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 |
2,308,233 |
(C)5→4 |
intergenic (+176/‑161) |
h16_B2050 → / → h16_B2051 |
response regulator containing a GGDEF effector domain/conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260480 | 2,308,229 | 0 | C | . | 100.0%
| 96.0
/ NA
| 22 | intergenic (+172/‑165) | h16_B2050/h16_B2051 | response regulator containing a GGDEF effector domain/conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base C (0/0); new base . (10/12); total (10/12) |
GGCCACCGGCCAACCGGGCCACCAGCCCGGCCAACGTCCCGCCAGGCCCCGCACCTGCGGGCCTGGCCGGCCCCGCCACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAGCCCCCGCGCCTGTCTCGCCCCTGGGTTGATACCTATCGTTGCATCACGACAGGTGCAATCGCTGCGCCTGCAACAACAGACAGCCAACTGGCCACGCGACCGGCGCGCCCCCGCGCG > AM260480/2308101‑2308345
|
ggcCACCGGCCAACCGGGCCACCAGCCCGGCCAACGTCCCGCCAGGCCCCGCACCTGCGGGCCTGGCCGGCCCCGCCACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAGccccgc > 1:533148/1‑132 (MQ=255)
gcCACCGGCCAACCGGGCCACCAGCCCGGCCAACGTCCCGCCAGGCCCCGCACCTGCGGGCCTGGCCGGCCCCGCCACACACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAGccccgcg < 1:709726/134‑4 (MQ=255)
aCCGGCCAACCGGGCCACCAGCCCGGCCAACGTCCCGCCAGGCCCCGCACCTGCGGGCCTGGCCGGCCCCGCCACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAG‑CCCCGCGCCt < 2:795154/134‑1 (MQ=255)
aCCGGCCAACCGGGCCACCAGCCCGGCCAACGTCCCGCCAGGCCCCGCACCTGCGGGCCTGGCCGGCCCCGCCACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAG‑CCCCGCGCCt < 2:533148/134‑1 (MQ=255)
cGGCCAACCGGGCCACCAGCCCGGCCAACGTCCCGCCAGGCCCCGCACCTGCGGGCCTGGCCGGCCCCGCCACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAG‑CCCCGCGCCTGt < 1:644526/134‑1 (MQ=255)
aCCGGGCCACCAGCCCGGCCAACGTCCCGCCAGGCCCCGCACCTGCGGGCCTGGCCGGCCCCGCCACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAG‑CCCCGCGCCTGtctc < 2:849359/131‑1 (MQ=255)
aCCGGGCCACCAGCCCGGCCAACGTCCCGCCAGGCCCCGCACCTGCGGGCCTGGCCGGCCCCGCCACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAG‑CCCCGCGCCTGtctc > 1:849359/1‑131 (MQ=255)
gCCACCAGCCCGGCCAACGTCCCGCCAGGCCCCGCACCTGCGGGCCTGGCCGGCCCCGCCACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAG‑CCCCGCGCCTGTCTCGCCCCTgg > 1:375961/1‑134 (MQ=255)
caGCCCGGCCAACGTCCCGCCAGGCCCCGCACCTGCGGGCCTGGCCGGCCCCGCCACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAG‑CCCCGCGCCTGTCTCGCCCCTGGGTTGa < 2:833246/134‑1 (MQ=255)
caGCCCGGCCAACGTCCCGCCAGGCCCCGCACCTGCGGGCCTGGCCGGCCCCGCCACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAG‑CCCCGCGCCTGTCTCGCCCCTGGGTTGa > 2:541378/1‑134 (MQ=255)
ggCCTGGCCGGCCCCGCCACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAG‑CCCCGCGCCTGTCTCGCCCCTGGGTTGATACCTATCGTTGCATCACGACAGGTGCAATCGCTg < 1:237605/132‑1 (MQ=255)
ggCCTGGCCGGCCCCGCCACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAG‑CCCCGCGCCTGTCTCGCCCCTGGGTTGATACCTATCGTTGCATCACGACAGGTGCAATCGCTg > 2:237605/1‑132 (MQ=255)
gCCTGGCCGGCCCCGCCACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAGccc > 1:252692/1‑71 (MQ=255)
gCCTGGCCGGCCCCGCCACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAGccc < 2:252692/71‑1 (MQ=255)
gCCTGGCCGGCCCCGCCACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAG‑CCCCGCGCCTGTCTCGCCCCTGGGTTGATACCTATCGTTGCATCACGACAGGTGCAATCGCTgcgc > 2:211075/1‑134 (MQ=255)
gccggccCCGCCACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAGccc > 2:931830/1‑66 (MQ=255)
gccggccCCGCCACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAGccc < 1:931830/66‑1 (MQ=255)
ggccCCGCCACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAG‑CCCCGCGCCTGTCTCGc > 1:704112/1‑77 (MQ=255)
ggccCCGCCACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAG‑CCCCGCGCCTGTCTCGc < 2:704112/77‑1 (MQ=255)
ccGCCACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAG‑CCCCGCGCCTGTCTCGCCCCTGGGTTGATACCTATCGTTGCATCACGACAGGTGCAATCGCTGCGCCTGCAACAacag < 2:375961/134‑1 (MQ=255)
gCCACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAG‑CCCCGCGCCTGTCTCGCCCCTGGGTTGATACCTATCGTTGCATCACGACAGGTGCAATCGCTGCGCCTGCAACAacaga > 2:195781/1‑133 (MQ=255)
gcacgcacgcGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAG‑CCCCGCGCCTGTCTCGCCCCTGGGTTGATACCTATCGTTGCATCACGACAGGTGCAATCGCTGCGCCTGCAACAACAGACAGcc > 1:646639/1‑133 (MQ=255)
gTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAG‑CCCCGCGCCTGTCTCGCCCCTGGGTTGATACCTATCGTTGCATCACGACAGGTGCAATCGCTGCGCCTGCAACAACAGACAGCCAACTGGCCAcg < 2:646639/134‑1 (MQ=255)
gAATTGTCCGACATGCGATTCGGAG‑CCCCGCGCCTGTCTCGCCCCTGGGTTGATACCTATCGTTGCATCACGACAGGTGCAATCGCTGCGCCTGCAACAACAGACAGCCAACTGGCCACGCGACCGGCGCGccc > 2:572930/1‑134 (MQ=255)
aaTTGTCCGACATGCGATTCGGAG‑CCCCGCGCCTGTCTCGCCCCTGGGTTGATACCTATCGTTGCATCACGACAGGTGCAATCGCTGCGCCTGCAACAACAGACAGCCAACTGGCCACGCGACCGGCGCGcccc < 1:211075/134‑1 (MQ=255)
tCCGACATGCGATTCGGAG‑CCCCGCGCCTGTCTCGCCCCTGGGTTGATACCTATCGTTGCATCACGACAGGTGCAATCGCTGCGCCTGCAACAACAGACAGCCAACTGGCCACGCGACCGGCGCGCCCCcgcgc < 1:541378/134‑1 (MQ=255)
ccGACATGCGATTCGGAG‑CCCCGCGCCTGTCTCGCCCCTGGGTTGATACCTATCGTTGCATCACGACAGGTGCAATCGCTGCGCCTGCAACAACAGACAGCCAACTGGCCACGCGACCGGCGCGCCCCcgcgcg > 1:858970/1‑134 (MQ=255)
