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
|
154 |
26.6 |
2069536 |
90.2% |
1866721 |
108.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
AM260479 |
787,769 |
+T |
intergenic (‑549/+743) |
h16_A0728 ← / ← h16_A0729 |
response regulator containing CheY‑like receiver, AAA‑type ATPase, and DNA‑binding domains/transcriptional regulator, LysR‑family |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260479 | 787,768 | 1 | . | T | 100.0%
| 114.8
/ NA
| 30 | intergenic (‑548/+744) | h16_A0728/h16_A0729 | response regulator containing CheY‑like receiver, AAA‑type ATPase, and DNA‑binding domains/transcriptional regulator, LysR‑family |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base T (14/16); total (14/16) |
ACGACCCCTGCACCTGGCCAGCCGATGCGGACCAGTTCCTGCCGCGTGGCCCACGCTTACAGCGCCAGTCCGAATCCCGCCCTGGGATGCGGGGTCGTCCTGAAACTGATCTTCGGCGAACCCGTGCCAGTGTG‑TGCCGCTTCGGTTTCAGACGTCCCCCTGTTCCGGGCTTCTGTTCGCGCGGACATATGTGCGACGAACGTGCCAGATATGGCTAATCCTTTGATAACAAAAGGAAAAGGAAA‑TTTCGGCTG > AM260479/787635‑787888
|
acgacCCCTGCACCTGGCCAGCCGATGCGGACCAGTTCCTGCCGCGTGGCCCACGCTTACAGCGCCAGTCCGAATCCCGCCCTGGGATGCGGGGTCGTCCTGAAACTGATCTTCGGCGAACCCGTGCCAgtgtg > 1:263035/1‑134 (MQ=255)
ccccTGCACCTGGCCAGCCGATGCGGACCAGTTCCTGCCGCGTGGCCCACGCTTACAGCGCCAGTCCGAATCCCGCCCTGGGATGCGGGGTCGTCCTGAAACTGATCTTCGGCGAACCCGTGCCAgtgtg‑ttgc < 1:850655/134‑4 (MQ=255)
cccTGCACCTGGCCAGCCGATGCGGACCAGTTCCTGCCGCGTGGCCCACGCTTACAGCGCCAGTCCGAATCCCGCCCTGGGATGCGGGGTCGTCCTGAAACTGATCTTCGGCGAACCCGTGCCAgtgtg‑ttgcc > 1:906588/1‑130 (MQ=255)
ccAGCCGATGCGGACCAGTTCCTGCCGCGTGGCCCACGCTTACAGCGCCAGTCCGAATCCCGCCCTGGGATGCGGGGTCGTCCTGAAACTGATCTTCGGCGAACCCGTGCCAGTGTGTTGCCGCTTCGGTTTCa < 2:345918/134‑1 (MQ=255)
ccAGCCGATGCGGACCAGTTCCTGCCGCGTGGCCCACGCTTACAGCGCCAGTCCGAATCCCGCCCTGGGATGCGGGGTCGTCCTGAAACTGATCTTCGGCGAACCCGTGCCAGTGTGTTGCCGCTTCGGTTTCa < 2:18068/134‑1 (MQ=255)
aGCCGATGCGGACCAGTTCCTGCCGCGTGGCCCACGCTTACAGCGCCAGTCCGAATCCCGCCCTGGGATGCGGGGTCGTCCTGAAACTGATCTTCGGCGAACCCGTGCCAgtgtg‑ttgcc > 2:149129/1‑116 (MQ=255)
