Δ1 bp |
coding (2631/2652 nt) |
glnE → |
glutamine synthetase adenylyltransferase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260479 | 1,231,141 | 0 | A | . | 94.4%
| 137.5
/ 2.5
| 36 | coding (2630/2652 nt) | glnE | glutamine synthetase adenylyltransferase |
| Reads supporting (aligned to +/- strand): ref base A (2/0); new base . (18/16); total (20/16) |
| Fisher's exact test for biased strand distribution p-value = 4.92e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.52e-01 |
CCGCAAGGTCGCCGAAGGCCATCCCAACCCGACCGACCTGTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCACGGGTGCAGTACCTGGTGCTGCTGCACAACCCGGGCGCACCCGCAGCTGACGCGCAACGCGGGGCAATATCGCGCTGCTGCGCGCAGCGGGCGAGCTGGGCCTGATCGACGCACCGCTGGCACTGGCGGTGGGCGATGCCTACCGGCTGTTCCG > AM260479/1231028‑1231267
|
ccgcAAGGTCGCCGAAGGCCATCCCAACCCGACCGACCTGTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGa > 2:391559/1‑134 (MQ=255)
aaGGTCGCCGAAGGCCATCCCAACCCGACCGACCTGTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGAcgcg < 1:239097/134‑1 (MQ=255)
gTCGCCGAAGGCCATCCCAACCCGACCGACCTGTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCaa > 2:964206/1‑134 (MQ=255)
gCCGAAGGCCATCCCAACCCGACCGACCTGTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAAcg < 1:391559/133‑1 (MQ=255)
accTGTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCGctgctg < 2:543752/128‑1 (MQ=255)
accTGTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCGCTGCTgcgcg > 1:80340/1‑132 (MQ=255)
accTGTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCActgctg > 1:543752/1‑128 (MQ=255)
ccTGTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCGCTGCTGCGCGCAg > 2:505440/1‑134 (MQ=255)
ccTGTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCGCTGCTGCGCGCAg < 2:199056/134‑1 (MQ=255)
gTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCAc > 2:804572/1‑85 (MQ=255)
gTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCAc < 1:804572/85‑1 (MQ=255)
tCGCGGCGGCATGGTCGATATCGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCGCTGCTGCGCGCAGCGGGCGAGCTGGGCCTGATCg < 2:80340/134‑1 (MQ=255)
tCGCGGCGGCATGGTCGATATCGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCGCTGCTGCGCGCAGCGGGCGAGCTGGGCCTGATCg < 1:964206/134‑1 (MQ=255)
gcggcgGCATGGTCGATATCGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGAc < 1:435625/76‑1 (MQ=255)
gcggcgGCATGGTCGATATCGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGAc > 2:435625/1‑76 (MQ=255)
ggcggcATGGTCGATATCGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCGCTGCTGCGCGCAGCGGGCGAGCTGGGCCTGATCGACGc < 1:505440/134‑1 (MQ=255)
ggcggcATGGTCGATATCGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCGCTGCTGCGCGCAGCGGGCGAGCTGGGCCTGATCGACGc > 2:456121/1‑134 (MQ=255)
cATGGTCGATATCGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCGCTGCTGCGCGCAGCGGGCGAGCTGGGCCTGATCGACGccacgc > 2:831717/1‑129 (MQ=255)
acggTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCGCTGCTGCGCGCAGCGGGCGAGCTGGGCCTGATCGACGCCACGCTGGCACTGGCGGTGGGCGa > 2:263566/3‑134 (MQ=255)
tGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCGCTGCTGCGCGCAGCGGGCGAGCt > 2:351006/1‑91 (MQ=255)
tGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCGCTGCTGCGCGCAGCGGGCGAGCt < 1:351006/91‑1 (MQ=255)
tGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCGCTGCTGCGCGCAGCGGGCGAGCTGGGCCTGATc < 1:807879/101‑1 (MQ=255)
tGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCGCTGCTGCGCGCAGCGGGCGAGCTGGGCCTGATc > 2:807879/1‑101 (MQ=255)
tGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCGCTGCTGCGCGCAGCGGGCGAGCTGGGCCTGATCGACGc > 2:54743/1‑106 (MQ=255)
tGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCGCTGCTGCGCGCAGCGGGCGAGCTGGGCCTGATCGACGc < 1:54743/106‑1 (MQ=255)
tGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCGCTGCTGCGCGCAGCGGGCGAGCTGGGCCTGATCGACGCCACGCTGGCACTGGCGGTGGGCGATGcc > 2:180980/1‑134 (MQ=255)
tGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCGCTGCTGCGCGCAGCGGGCGAGCTGGGCCTGATCg < 2:483612/93‑1 (MQ=255)
tGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCGCTGCTGCGCGCAGCGGGCGAGCTGGGCCTGATCg > 1:483612/1‑93 (MQ=255)
ctgctgcAC‑AGCCGGGCGCACCCGCAGCTGACGCGCGACGC‑GGGCAATATCGCGCTGCTGCGCGCAGCGGGCGAGCTGGGCCTGATCGACGCCACGCTGGCACTGGCGGTGGGCGATGCCTACCGGCTGTTCcg > 2:1010246/1‑134 (MQ=255)
ctgctgcAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCGCTGCTgcgc > 1:690133/1‑63 (MQ=37)
ctgctgcAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCGCTGCTgcgc < 2:690133/63‑1 (MQ=37)
ctgctgcAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCGCTGCTGCGCGCAGCGGGCGAGCGGGGCCTGATCGACGCCACGCTGGCACTGGCGGTGGGCGATGCCTACCGGCTGTTCcg > 2:666524/1‑134 (MQ=255)
gctgcACAG‑CCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCGCTGCTGCGCGCAGCGGGCGAGCTGGGCCTGATCGACGcca > 2:106486/1‑90 (MQ=255)
gctgcACAG‑CCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCGCTGCTGCGCGCAGCGGGCGAGCTGGGCCTGATCGACGcca > 2:429631/1‑90 (MQ=255)
gctgcAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCGCTGCTGCGCGCAGCGGGCGAGCTGGGCCTGATCGACGcca < 1:106486/92‑3 (MQ=255)
gctgcAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCGCTGCTGCGCGCAGCGGGCGAGCTGGGCCTGATCGACGcca < 1:429631/92‑3 (MQ=255)
|
CCGCAAGGTCGCCGAAGGCCATCCCAACCCGACCGACCTGTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCACGGGTGCAGTACCTGGTGCTGCTGCACAACCCGGGCGCACCCGCAGCTGACGCGCAACGCGGGGCAATATCGCGCTGCTGCGCGCAGCGGGCGAGCTGGGCCTGATCGACGCACCGCTGGCACTGGCGGTGGGCGATGCCTACCGGCTGTTCCG > AM260479/1231028‑1231267
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GCCGCCGCGCTGCGCGACGAGATCATGCAGATGCGCCGCAAGGTCGCCGAAGGCCATCCCAACCCGACCGACCTGTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCACGGGTGCAGTACCTGGTGCTGCTGCACAACCCGGGCGCACCCGCAGCTGACGCGCAACGCGGGGCAATATCGCGCTGCTGCGCGCAGCGGGCGAGCTGGGCCTGATCGACGCACCGCTGGCACTGGCGGTGGGCGATGCCTACCGGCTGTTCCGCGCGC > AM260479/1230993‑1231272
|
cggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacagATCCCAACCCGACCGACCTGTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCACAGC < GWNJ‑0478:712:GW2002102894th:2:2107:13768:24396/95‑1 (MQ=60)
cgtctcgtgggctcggagatgtgtataagagacagCAACCCGACCGACCTGTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGC < GWNJ‑0478:712:GW2002102894th:2:2202:4315:60960/115‑1 (MQ=60)
atgtagctccgtctcgtgggctcggagatgtgtataagagacaGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAA < GWNJ‑0478:712:GW2002102894th:2:1213:11946:56284/107‑1 (MQ=60)
