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 |
637,111 |
+G |
intergenic (‑164/+218) |
adk ← / ← kdsB |
adenylate kinase/3‑Deoxy‑manno‑octulosonate cytidylyltransferase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260479 | 637,107 | 1 | . | G | 100.0%
| 140.2
/ NA
| 37 | intergenic (‑160/+222) | adk/kdsB | adenylate kinase/3‑Deoxy‑manno‑octulosonate cytidylyltransferase |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base G (18/19); total (18/19) |
GGCGGGAGATCAGAAGGAGGGTAACGCCGTAACTTGACGCAGGACTTACTGCGGTCCTGATGCGTTCTGACTGCGTTCAGCGCGGGCACTGCTCAGGCGTACCCACGCATACGGCCGGCGGCGGCTGCCA‑GGGGATGGCGGCGCGGCACACCGGACGGGCTCTATCTTTATCTCCCCACCGAGCCTTGGCCGGAGGCACGCTTGCGCATGCCGGCCGGGCGGCTCTGTATCGGCAAGCATTATGCCAT > AM260479/636978‑637225
|
ggCGGGAGATCAGAAGGAGGGTAACGCCGTAACTTGACGCAGGACTTACTGCGGTCCTGATGCGTTCTGACTGCGTTCAGCGCGGGCACTGCTCAGGCGTACCCACGCATACGGCCGGCGGCGGCTGCCA‑gggg > 1:156634/1‑134 (MQ=255)
aGAAGGAGGGTAACGCCGTAACTTGACGCAGGACTTACTGCGGTCCTGATGCGTTCTGACTGCGTTCAGCGCGGGCACTGCTCAGGCGTACCCACGCATACGGCCGGCGGCGGCTGCCAGGGGGATGgcggcgc > 2:812539/1‑134 (MQ=255)
aGAAGGAGGGTAACGCCGTAACTTGACGCAGGACTTACTGCGGTCCTGATGCGTTCTGACTGCGTTCAGCGCGGGCACTGCTCAGGCGTACCCACGCATACGGCCGGCGGCGGCTGCCAGGGGGATGgcggcgc > 1:265807/1‑134 (MQ=255)
gggTAACGCCGTAACTTGACGCAGGACTTACTGCGGTCCTGATGCGTTCTGACTGCGTTCAGCGCGGGCACTGCTCAGGCGTACCCACGCATACGGCCGGCGGCGGCTGCCAGGGGGATGGCGGCGCGGCacac < 1:812539/134‑1 (MQ=255)
ggTAACGCCGTAACTTGACGCAGGACTTACTGCGGTCCTGATGCGTTCTGACTGCGTTCAGCGCGGGCACTGCTCAGGCGTACCCACGCATACGGCCGGCGGCGGCTGCCAGGGGGATGGCGGCGCGGCACAcc < 1:198313/134‑1 (MQ=255)
cGCCGTAACTTGACGCAGGACTTACTGCGGTCCTGATGCGTTCTGACTGCGTTCAGCGCGGGCACTGCTCAGGCGTACCCACGCATACGGCCGGCGGCGGCTGCCAGGGGGATGGCGGCGCGGCACACCGGACg < 2:156634/134‑1 (MQ=255)
cGCCGTAACTTGACGCAGGACTTACTGCGGTCCTGATGCGTTCTGACTGCGTTCAGCGCGGGCACTGCTCAGGCGTACCCACGCATACGGCCGGCGGCGGCTGCCAGGGGGATGGCGGCGCGGCACACCGGACg < 2:265807/134‑1 (MQ=255)