aGCCGATGCGGACCAGTTCCTGCCGCGTGGCCCACGCTTACAGCGCCAGTCCGAATCCCGCCCTGGGATGCGGGGTCGTCCTGAAACTGATCTTCGGCGAACCCGTGCCAgtgtg‑ttgcc < 1:149129/120‑5 (MQ=255)
cTGCCGCGTGGCCCACGCTTACAGCGCCAGTCCGAATCCCGCCCTGGGATGCGGGGTCGTCCTGAAACTGATCTTCGGCGAACCCGTGCCAGTGTGTTGCCGCTTCGGTTTCAGACGTCCCCCTGTTCCGGGCt < 1:38624/134‑1 (MQ=255)
gcgTGGCCCACGCTTACAGCGCCAGTCCGAATCCCGCCCTGGGATGCGGGGTCGTCCTGAAACTGATCTTCGGCGAACCCGTGCCAGTGTGTTGCCGCTTCGGTTTCAGACGTCCCCCTGTTCCGGGCTTCTGt < 2:263035/134‑1 (MQ=255)
gcgTGGCCCACGCTTACAGCGCCAGTCCGAATCCCGCCCTGGGATGCGGGGTCGTCCTGAAACTGATCTTCGGCGAACCCGTGCCAGTGTGTTGCCGCTTCGGTTTCAGACGTCCCCCTGTTCCGGGCTTCTGt < 1:558208/134‑1 (MQ=255)
tGGCCCACGCTTACAGCGCCAGTCCGAATCCCGCCCTGGGATGCGGGGTCGTCCTGAAACTGATCTTCGGCGAACCCGTGCCAGTGTGTTGCCGCTTCGGTTTCAGACGTCCCCCTGTTCCGGGCTTCTGTTcg > 2:870192/1‑134 (MQ=255)
cccACGCTTACAGCGCCAGTCCGAATCCCGCCCTGGGATGCGGGGTCGTCCTGAAACTGATCTTCGGCGAACCCGTGCCAGTGTGTTGCCGCTTCGGTTTCAGACGTCCCCCTGTTCCGGGCTTCTGTTcgcgc > 2:241020/1‑134 (MQ=255)
gcCAGTCCGAATCCCGCCCTGGGATGCGGGGTCGTCCTGAAACTGATCTTCGGCGAACCCGTGCCAGTGTGTTGCCGCTTCGGTTTCAGACGTCCCCCTGTTCCGGGCTTCTGTTCGCGCGGACATATGTGcga < 1:241020/134‑1 (MQ=255)
tCCGAATCCCGCCCTGGGATGCGGGGTCGTCCTGAAACTGATCTTCGGCGAACCCGTGCCAGTGTGTTGCCGCTTCGGTTTCAGACGTCCCCCTGTTCCGGGCTTCTGTTCGCGCGGACATATGTGcg < 1:98618/128‑1 (MQ=255)
tCCGAATCCCGCCCTGGGATGCGGGGTCGTCCTGAAACTGATCTTCGGCGAACCCGTGCCAGTGTGTTGCCGCTTCGGTTTCAGACGTCCCCCTGTTCCGGGCTTCTGTTCGCGCGGACATATGTGcg > 2:98618/1‑128 (MQ=255)
tCCGAATCCCGCCCTGGGATGCGGGGTCGTCCTGAAACTGATCTTCGGCGAACCCGTGCCAGTGTGTTGCCGCTTCGGTTTCAGACGTCCCCCTGTTCCGGGCTTCTGTTCGCGCGGACATATGTGCGACGAAc < 1:981475/134‑1 (MQ=255)
aaTCCCGCCCTGGGATGCGGGGTCGTCCTGAAACTGATCTTCGGCGAACCCGTGCCAGTGTGTTGCCGCTTCGGTTTCAGACGTCCCCCTGTTCCGGGCTTCTGTTCGCGCGGACATATGTGcg < 2:355468/124‑1 (MQ=255)
aaTCCCGCCCTGGGATGCGGGGTCGTCCTGAAACTGATCTTCGGCGAACCCGTGCCAGTGTGTTGCCGCTTCGGTTTCAGACGTCCCCCTGTTCCGGGCTTCTGTTCGCGCGGACATATGTGcg > 1:355468/1‑124 (MQ=255)