cGACATGCGATTCGGAG‑CCCCGCGCCTGTCTCGCCCCTGGGTTGATACCTATCGTTGCATCACGACAGGTGCAATCGCTGCGCCTGCAACAACAGACAGCCAACTGGCCACGCGACCGGCGCGCCCCcgcgcg < 1:572930/133‑1 (MQ=255)
|
GGCCACCGGCCAACCGGGCCACCAGCCCGGCCAACGTCCCGCCAGGCCCCGCACCTGCGGGCCTGGCCGGCCCCGCCACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAGCCCCCGCGCCTGTCTCGCCCCTGGGTTGATACCTATCGTTGCATCACGACAGGTGCAATCGCTGCGCCTGCAACAACAGACAGCCAACTGGCCACGCGACCGGCGCGCCCCCGCGCG > AM260480/2308101‑2308345
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 35 ≤ 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
CAGTTACACACTGGCGGCCACCGGCCAACCGGGCCACCAGCCCGGCCAACGTCCCGCCAGGCCCCGCACCTGCGGGCCTGGCCGGCCCCGCCACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAGCCCCCGCGCCTGTCTCGCCCCTGGGTTGATACCTATCGTTGCATCACGACAGGTGCAATCGCTGCGCCTGCAACAACAGACAGCCAACTGGCCACGCGACCGGCGCGCCCCCGCGCGGGCATGGGCCAGATCGTCTCTGACTCCTCCAACAG > AM260480/2308086‑2308380
|
CAGTTACACACTGGCGGCCACCGGCCAACCGGGCCACCAGCCCGGCCAACGTCCCGCCAGGCCCCGCACCTGCGGGCCTGGCCGGCCCCGCCACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAG‑CCCCGCG > GWNJ‑0478:712:GW2002102894th:2:2101:18084:71970/1‑150 (MQ=60)
ACACTGGCGGCCACAGGCCAACCGGGCCACCAGCCCGGCCAACGTCCCGCCAGGCCCCGCACCTGCGGGCCTGGCCGGCCCCGCCACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAG‑CCCCGCGCCTGTCT < GWNJ‑0478:712:GW2002102894th:2:2209:7609:20241/150‑1 (MQ=60)
ggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacagGCACCTGCGGGCCTGGCCGGCCCCGCCACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAG‑CCCCGCGCCTGTCTCGCC < GWNJ‑0478:712:GW2002102894th:2:2211:20399:98585/96‑1 (MQ=60)
GGCGGCCACCGGCCAACCGGGCCACCAGCCCGGCCAACGTCCCGCCAGGCCCCGCACCTGCGGGCCTGGCCGGCCCCGCCACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAG‑CCCCGCGCCTGTCTCGCCC > GWNJ‑0478:712:GW2002102894th:2:2205:12537:91212/1‑150 (MQ=60)
GGCCACCGGCCAACCGGGCCACCAGCCCGGCCAACGTCCCGCCAGGCCCCGCACCTGCGGGCCTGGCCGGCCCCGCCACACACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAG‑CCCCGCGCCTGTCTCGCCCCTG < GWNJ‑0478:712:GW2002102894th:2:2112:16694:14085/150‑1 (MQ=60)
CCACCGGCCAACCGGGCCACCAGCCCGGCCAACGTCCCGCCAGGCCCCGCACCTGCGGGCCTGGCCGGCCCCGCCACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAG‑CCCCGCGCCTGTCTCGCCCCTGGG > GWNJ‑0478:712:GW2002102894th:2:1208:13464:83828/1‑150 (MQ=60)
CCGGCCAACCGGGCCACCAGCCCGGCCAACGTCCCGCCAGGCCCCGCACCTGCGGGCCTGGCCGGCCCCGCCACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAG‑CCCCGCGCCTGTCTCGCCCCTGGGTTG < GWNJ‑0478:712:GW2002102894th:2:2109:12443:31399/150‑1 (MQ=60)