cAGGACTTACTGCGGTCCTGATGCGTTCTGACTGCGTTCAGCGCGGGCACTGCTCAGGCGTACCCACGCATACGGCCGGCGGCGGCTGCCAGGGGGATGGCGGCGCGGCACACCGGACGGGCTCTATCTTTAtc > 2:878931/1‑134 (MQ=255)
aCTTACTGCGGTCCTGATGCGTTCTGACTGCGTTCAGCGCGGGCACTGCTCAGGCGTACCCACGCATACGGCCGGCGGCGGCTGCCAGGGGGATGGCGGCGCGGCACACCGGACGGGCTCTATCTTTATCTccc < 1:878931/134‑1 (MQ=255)
gACTGCGTTCAGCGCGGGCACTGCTCAGGCGTACCCACGCATACGGCCGGCGGCGGCTGCCAGGGGGATGGCGGCGCGGCACACCGGACGGGCTCTATCTTTATCTCCCCACCGAGCCTTGGCCGGAGGCACGc > 1:794213/1‑134 (MQ=255)
cTGCGTTCAGCGCGGGCACTGCTCAGGCGTACCCACGCATACGGCCGGCGGCGGCTGCCAGGGGGATGGCGGCGCGGCACACCGGACGGGct > 2:886566/1‑92 (MQ=255)
cTGCGTTCAGCGCGGGCACTGCTCAGGCGTACCCACGCATACGGCCGGCGGCGGCTGCCAGGGGGATGGCGGCGCGGCACACCGGACGGGct < 1:886566/92‑1 (MQ=255)
aGCGCGGGCACTGCTCAGGCGTACCCACGCATACGGCCGGCGGCGGCTGCCAGGGGGATggcgg < 1:161291/64‑1 (MQ=255)
aGCGCGGGCACTGCTCAGGCGTACCCACGCATACGGCCGGCGGCGGCTGCCAGGGGGATggcgg > 2:161291/1‑64 (MQ=255)
gcgcGGGCACTGCTCAGGCGTACCCACGCATACGGCCGGCGGCGGCTGCCAGGGGGATGGCGGCGCGGCACACCGGACGGGCTCTATCTTTATCTCCCCACCGAGCCTTGGCCGGAGGCACGCTTGCGCATgcc > 2:261730/1‑134 (MQ=255)
gggCACTGCTCAGGCGTACCCACGCATACGGCCGGCGGCGGCTGCCAGGGGGATGGCGGCGCGGCACACCGGACGGGCTCTATCTTTATCTCCCCACCGAGCCTTGGCCGGAGGCACGCTTGCGCATgccggcc > 2:548167/1‑134 (MQ=255)
cGTACCCACGCATACGGCCGGCGGCGGCTGCCAGGGGGATGGCGGCGCGGCACACCGGACGGGCTCTATCTTTATCTCCCCACCGAGCCTTGGCCGGAGGCACGCTTGCGCATGCCGGCCGGGCGGCTCTGTAt < 1:353650/134‑1 (MQ=255)
cGTACCCACGCATACGGCCGGCGGCGGCTGCCAGGGGGATGGCGGCGCGGCACACCGGACGGGCTCTATCTTTATCTCCCCACCGAGCCTTGGCCGGAGGCACGCTTGCGCATGCCGGCCGGGCGGCTCTGTAt < 1:261730/134‑1 (MQ=255)
gTACCCACGCATACGGCCGGCGGCGGCTGCCAGGGGGATGgcggcgcggc < 1:159476/50‑1 (MQ=38)
gTACCCACGCATACGGCCGGCGGCGGCTGCCAGGGGGATGgcggcgcggc > 2:159476/1‑50 (MQ=39)
aCCCACGCATACGGCCTGCGGCGGCTGCCAGGGGGATGGCGGCGCGGCACACCGGACg < 1:164803/58‑1 (MQ=38)
aCCCACGCATACGGCCTGCGGCGGCTGCCAGGGGGATGGCGGCGCGGCACACCGGACg > 2:164803/1‑58 (MQ=38)
aCGCATACGGCCGGCGGCGGCTGCCAGGGGGATGGCGGCGCGGCACACCGGACGGGCTCTATCTTTATCTCCCCACCGAGCCTTGGCCGGAGGCACGCTTGCGCATGCCGGCCGGGCGGCTCTGTATCGGCAAg < 1:907752/134‑1 (MQ=255)