aTCCCGCCCTGGGATGCGGGGTCGTCCTGAAACTGATCTTCGGCGAACCCGTGCCAGTGTGTTGCCGCTTCGGTTTCAGACGTCCCCCTGTTCCGGGCTTCTGTTCGCGCGGACATATGTGCGACGAACGTGcc < 2:906588/134‑1 (MQ=255)
ccGCCCTGGGATGCGGGGTCGTCCTGAAACTGATCTTCGGCGAACCCGTGCCAGTGTGTTGCCGCTTCGGTTTCa < 1:721701/75‑1 (MQ=255)
ccGCCCTGGGATGCGGGGTCGTCCTGAAACTGATCTTCGGCGAACCCGTGCCAGTGTGTTGCCGCTTCGGTTTCa > 2:721701/1‑75 (MQ=255)
tGGGATGCGGGGTCGTCCTGAAACTGATCTTCGGCGAACCCGTGCCAGTGTGTTGCCGCTTCGGTTTCAGACGTCCCCCTGTTCCGGGCTTCTGTTCGCGCGGACATATGTGCGACGaa > 1:224045/1‑119 (MQ=255)
tGGGATGCGGGGTCGTCCTGAAACTGATCTTCGGCGAACCCGTGCCAGTGTGTTGCCGCTTCGGTTTCAGACGTCCCCCTGTTCCGGGCTTCTGTTCGCGCGGACATATGTGCGACGaa < 2:224045/119‑1 (MQ=255)
tGGGATGCGGGGTCGTCCTGAAACTGATCTTCGGCGAACCCGTGCCAGTGTGTTGCCGCTTCGGTTTCAGACGTCCCCCTGTTCCGGGCTTCTGTTCGCGCGGACATATGTGCGACGAACGTGCCAGATATGGc > 1:189820/1‑134 (MQ=255)
gCGGGGTCGTCCTGAAACTGATCTTCGGCGAACCCGTGCCAGTGTGTTGCCGCTTCGGTTTCAGACGTCCCCCTGTTCCGGGCTTCTGTTCGCGCGGACATATGTGCGACGaa > 1:920476/1‑113 (MQ=255)
gCGGGGTCGTCCTGAAACTGATCTTCGGCGAACCCGTGCCAGTGTGTTGCCGCTTCGGTTTCAGACGTCCCCCTGTTCCGGGCTTCTGTTCGCGCGGACATATGTGCGACGaa < 2:920476/113‑1 (MQ=255)
ccTGAAACTGATCTTCGGCGAACCCGTGCCAGTGTGTTGCCGCTTCGGTTTCAGACGTCCCCCTGTTCCGGGCTTCTGTTCGCGCGGACATATGTGCGACGAACGTGCCAGATATGGCTAATCCTTTGATAAc > 1:924436/1‑133 (MQ=255)
tCGGCGAACCCGTGCCAGTGTGTTGCCGCTTCGGTTTCa > 2:692078/1‑39 (MQ=255)
tCGGCGAACCCGTGCCAGTGTGTTGCCGCTTCGGTTTCa < 1:692078/39‑1 (MQ=255)
tCGGCGAACCCGTGCCAGTGTGTTGCCGCTTCGGTTTCAGACGTCCCCCTGTTCCGGGCTTCTGTTCGCGCGGACATATGTGCGACGAACGTGCCAGATATGGCTAATCCTTTGATAACaaaaggaaaagg > 2:664595/1‑131 (MQ=255)
tCGGCGAACCCGTGCCAGTGTGTTGCCGCTTCGGTTTCAGACGTCCCCCTGTTCCGGGCTTCTGTTCGCGCGGACATATGTGCGACGAACGTGCCAGATATGGCTAATCCTTTGATAACAAAaggaaaaggaaa > 1:163130/1‑134 (MQ=255)
cGGCGAACCCGTGCCAGTGTGTTGCCGCTTCGGTTTCAGACGTCCCCCTGTTCCGGGCTTCTGTTCGCGCGGACATATGTGCGACGAACGTGCCAGATATGGCTAATCCTTTGATAACAaaaggaaaagga < 1:664595/131‑1 (MQ=255)