GCCCCGCACCTGCGGGCCTGGCCGGCCCCGCCACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAG‑CCCCGCGCCTGTCTCGCCCtgtctcttatacacatctccgagcccacgagacggagctacatctcgt > GWNJ‑0478:712:GW2002102894th:2:1116:10063:64774/1‑102 (MQ=60)
CCTGCGGGCCTGGCCGGCCCCGCCACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAG‑CCCCGCGCCTGTCTCGCCCCTGGGTTGATACCctgtctcttatacacatctccgagcccacgagacggagctac > GWNJ‑0478:712:GW2002102894th:2:2113:12165:80321/1‑107 (MQ=60)
GCGGGCCTGGCCGGCCCCGCCACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAG‑CCCCGCGCCTGTCTCGCCCCTGGGTTGATACCTATCGTTGCATCACGACAGGTGCAATCGCTGCGCCTGCAACAACAG < GWNJ‑0478:712:GW2002102894th:2:1114:9825:78874/150‑1 (MQ=60)
GGCCGGCCCCGCCACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAG‑CCCCGCGCCTGTCTCGCCCCTGGGTTGATACCTATCGTTGCATCACGACAGGTGCAATCGCTGCGCCTGCAACAACAGACAGCCA > GWNJ‑0478:712:GW2002102894th:2:2109:16598:44593/1‑149 (MQ=60)
GCTTGTCGGAATTGTCCGACATGCGATTCGGAG‑CCCCGCGCCTGTCTCGCCCCTGGGTTGATACCTATCGTTGCATCACGACAGGTGCAATCGCTGCGCCTGCAACAACAGACAGCCAACTGGCCACGCGACCGGCGCGCCCCCGCGCGG > GWNJ‑0478:712:GW2002102894th:2:2209:18820:50831/1‑150 (MQ=60)
GAATTGTCCGACATGCGATTCGGAG‑CCCCGCGCCTGTCTCGCCCCTGGGTTGATACCTATCGTTGCATCACGACAGGTGCAATCGCTGCGCCTGCAACAACAGACAGCCAACTGGCCACGCGACCGGCGCGCCCCCGCGCGGGCATGGGC < GWNJ‑0478:712:GW2002102894th:2:1115:8171:33968/150‑1 (MQ=60)
GTCCGACATGCGATTCGGAG‑CCCCGCGCCTGTCTCGCCCCTGGGTTGATACCTATCGTTGCATCACGACAGGTGCAATCGCTGCGCCTGCAACAACAGACAGCCAACTGGCCACGCGACCGGCGCGCCCCCGCGCGGGCATGGGCCAGAT < GWNJ‑0478:712:GW2002102894th:2:2103:9977:31430/150‑1 (MQ=60)
CCGACATGCGATTCGGAG‑CCCCGCGCCTGTCTCGCCCCTGGGTTGATACCTATCGTTGCATCACGACAGGTGCAATCGCTGCGCCTGCAACAACAGACAGCCAACTGGCCACGCGACCGGCGCGCCCCCGCGCGGGCATGGGCCAGATC < GWNJ‑0478:712:GW2002102894th:2:2105:6921:59283/149‑1 (MQ=60)
CGATTCGGAG‑CCCCGCGCCTGTCTCGCCCCTGGGTTGATACCTATCGTTGCATCACGACAGGTGCAATCGCTGCGCCTGCAACAACAGACAGCCAACTGGCCACGCGACCGGCGCGCCCCCGCGCGGGCATGGGCCAGATCGTCTCTGAC > GWNJ‑0478:712:GW2002102894th:2:1107:8540:56743/1‑150 (MQ=60)
CCCGCGCCTGTCTCGCCCCTGGGTTGATACCTATCGTTGCATCACGACAGGTGCAATCGCTGCGCCTGCAACAACAGACAGCCAACTGGCCACGCGACCGGCGCGCCCCCGCGCGGGCATGGGCCAGATCGTCTCTGACTCCTCCAACAG < GWNJ‑0478:712:GW2002102894th:2:2210:18989:22752/150‑1 (MQ=60)
|
CAGTTACACACTGGCGGCCACCGGCCAACCGGGCCACCAGCCCGGCCAACGTCCCGCCAGGCCCCGCACCTGCGGGCCTGGCCGGCCCCGCCACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAGCCCCCGCGCCTGTCTCGCCCCTGGGTTGATACCTATCGTTGCATCACGACAGGTGCAATCGCTGCGCCTGCAACAACAGACAGCCAACTGGCCACGCGACCGGCGCGCCCCCGCGCGGGCATGGGCCAGATCGTCTCTGACTCCTCCAACAG > AM260480/2308086‑2308380
|
| 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: ‑ |