cGCATACGGCCGGCGGCGGCTGCCAGGGGGATGGCGGCGCGGCACACCGGACGGGCTCTATCTTTATCTCCCCACCGAGCCTTGGCCGGAGGCACGCTTGCGCATGCCGGCCGggc > 2:874092/1‑116 (MQ=255)
cGCATACGGCCGGCGGCGGCTGCCAGGGGGATGGCGGCGCGGCACACCGGACGGGCTCTATCTTTATCTCCCCACCGAGCCTTGGCCGGAGGCACGCTTGCGCATGCCGGCCGggc < 2:988217/116‑1 (MQ=255)
cGCATACGGCCGGCGGCGGCTGCCAGGGGGATGGCGGCGCGGCACACCGGACGGGCTCTATCTTTATCTCCCCACCGAGCCTTGGCCGGAGGCACGCTTGCGCATGCCGGCCGggc > 1:988217/1‑116 (MQ=255)
cGCATACGGCCGGCGGCGGCTGCCAGGGGGATGGCGGCGCGGCACACCGGACGGGCTCTATCTTTATCTCCCCACCGAGCCTTGGCCGGAGGCACGCTTGCGCATGCCGGCCGggc < 1:874092/116‑1 (MQ=255)
cGCATACGGCCGGCGGCGGCTGCCAGGGGGATGGCGGCGCGGCACACCGGACGGGCTCTATCTTTATCTCCCCACCGAGCCTTGGCCGGAGGCACGCTTGCGCATGCCGGCCGGGCGGCTCTGTATCGGCAAg > 2:907752/1‑133 (MQ=255)
aCGGCCGGCGGCGGCTGCCAGGGGGATGGCGGCGCGGCACAcc > 1:832382/1‑43 (MQ=38)
aCGGCCGGCGGCGGCTGCCAGGGGGATGGCGGCGCGGCACAcc < 2:832382/43‑1 (MQ=38)
aCGGCCGGCGGCGGCTGCCAGGGGGATGGCGGCGCGGCACACCGGACGGGCTCTATCTTTATCTCCCCACCGAGCCTTGGCCGGAGGCACGCTTGCGCATGCCGGCCGGGCGGctct > 2:103570/1‑117 (MQ=255)
aCGGCCGGCGGCGGCTGCCAGGGGGATGGCGGCGCGGCACACCGGACGGGCTCTATCTTTATCTCCCCACCGAGCCTTGGCCGGAGGCACGCTTGCGCATGCCGGCCGGGCGGctct < 1:103570/117‑1 (MQ=255)
aCGGCCGGCGGCGGCTGCCAGGGGGATGGCGGCGCGGCACACCGGACGGGCTCTATCTTTATCTCCCCACCGAGCCTTGGCCGGAGGCACGCTTGCGCATGCCGGCCGGGCGGCTCTGTATCGGCAAGCATTAt > 2:855848/1‑134 (MQ=255)
cggcggcggCTGCCAGGGGGATGGCGGCGCGGCacac < 2:631599/37‑1 (MQ=25)
cggcggcggCTGCCAGGGGGATGGCGGCGCGGCacac > 1:631599/1‑37 (MQ=25)
cggcggcggCTGCCAGGGGGATGGCGGCGCGGCACACCGGACGGGCTCTATCTTTATCTCCCCACCGAGCCTTGGCCGGAGGCACGCTTGCGCATGCCGGCCGGGCGGCTCTGTATCGGCAAGCATTATGCCAt < 1:548167/134‑1 (MQ=255)
gcggcTGCCAGGGGGATGGCGGCGCGGCACACCGGACGGGCTCTATCTTTATCTCCCCACCGAGCCTTGGCCGGAGGc > 2:619873/1‑78 (MQ=255)
gcggcTGCCAGGGGGATGGCGGCGCGGCACACCGGACGGGCTCTATCTTTATCTCCCCACCGAGCCTTGGCCGGAGGc < 1:619873/78‑1 (MQ=255)
|
GGCGGGAGATCAGAAGGAGGGTAACGCCGTAACTTGACGCAGGACTTACTGCGGTCCTGATGCGTTCTGACTGCGTTCAGCGCGGGCACTGCTCAGGCGTACCCACGCATACGGCCGGCGGCGGCTGCCA‑GGGGATGGCGGCGCGGCACACCGGACGGGCTCTATCTTTATCTCCCCACCGAGCCTTGGCCGGAGGCACGCTTGCGCATGCCGGCCGGGCGGCTCTGTATCGGCAAGCATTATGCCAT > AM260479/636978‑637225