cGGCGAACCCGTGCCAGTGTGTTGCCGCTTCGGTTTCAGACGTCCCCCTGTTCCGGGCTTCTGTTCGCGCGGACATATGTGCGACGAACGTGCCAGATATGGCTAATCCTTTGATAACAAAAGGAAAAGGAAA‑t > 2:229262/1‑134 (MQ=255)
cGAACCCGTGCCAGTGTGTTGCCGCTTCGGTTTCAGACGTCCCCCTGTTCCGGGCTTCTGTTCGCGCGGACATATGTGCGACGAACGTGCCAGATATGGCTAATCCTTTGATAACAAAAGGAAAAGGAAA‑tttt < 2:189820/134‑2 (MQ=255)
cGTGCCAGTGTGTTGCCGCTTCGGTTTCAGACGTCCCCCTGTTCCGGGCTTCTGTTCGCGCGGACATATGTGCGACGAACGTGCCAGATATGGCTAATCCTTTGATAACAAAAGGAAAAGGAAATTTTCGGCTg > 2:410630/1‑134 (MQ=255)
|
ACGACCCCTGCACCTGGCCAGCCGATGCGGACCAGTTCCTGCCGCGTGGCCCACGCTTACAGCGCCAGTCCGAATCCCGCCCTGGGATGCGGGGTCGTCCTGAAACTGATCTTCGGCGAACCCGTGCCAGTGTG‑TGCCGCTTCGGTTTCAGACGTCCCCCTGTTCCGGGCTTCTGTTCGCGCGGACATATGTGCGACGAACGTGCCAGATATGGCTAATCCTTTGATAACAAAAGGAAAAGGAAA‑TTTCGGCTG > AM260479/787635‑787888
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ 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: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CCGCTAATCTTGTCGACGACCCCTGCACCTGGCCAGCCGATGCGGACCAGTTCCTGCCGCGTGGCCCACGCTTACAGCGCCAGTCCGAATCCCGCCCTGGGATGCGGGGTCGTCCTGAAACTGATCTTCGGCGAACCCGTGCCAGTGTG‑TGCCGCTTCGGTTTCAGACGTCCCCCTGTTCCGGGCTTCTGTTCGCGCGGACATATGTGCGACGAACGTGCCAGATATGGCTAATCCTTTGATAACAAAAGGAAAAGGAAA‑TTTCGGCTGGCC > AM260479/787620‑787891
|
CCGCTAATCTTGTCGACGACCCCTGCACCTGGCCAGCCGATGCGGACCAGTTCCTGCCGCGTGGCCCACGCTTACAGCGCCAGTCCGAATCCCGCCCTGGGATGCGGGGTCGTCCTGAAACTGATCTTCGGCGAACCCGTGCCAGTGTG‑T > GWNJ‑0478:712:GW2002102894th:2:1201:5977:55150/1‑150 (MQ=60)
AATCTTGTCGACGACCCCTGCACCTGGCCAGCCGATGCGGACCAGTTCCTGCCGCGTGGCCCACGCTTACAGCGCCAGTCCGAATCCCGCCCTGGGATGCGGGGTCGTCCTGAAACTGATCTTCGGCGAACCCGTGCCAGTGTGTTGCCG > GWNJ‑0478:712:GW2002102894th:2:2208:18529:75446/1‑150 (MQ=60)
ttttttttttcaagcagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacagGTCCGAATCCCGCCCTGGGATGCGGGGTCGTCCTGAAACTGATCTTCGGCGAACCCGTGCCAGTGTGTTGCCG < GWNJ‑0478:712:GW2002102894th:2:1112:3092:70750/73‑1 (MQ=60)
ACCCCTGCACCTGGCCAGCCGATGCGGACCAGTTCCTGCCGCGTGGCCCACGCTTACAGCGCCAGTCCGAATCCCGCCCTGGGATGCGGGGTCGTCCTGAAACTGATCTTCGGCGAACCCGTGCCAGTGTGTTGCCGCTTCGGTTTCAGA < GWNJ‑0478:712:GW2002102894th:2:2209:11934:24994/150‑1 (MQ=60)
