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
|
152 |
24.9 |
2083062 |
91.6% |
1908084 |
109.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
AM260480 |
2,737,510 |
T→G |
intergenic (‑227/+17) |
h16_B2423 ← / ← h16_B2424 |
periplasmic solute binding protein/Hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260480 | 2,737,510 | 0 | T | G | 100.0%
| 90.0
/ NA
| 24 | intergenic (‑227/+17) | h16_B2423/h16_B2424 | periplasmic solute binding protein/Hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base G (12/12); total (12/12) |
GCGCATGGCCAGCGGCCGGCAGGGCAAGCGCGGCGCCCGCGAGGGCGCGCGCCAGCCAGCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAACGACAATGGCTTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAATGGCGGGCGCCTGGGTGGCGGCGGGCAGCGTGGCAGTGGCCGGGGCCGCGGGCGCCACGGCCATG > AM260480/2737394‑2737638
|
gcgcATGGCCAGCGGCCGGCAGGGCAAGCGCGGCGCCCGCGAGGGCGCGCGCCAGCCAGCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGttt > 2:719022/1‑133 (MQ=255)
tGGCCAGCGGCCGGCAGGGCAAGCGCGGCGCCCGCGAGGGCGCGCGCCAGCCAGCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACg < 1:589710/118‑1 (MQ=255)
tGGCCAGCGGCCGGCAGGGCAAGCGCGGCGCCCGCGAGGGCGCGCGCCAGCCAGCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAgg > 1:685861/1‑132 (MQ=255)
tGGCCAGCGGCCGGCAGGGCAAGCGCGGCGCCCGCGAGGGCGCGCGCCAGCCAGCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAgg > 1:745386/1‑132 (MQ=255)
tGGCCAGCGGCCGGCAGGGCAAGCGCGGCGCCCGCGAGGGCGCGCGCCAGCCAGCGCCACGCGCGTGTTGCCGCGCGGCGGGAAGCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACg > 2:589710/1‑118 (MQ=255)
ccggcAGGGCAAGCGCGGCGCCCGCGAGGGCGCGCGCCAGCCAGCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGgcg < 1:311238/134‑1 (MQ=255)
gcgcCCGCGAGGGCGCGCGCCAGCCAGCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGc > 1:790793/1‑133 (MQ=255)
cgcCCGCGAGGGCGCGCGCCAGCCAGCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTAATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCaa < 1:38608/134‑1 (MQ=255)
gAGGGCGCGCGCCAGCCAGCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAAc < 2:878013/134‑1 (MQ=255)
gcgcgcCAGCCAGCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAAt > 1:833593/1‑134 (MQ=255)
gcgcCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCcgc > 1:129551/1‑104 (MQ=255)
gcgcCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCcgc < 2:129551/104‑1 (MQ=255)
cgcgcgTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAATGGCGGGCGCCTGGGTggc < 1:725380/134‑1 (MQ=255)
cgcgTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAATGGCGGGCGCCTGGGTggcgg < 2:790793/134‑1 (MQ=255)
cgTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCGAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAgg > 1:23495/1‑101 (MQ=255)
cgTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCGAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAgg < 2:23495/101‑1 (MQ=255)
gtgtTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAATGGCGGGCGCCTGGGTGGcggcgg > 1:75883/1‑134 (MQ=255)
ggcggGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAATGGCGGGCGCCTGGGTGGCGGCGGGCAGCGTGGCAg > 1:977878/1‑134 (MQ=255)
cggGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAATGGCGGGCGCCTGGGTGGCGGCGGGCAGCGTGGCAGTg > 1:915205/1‑134 (MQ=255)
tCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAATGGCGGGCGCCTGGGTGGCGGCGGGCAGCGTGGCAGTGGCCggg < 2:75883/134‑1 (MQ=255)
aGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAATGGCGGGCGcc > 2:275090/1‑90 (MQ=255)
aGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAATGGCGGGCGcc < 1:275090/90‑1 (MQ=255)
agcgacaTGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAATGGCGGGCGCCTGGGTGGCGGCGGGCAGCGTGGCAGTGGCCGGGGCCGCGGGCGCCACg < 1:719022/128‑1 (MQ=255)
aTGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAATGGCGGGCGCCTGGGTGGCGGCGGGCAGCGTGGCAGTGGCCGGGGCCGCGGGCGCCACGGCCATg < 2:915205/134‑1 (MQ=255)
|
GCGCATGGCCAGCGGCCGGCAGGGCAAGCGCGGCGCCCGCGAGGGCGCGCGCCAGCCAGCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAACGACAATGGCTTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAATGGCGGGCGCCTGGGTGGCGGCGGGCAGCGTGGCAGTGGCCGGGGCCGCGGGCGCCACGGCCATG > AM260480/2737394‑2737638
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ 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
GGGCCGGTGCCGGCGTGTAGGTGGCCTGCGCATGGCCAGCGGCCGGCAGGGCAAGCGCGGCGCCCGCGAGGGCGCGCGCCAGCCAGCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAACGACAATGGCTTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAATGGCGGGCGCCTGGGTGGCGGCGGGCAGCGTGGCAGTGGCCGGGGCCGCGGGCGCCACGGCCATGGGTGCGGTGTCC > AM260480/2737367‑2737650