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 38 ≤ 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
GTTTTTAATCTGTATGGCGGGAGATCAGAAGGAGGGTAACGCCGTAACTTGACGCAGGACTTACTGCGGTCCTGATGCGTTCTGACTGCGTTCAGCGCGGGCACTGCTCAGGCGTACCCACGCATACGGCCGGCGGCGGCTGCCA‑GGGGATGGCGGCGCGGCACACCGGACGGGCTCTATCTTTATCTCCCCACCGAGCCTTGGCCGGAGGCACGCTTGCGCATGCCGGCCGGGCGGCTCTGTATCGGCAAGCATTATGCCATGAGGCGGCGCCAAATCGGCCCGAAATCCGCC > AM260479/636963‑637256
|
aagagacagCTGTATGGCGGGAGATCAGAAGGAGGGTAACGCCGTAACTTGACGCAGGACTTACTGCGGTCCTGATGCGTTCTGACTGCGTTCAGCGCGGGCACTGCTCAGGCGTACCCACGCATACGGCCGGCGGCGGCTGCCA‑GGGGG < GWNJ‑0478:712:GW2002102894th:2:1210:1756:96398/141‑1 (MQ=60)
GTTTTTAATCTGTATGGCGGGAGATCAGAAGGAGGGTAACGCCGTAACTTGACGCAGGACTTACTGCGGTCCTGATGCGTTCTGACTGCGTTCAGCGCGGGCACTGCTCAGGCGTACCCACGCATACGGCCGGCGGCGGCTGCCA‑GGGGG > GWNJ‑0478:712:GW2002102894th:2:1110:3825:20761/1‑150 (MQ=60)
ctttctgtcttctctttttcacgcttcctttttttttttttttcaagcagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacagGTACCCACGCATACGGCCGGCGGCGGCTGCCA‑GGGGgat < GWNJ‑0478:712:GW2002102894th:2:1211:13116:43146/39‑4 (MQ=60)
GTATGGCGGGAGATCAGAAGGAGGGTAACGCCGTAACTTGACGCAGGACTTACTGCGGTCCTGATGCGTTCTGACTGCGTTCAGCGCGGGCACTGCTCAGGCGTACCCACGCATACGGCCGGCGGCGGCTGCCAGGGGGATGGCGGCGCG > GWNJ‑0478:712:GW2002102894th:2:1201:12703:94164/1‑150 (MQ=60)
acggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacagGTTCTGACTGCGTTCAGCGCGGGCACTGCTCAGGCGTACCCACGCATACGGCCGGCGGCGGCTGCCAGGGGGATGGCGGCGCGGCACACCGGAC < GWNJ‑0478:712:GW2002102894th:2:1110:14884:48999/94‑1 (MQ=60)
tttcaagcagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacagGGGCACTGCTCAGGCGTACCCACGCATACGGCCGGCGGCGGCTGCCAGGGGGATGGCGGCGCGGCACACCGGACGGGCTC < GWNJ‑0478:712:GW2002102894th:2:1110:8693:38390/80‑1 (MQ=60)
AGGGTAACGCCGTAACTTGACGCAGGACTTACTGCGGTCCTGATGCGTTCTGACTGCGTTCAGCGCGGGCACTGCTCAGGCGTACCCACGCATACGGCCGGCGGCGGCTGCCAGGGGGATGGCGGCGCGGCACACCGGACGGGCTCTATC < GWNJ‑0478:712:GW2002102894th:2:2204:10476:14902/150‑1 (MQ=60)