CCCCTGCACCTGGCCAGCCGATGCGGACCAGTTCCTGCCGCGTGGCCCACGCTTACAGCGCCAGTCCGAATCCCGCCCTGGGATGCGGGGTCGTCCTGAAACTGATCTTCGGCGAACCCGTGCCAGTGTGTTGCCGCTTCGGTTTCAGAC < GWNJ‑0478:712:GW2002102894th:2:1111:12929:79711/150‑1 (MQ=60)
tttgtttttttttttttcaagcagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacaGTCCTGAAACTGATCTTCGGCGAACCCGTGCCAGTGTGTTGCCGCTTCGGTTTCAGACGTCCCCC < GWNJ‑0478:712:GW2002102894th:2:2105:12849:53232/65‑1 (MQ=60)
gatgtagctccgtctcgtgggctcggagatgtgtataagagacagGCGCCAGTCCGAATCCCGCCCTGGGATGCGGGGTCGTCCTGAAACTGATCTTCGGCGAACCCGTGCCAGTGTGTTGCCGCTTCGGTTTCAGACGTCCCCCTGTTC < GWNJ‑0478:712:GW2002102894th:2:2115:9494:9819/105‑1 (MQ=60)
ttttttttttttttcaagcagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacaGTCCTGAAACTGATCTTCGGCGAACCCGTGCCAGTGTGTTGCCGCTTCGGTTTCAGACGTCCCCCTGTTC < GWNJ‑0478:712:GW2002102894th:2:2113:2392:35389/70‑1 (MQ=60)
CCTGCCGCGTGGCCCACGCTTACAGCGCCAGTCCGAATCCCGCCCTGGGATGCGGGGTCGTCCTGAAACTGATCTTCGGCGAACCCGTGCCAGTGTGTTGCCGCTTCGGTTTCAGACGTCCCCCTGTTCCGGGCTTCTGTTCGCGCGGAC < GWNJ‑0478:712:GW2002102894th:2:1105:21064:67066/150‑1 (MQ=60)
CGCGTGGCCCACGCTTACAGCGCCAGTCCGAATCCCGCCCTGGGATGCGGGGTCGTCCTGAAACTGATCTTCGGCGAACCCGTGCCAGTGTGTTGCCGCTTCGGTTTCAGACGTCCCCCTGTTCCGGGCTTCTGTTCGCGCGGACATATG < GWNJ‑0478:712:GW2002102894th:2:2102:12533:85175/150‑1 (MQ=60)
TACAGCGCCAGTCCGAATCCCGCCCTGGGATGCGGGGTCGTCCTGAAACTGATCTTCGGCGAACCCGTGCCAGTGTGTTGCCGCTTCGGTTTCAGACGTCCCCCTGTTCCGGGCTTCTGTTCGCGCGGACATATGTGCGACGAACGTGCC > GWNJ‑0478:712:GW2002102894th:2:1206:7856:73640/1‑150 (MQ=60)
GCGCCAGTCCGAATCCCGCCCTGGGATGCGGGGTCGTCCTGAAACTGATCTTCGGCGAACCCGTGCCAGTGTGTTGCCGCTTCGGTTTCAGACGTCCCCCTGTTCCGGGCTTCTGTTCGCGCGGACATATGTGCGACGAACGTGCCAGAT < GWNJ‑0478:712:GW2002102894th:2:1106:6292:67434/150‑1 (MQ=60)
CGCCAGTCCGAATCCCGCCCTGGGATGCGGGGTCGTCCTGAAACTGATCTTCGGCGAACCCGTGCCAGTGTGTTGCCGCTTCGGTTTCAGACGTCCCCCTGTTCCGGGCTTCTGTTCGCGCGGACATATGTGCGACGAACGTGCCAGATA < GWNJ‑0478:712:GW2002102894th:2:1116:19555:11623/150‑1 (MQ=60)