|
GGGCCGGTGCCGGCGTGTAGGTGGCCTGCGCATGGCCAGCGGCCGGCAGGGCAAGCGCGGCGCCCGCGAGGGCGCGCGCCAGCCAGCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAAC < GWNJ‑0478:712:GW2002102894th:2:2102:16887:36428/149‑1 (MQ=60)
ggctcggagatgtgtataagagacagctacacGCCGGCAGGGCAAGCGCGGCGCCCGCGAGGGCGCGCGCCAGCCAGCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTT < GWNJ‑0478:712:GW2002102894th:2:2104:18106:61247/118‑1 (MQ=60)
tcaagcagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacagtccctgattcccgcCGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTT < GWNJ‑0478:712:GW2002102894th:2:1101:3388:44621/68‑1 (MQ=60)
AGTAGGTGGCCTGCGCATGGCCAGCGGCCGGCAGGGCAAGCGCGGCGCCCGCGAGGGCGCGCGCCAGCCAGCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGG < GWNJ‑0478:712:GW2002102894th:2:2104:2839:75285/150‑1 (MQ=60)
TAGGTGGCCTGCGCATGGCCAGCGGCCGGCAGGGCAAGCGCGGCGCCCGCGAGGGCGCGCGCCAGCCAGCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGG > GWNJ‑0478:712:GW2002102894th:2:2114:11510:13397/1‑148 (MQ=60)
TAGGTGGCCTGCGCATGGCCAGCGGCCGGCAGGGCAAGCGCGGCGCCCGCGAGGGCGCGCGCCAGCCAGCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGG > GWNJ‑0478:712:GW2002102894th:2:2110:2335:75898/1‑148 (MQ=60)
GCCGGCAGGGCAAGCGCGGCGCCCGCGAGGGCGCGCGCCAGCCAGCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGG < GWNJ‑0478:712:GW2002102894th:2:1205:6002:71359/150‑1 (MQ=60)
GGCAGGGCAAGCGCGGCGCCCGCGAGGGCGCGCGCCAGCCAGCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCA > GWNJ‑0478:712:GW2002102894th:2:2201:18874:91429/1‑149 (MQ=60)
tccctgattcccgcCGCGCGCCAGCCAGCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAATG > GWNJ‑0478:712:GW2002102894th:2:2204:14850:86349/15‑150 (MQ=60)
GCGCCCGCGAGGGCGCGCGCCAGCCAGCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTAATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAATGG < GWNJ‑0478:712:GW2002102894th:2:1105:13843:68354/150‑1 (MQ=60)
GGCGCGCGCCAGCCAGCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCctgtctcttatacac > GWNJ‑0478:712:GW2002102894th:2:1109:8980:64673/1‑134 (MQ=60)
AGCCAGCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCGAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAATGGCGctgtctcttatacacatct > GWNJ‑0478:712:GW2002102894th:2:1103:16592:67811/1‑131 (MQ=60)
GCCAGCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAATGGCGGGCGCCTGGGTGGCGGCGGG > GWNJ‑0478:712:GW2002102894th:2:1107:10237:25253/1‑150 (MQ=60)
cgtgggctcggagatgtgtataagagacaGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAATGGCGGGCGCCTGGGTGGCGGCGGGC < GWNJ‑0478:712:GW2002102894th:2:1203:19576:26794/121‑1 (MQ=60)
ACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAATGGCGGGCGCCTGGGTGGCGGCGGGCAGCGTGGC < GWNJ‑0478:712:GW2002102894th:2:2115:9729:4789/150‑1 (MQ=60)
CGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAATGGCGGGCGCCTGGGTGGCGGCGGGCAGCGTGGCAGT > GWNJ‑0478:712:GW2002102894th:2:2213:8053:60278/1‑150 (MQ=60)
CGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAATGGCGGGCGCCTGGGTGGCGGCGGGCAGCGTGGCAGTGG > GWNJ‑0478:712:GW2002102894th:2:2211:16455:3732/1‑150 (MQ=60)
GTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAATGGCGGGCGCCTGGGTGGCGGCGGGCAGCGTGGCAGTGGCCGGGGCCGCGGGCGCCACGGCCATGGGTGCGG > GWNJ‑0478:712:GW2002102894th:2:2205:18194:20487/1‑150 (MQ=60)
cagcgacATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAATGGCGGGCGCCTGGGTGGCGGCGGGCAGCGTGGCAGTGGCCGGGGCCGCGGGCGCCACGGCCActgccacgctg < GWNJ‑0478:712:GW2002102894th:2:2112:13106:67073/143‑12 (MQ=60)
gcgacATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAATGGCGGGCGCCTGGGTGGCGGCGGGCAGCGTGGCAGTGGCCGGGGCCGCGGGCGCCACGGCCATGGGctgtctctt > GWNJ‑0478:712:GW2002102894th:2:1114:6519:30740/6‑141 (MQ=60)
gcgacATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAATGGCGGGCGCCTGGGTGGCGGCGGGCAGCGTGGCAGTGGCCGGGGCCGCGGGCGCCACGGCCATGGGTGCGGTGTC > GWNJ‑0478:712:GW2002102894th:2:1204:13346:81106/6‑150 (MQ=60)
CGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAATGGCGGGCGCCTGGGTGGCGGCGGGCAGCGTGGCAGTGGCCGGGGCCGCGGGCGCCACGGCCATGGGTGCGGTGTCC > GWNJ‑0478:712:GW2002102894th:2:2211:5824:19459/1‑150 (MQ=60)
|
GGGCCGGTGCCGGCGTGTAGGTGGCCTGCGCATGGCCAGCGGCCGGCAGGGCAAGCGCGGCGCCCGCGAGGGCGCGCGCCAGCCAGCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAACGACAATGGCTTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAATGGCGGGCGCCTGGGTGGCGGCGGGCAGCGTGGCAGTGGCCGGGGCCGCGGGCGCCACGGCCATGGGTGCGGTGTCC > AM260480/2737367‑2737650
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