GGGTAACGCCGTAACTTGACGCAGGACTTACTGCGGTCCTGATGCGTTCTGACTGCGTTCAGCGCGGGCACTGCTCAGGCGTACCCACGCATACGGCCGGCGGCGGCTGCCAGGGGGATGGCGGCGCGGCACACCGGACGGGCTCTATCT < GWNJ‑0478:712:GW2002102894th:2:1112:10778:70528/150‑1 (MQ=60)
cagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacaGGCACTGCTCAGGCGTACCCACGCATACGGCCTGCGGCGGCTGCCAGGGGGATGGCGGCGCGGCACACCGGACGGGCTCTATCTTTATC < GWNJ‑0478:712:GW2002102894th:2:1110:3583:69984/89‑1 (MQ=60)
gggctcggagatgtgtataagagacagCCTGATGCGTTCTGACTGCGTTCAGCGCGGGCACTGCTCAGGCGTACCCACGCATACGGCCGGCGGCGGCTGCCAGGGGGATGGCGGCGCGGCACACCGGACGGGCTCTATCTTTATCTCCC < GWNJ‑0478:712:GW2002102894th:2:2207:12996:82788/122‑1 (MQ=60)
GACTTACTGCGGTCCTGATGCGTTCTGACTGCGTTCAGCGCGGGCACTGCTCAGGCGTACCCACGCATACGGCCGGCGGCGGCTGCCAGGGGGATGGCGGCGCGGCACACCGGACGGGCTCTATCTTTATCTCCCCACCGAGCCTTGGCC < GWNJ‑0478:712:GW2002102894th:2:2207:19264:35979/150‑1 (MQ=60)
GTCCTGATGCGTTCTGACTGCGTTCAGCGCGGGCACTGCTCAGGCGTACCCACGCATACGGCCGGCGGCGGCTGCCAGGGGGATGGCGGCGCGGCACACCGGACGGGCTCTATCTTTATCTCCCCACCGAGCCTTGGCCGGAGGCACGCT > GWNJ‑0478:712:GW2002102894th:2:2203:19469:91167/1‑150 (MQ=60)
gtagctccgtctcgtgggctcggagatgtgtataagagacagCGCATACGGCCGGCGGCGGCTGCCAGGGGGATGGCGGCGCGGCACACCGGACGGGCTCTATCTTTATCTCCCCACCGAGCCTTGGCCGGAGGCACGCTTGCGCATGCC < GWNJ‑0478:712:GW2002102894th:2:2108:15039:19936/108‑1 (MQ=60)
acagGCTCAGGCGTACCCACGCATACGGCCGGCGGCGGCTGCCAGGGGGATGGCGGCGCGGCACACCGGACGGGCTCTATCTTTATCTCCCCACCGAGCCTTGGCCGGAGGCACGCTTGCGCATGCCGGCCGGGCGGCTCTGTATCGGCA < GWNJ‑0478:712:GW2002102894th:2:2207:5435:6299/146‑1 (MQ=60)
GCTCAGGCGTACCCACGCATACGGCCGGCGGCGGCTGCCAGGGGGATGGCGGCGCGGCACACCGGACGGGCTCTATCTTTATCTCCCCACCGAGCCTTGGCCGGAGGCACGCTTGCGCATGCCGGCCGGGCGGCTCTGTATCGGCActgt > GWNJ‑0478:712:GW2002102894th:2:2214:17527:80726/1‑146 (MQ=60)
cagGGCGTACCCACGCATACGGCCGGCGGCGGCTGCCAGGGGGATGGCGGCGCGGCACACCGGACGGGCTCTATCTTTATCTCCCCACCGAGCCTTGGCCGGAGGCACGCTTGCGCATGCCGGCCGGGCGGCTCTGTATCGGCAAGCATT < GWNJ‑0478:712:GW2002102894th:2:1106:8357:93518/147‑1 (MQ=60)