GTCCGAATCCCGCCCTGGGATGCGGGGTCGTCCTGAAACTGATCTTCGGCGAACCCGTGCCAGTGTGTTGCCGCTTCGGTTTCAGACGTCCCCCTGTTCCGGGCTTCTGTTCGCGCGGACATATGTGCGACGAACGTGCCAGATATGGCT > GWNJ‑0478:712:GW2002102894th:2:1112:16447:19876/1‑150 (MQ=60)
GTCCGAATCCCGCCCTGGGATGCGGGGTCGTCCTGAAACTGATCTTCGGCGAACCCGTGCCAGTGTGTTGCCGCTTCGGTTTCAGACGTCCCCCTGTTCCGGGCTTCTGTTCGCGCGGACATATGTGCGACGAACGTGCCAGATATGGCT < GWNJ‑0478:712:GW2002102894th:2:2214:10800:9185/150‑1 (MQ=60)
GTCCGAATCCCGCCCTGGGATGCGGGGTCGTCCTGAAACTGATCTTCGGCGAACCCGTGCCAGTGTGTTGCCGCTTCGGTTTCAGACGTCCCCCTGTTCCGGGCTTCTGTTCGCGCGGACATATGTGCGACGAACGTGCCAGATATGGCC > GWNJ‑0478:712:GW2002102894th:2:1114:7386:15109/1‑150 (MQ=60)
ATCCCGCCCTGGGATGCGGGGTCGTCCTGAAACTGATCTTCGGCGAACCCGTGCCAGTGTGTTGCCGCTTCGGTTTCAGACGTCCCCCTGTTCCGGGCTTCTGTTCGCGCGGACATATGTGCGACGAACGTGCCAGATATGGCctgtctc > GWNJ‑0478:712:GW2002102894th:2:2211:9589:59802/1‑143 (MQ=60)
GGGATGCGGGGTCGTCCTGAAACTGATCTTCGGCGAACCCGTGCCAGTGTGTTGCCGCTTCGGTTTCAGACGTCCCCCTGTTCCGGGCTTCTGTTCGCGCGGACATATGTGCGACGAACGTGCCAGATATGGCTAATCCTTTGATAACA > GWNJ‑0478:712:GW2002102894th:2:2211:14977:81968/1‑149 (MQ=60)
TCCTGAAACTGATCTTCGGCGAACCCGTGCCAGTGTGTTGCCGCTTCGGTTTCAGACGTCCCCCTGTTCCGGGCTTCTGTTCGCGCGGACATATGTGCGACGAACGTGCCAGATATGGCTAATCCTTTGATAACAAAAGGAAAAGGAAA‑T > GWNJ‑0478:712:GW2002102894th:2:1110:8024:63382/1‑150 (MQ=60)
TCGGCGAACCCGTGCCAGTGTGTTGCCGCTTCGGTTTCAGACGTCCCCCTGTTCCGGGCTTCTGTTCGCGCGGACATATGTGCGACGAACGTGCCAGATATGGCTAATCCTTTGATAACAAAAGGAAAAGGAAATTTTCGGCTGGCC < GWNJ‑0478:712:GW2002102894th:2:2111:15766:72882/147‑1 (MQ=60)
|
CCGCTAATCTTGTCGACGACCCCTGCACCTGGCCAGCCGATGCGGACCAGTTCCTGCCGCGTGGCCCACGCTTACAGCGCCAGTCCGAATCCCGCCCTGGGATGCGGGGTCGTCCTGAAACTGATCTTCGGCGAACCCGTGCCAGTGTG‑TGCCGCTTCGGTTTCAGACGTCCCCCTGTTCCGGGCTTCTGTTCGCGCGGACATATGTGCGACGAACGTGCCAGATATGGCTAATCCTTTGATAACAAAAGGAAAAGGAAA‑TTTCGGCTGGCC > AM260479/787620‑787891
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