CAAGGTCGCCGAAGGCCATCCCAACCCGACCGACCTGTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATAT < GWNJ‑0478:712:GW2002102894th:2:1116:14701:9021/150‑1 (MQ=60)
CGCCGAAGGCCATCCCAACCCGACCGACCTGTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCGC < GWNJ‑0478:712:GW2002102894th:2:1211:7513:5437/149‑1 (MQ=60)
ATCCCAACCCGACCGACCTGTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCGCTGCTGCGCGC > GWNJ‑0478:712:GW2002102894th:2:1107:8732:44789/1‑148 (MQ=60)
ATCCCAACCCGACCGACCTGTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCACTGCTGCGCGC > GWNJ‑0478:712:GW2002102894th:2:2102:12950:7892/1‑148 (MQ=60)
gtgggctcggagatgtgtataagagacaGATATCGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCGCTGCTGCGCGCAGCGGGCGAGCTGGGCCTGATCGACGC < GWNJ‑0478:712:GW2002102894th:2:1206:9434:54482/122‑1 (MQ=60)
agatgtgtataagagacaGATATCGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCGCTGCTGCGCGCAGCGGGCGAGCTGGGCCTGATCGACGCCACGCTGGCA < GWNJ‑0478:712:GW2002102894th:2:2202:13637:83109/132‑1 (MQ=60)
ATCGCGGCGGCATGGTCGATATCGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCGCTGCTGCGCGCAGCGGGCGAGCTGGGCCTGATCGACGCCACGCTGGCAC < GWNJ‑0478:712:GW2002102894th:2:2213:11689:46099/150‑1 (MQ=60)
CGGCGGCATGGTCGATATCGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCGCTGCTGCGCGCAGCGGGCGAGCTGGGCCTGATCGACGCCACGCTGGCACTGGC < GWNJ‑0478:712:GW2002102894th:2:1216:6901:46439/150‑1 (MQ=60)
gtataagagacaGATATCGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCGCTGCTGCGCGCAGCGGGCGAGCTGGGCCTGATCGACGCCACGCTGGCACTGGC < GWNJ‑0478:712:GW2002102894th:2:1102:7872:75164/137‑1 (MQ=60)
gggctcggagatgtgtataagagacagGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCGCTGCTGCGCGCAGCGGGCGAGCTGGGCCTGATCGACGCCACGCTGGCACTGGCGG < GWNJ‑0478:712:GW2002102894th:2:1108:2868:12598/122‑1 (MQ=60)
gggctcggagatgtgtataagagacagGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCGCTGCTGCGCGCAGCGGGCGAGCTGGGCCTGATCGACGCCACGCTGGCACTGGCGG < GWNJ‑0478:712:GW2002102894th:2:1213:18570:23169/122‑1 (MQ=60)
gtgtataagagacagACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCGCTGCTGCGCGCAGCGGGCGAGCTGGGCCTGATCGACGCCACGCTGGCACTGGCGGTGGGCGATGCCTACCGGC < GWNJ‑0478:712:GW2002102894th:2:2215:4297:92383/135‑1 (MQ=60)
TCAC‑GGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCGCTGCTGCGCGCAGCGGGCGAGCTGGGCCTGATCGACGCCACGCTGGCACctgtctcttatacacatctccgagccc > GWNJ‑0478:712:GW2002102894th:2:1214:14271:22539/1‑123 (MQ=60)
GTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCGCTGCTGCGCGCAGCGGGCGAGCTGctgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtc > GWNJ‑0478:712:GW2002102894th:2:2113:6004:44379/1‑93 (MQ=60)
GTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCGCctgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtcttctgcttgaaaaaaaaaaaaaaaaac > GWNJ‑0478:712:GW2002102894th:2:1108:5678:79063/1‑65 (MQ=60)
|
GCCGCCGCGCTGCGCGACGAGATCATGCAGATGCGCCGCAAGGTCGCCGAAGGCCATCCCAACCCGACCGACCTGTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCACGGGTGCAGTACCTGGTGCTGCTGCACAACCCGGGCGCACCCGCAGCTGACGCGCAACGCGGGGCAATATCGCGCTGCTGCGCGCAGCGGGCGAGCTGGGCCTGATCGACGCACCGCTGGCACTGGCGGTGGGCGATGCCTACCGGCTGTTCCGCGCGC > AM260479/1230993‑1231272
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