GGCGTACCCACGCATACGGCCGGCGGCGGCTGCCAGGGGGATGGCGGCGCGGCACACCGGACGGGCTCTATCTctgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtcttctgcttgaaaaaaaaaa > GWNJ‑0478:712:GW2002102894th:2:2205:11182:44101/1‑73 (MQ=60)
GCGTACCCACGCATACGGCCGGCGGCGGCTGCCAGGGGGATGGCGGCGCGGCACACCGGACGGGCTCTATCTTTATCTCCCCACCGAGCCTTGGCCGGAGGCACGCTTGCGCATGCCGGCCGGGCGGCTCTGTATCGGCAAGCATTATGC < GWNJ‑0478:712:GW2002102894th:2:1206:3837:71994/150‑1 (MQ=60)
GCGTACCCACGCATACGGCCGGCGGCGGCTGCCAGGGGGATGGCGGCGCGGCACACCGGACGGGCTCTATCTTTATCTCCCCACCGAGCCTTGGCCGGAGGCACGCTTGCGCATGCCGGCCGGGCGGCTCTGTATCGGCAAGCATTATGC < GWNJ‑0478:712:GW2002102894th:2:1201:5384:65014/150‑1 (MQ=60)
ACCCACGCATACGGCCGGCGGCGGCTGCCAGGGGGATGGCGGCGCGGCACACCGGACGGGCTCTATCctgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtcttctgcttgaaaaaaaaaaaaaaacg > GWNJ‑0478:712:GW2002102894th:2:2108:19983:94762/1‑67 (MQ=60)
CACGCATACGGCCGGCGGCGGCTGCCAGGGGGATGGCGGCGCGGCACACCGGACGGGCTCTATCTTTATCTCCCCACCGAGCCTTGGCCGGAGGCACGCTTGCGCATGCCGGCCGGGCGGCTCTGTATCGGCAAGCATTATGCCATGAGG < GWNJ‑0478:712:GW2002102894th:2:2211:5532:14923/150‑1 (MQ=60)
CCGGCGGCGGCTGCCAGGGGGATGGCGGCGCGGCACACCGGACGGGCTCTATCTTTATCTCCCCACCGAGCCTTGGCCGGAGGCACGCTTGCGCATGCCGGCCGGGCGGCTCTGTATCGGCAAGCATTATGCCATGAGGCGGCGCCAAAT < GWNJ‑0478:712:GW2002102894th:2:2102:16160:41496/150‑1 (MQ=60)
G‑GGGGATGGCGGCGCGGCACACCGGACGGGCTCTATCTTTATCTCCCCACCGAGCCTTGGCCGGAGGCACGCTTGCGCATGCCGGCCGGGCGGCTCTGTATCGGCAAGCATTATGCCATGAGGCGGCGCCAAATCGGCCCGAAATCCGCC > GWNJ‑0478:712:GW2002102894th:2:2113:2545:50200/1‑150 (MQ=60)
|
GTTTTTAATCTGTATGGCGGGAGATCAGAAGGAGGGTAACGCCGTAACTTGACGCAGGACTTACTGCGGTCCTGATGCGTTCTGACTGCGTTCAGCGCGGGCACTGCTCAGGCGTACCCACGCATACGGCCGGCGGCGGCTGCCA‑GGGGATGGCGGCGCGGCACACCGGACGGGCTCTATCTTTATCTCCCCACCGAGCCTTGGCCGGAGGCACGCTTGCGCATGCCGGCCGGGCGGCTCTGTATCGGCAAGCATTATGCCATGAGGCGGCGCCAAATCGGCCCGAAATCCGCC > AM260479/636963‑637256
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
