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 |
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%
| 81.5
/ NA
| 19 | 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 . (9/10); total (9/10) |
CCAGCCCGGCCAACGTCCCGCCAGGCCCCGCACCTGCGGGCCTGGCCGGCCCCGCCACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAGCCCCCGCGCCTGTCTCGCCCCTGGGTTGATACCTATCGTTGCATCACGACAGGTGCAATCGCTGCGCCTGCAACAACAGACAGCCAACTGGCCACGCGACCGGCGCGCCCCCGCGCGGGCATGGGC > AM260480/2308122‑2308354
|
ccaGCCCGGCCAACGTCCCGCCAGGCCCCGCACCTGCGGGCCTGGCCGGCCCCGCCACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAG‑CCCCGCGCCTGTCTCGCCCCTGGGtt > 2:437004/1‑133 (MQ=255)
ggCCAACGTCCCGCCAGGCCCCGCACCTGCGGGCCTGGCCGGCCCCGCCACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAG‑CCCCGCGCCTGTCTCGCCCCTGGGTTGATACCTa < 2:373817/134‑1 (MQ=255)
cTGCGGGCCTGGCCGGCCCCGCCACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAGcccc > 1:1024543/1‑78 (MQ=255)
cTGCGGGCCTGGCCGGCCCCGCCACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAGcccc < 2:1024543/78‑1 (MQ=255)
cGGGCCTGGCCGGCCCCGCCACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAG‑CCCCGCGCCTGTCTCGCCCCTGGGTTGATACCTATCGTTGCATCACGACAGGTGCAATCGCTg < 1:341621/134‑1 (MQ=255)
ggCCTGGCCGGCCCCGCCACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAG‑CCCCGCGCCTGTCTCGCCCCTGGGTTGATACCTATCGTTGCATCACGACAGGTGCAATCGCTgcg > 1:143334/1‑134 (MQ=255)
ccggccCCGCCACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAG‑CCCCGCGCCTGTCTCGCCCCTGGGTTGATACCTATCGTTGCATCa < 2:879660/107‑1 (MQ=255)
ccggccCCGCCACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAG‑CCCCGCGCCTGTCTCGCCCCTGGGTTGATACCTATCGTTGCATCa > 1:879660/1‑107 (MQ=255)
ggccCCGCCACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAGcccc > 1:812303/1‑64 (MQ=255)
ggccCCGCCACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAGcccc < 2:812303/64‑1 (MQ=255)
ggccCCGCCACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAG‑CCCCGCGCCTGTCTCGCCCCTGGGTTGATACCTATCGTTGCATCACGACAGGTGCAATCGCTGCGCCTGcaaca < 2:143334/134‑1 (MQ=255)
ggccCCGCCACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAG‑CCCCGCGCCTGTCTCGCCCCTGGGTTGATACCTATCGTTGCATCACGACAGGTGCAATCGCTGCGCCTGcaac > 1:594869/1‑133 (MQ=255)
gCCACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAG‑CCCCGCGCCTGTCTCGCCCCTGGGTTGATACCTATCGTTGCATCACGACAGGTGCAATCGCTGCGCCTGCAACAacaga > 1:455163/1‑133 (MQ=255)
gcacgcacgcGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAG‑CCCCGCGCCTGTCTCg > 1:85353/1‑65 (MQ=255)
gcacgcacgcGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAG‑CCCCGCGCCTGTCTCg < 2:85353/65‑1 (MQ=255)
aCCGCTTGTCGGAATTGTCCGACATGCGATTCGGAG‑CCCCGCGCCTGTCTCGCCCCt > 1:671280/1‑57 (MQ=255)
aCCGCTTGTCGGAATTGTCCGACATGCGATTCGGAG‑CCCCGCGCCTGTCTCGCCCCt < 2:671280/57‑1 (MQ=255)
cGCTTGTCGGAATTGTCCGACATGCGATTCGGAG‑CCCCGCGCCTGTCTCGCCCCTggg < 2:275115/58‑1 (MQ=255)
cGCTTGTCGGAATTGTCCGACATGCGATTCGGAG‑CCCCGCGCCTGTCTCGCCCCTggg > 1:275115/1‑58 (MQ=255)
tCCGACATGCGATTCGGAG‑CCCCGCGCCTGTCTCGCCCCTGGGTTGATACCTATCGTTGCATCACGACAGGTGCAATCGCTGCGCCTGCAACAACAGACAGCCAACTGGCCACGCGACCGGCGCGCCCCcgcgc < 2:455163/134‑1 (MQ=255)
cGACATGCGATTCGGAG‑CCCCGCGCCTGTCTCGCCCCTGGGTTGATACCTATCGTTGCATCACGACAGGTGCAATCGCTGCGCCTGCAACAACAGACAGCCAACTGGCCACGCGACCGGCGCGCCCCcgcgcg < 2:594869/133‑1 (MQ=255)
cGGAG‑CCCCGCGCCTGTCTCGCCCCTGGGTTGATACCTATCGTTGCATCACGACAGGTGCAATCGCTGCGCCTGCAACAACAGACAGCCAACTGGCCACGCGACCGGCGCGCCCCCGCGCGGGCATGGGc < 2:694401/130‑1 (MQ=255)
cGGAG‑CCCCGCGCCTGTCTCGCCCCTGGGTTGATACCTATCGTTGCATCACGACAGGTGCAATCGCTGCGCCTGCAACAACAGACAGCCAACTGGCCACGCGACCGGCGCGCCCCCGCGCGGGCATGGGc > 1:694401/1‑130 (MQ=255)
|
CCAGCCCGGCCAACGTCCCGCCAGGCCCCGCACCTGCGGGCCTGGCCGGCCCCGCCACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAGCCCCCGCGCCTGTCTCGCCCCTGGGTTGATACCTATCGTTGCATCACGACAGGTGCAATCGCTGCGCCTGCAACAACAGACAGCCAACTGGCCACGCGACCGGCGCGCCCCCGCGCGGGCATGGGC > AM260480/2308122‑2308354
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ 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
ACACTGGCGGCCACCGGCCAACCGGGCCACCAGCCCGGCCAACGTCCCGCCAGGCCCCGCACCTGCGGGCCTGGCCGGCCCCGCCACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAGCCCCCGCGCCTGTCTCGCCCCTGGGTTGATACCTATCGTTGCATCACGACAGGTGCAATCGCTGCGCCTGCAACAACAGACAGCCAACTGGCCACGCGACCGGCGCGCCCCCGCGCGGGCATGGGCCAGATCGTCTCTG > AM260480/2308093‑2308367
|
ACACTGGCGGCCACCGGCCAACCGGGCCACCAGCCCGGCCAACGTCCCGCCAGGCCCCGCACCTGCGGGCCTGGCCGGCCCCGCCACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAG‑CCCCGCGCCTGTCT < GWNJ‑0478:712:GW2002102894th:2:1201:18429:56606/150‑1 (MQ=60)
gatttggtggctctcgggacgactatgctttttttttttcaagcagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacaGTCCGACAAGCGATTCGGAG‑CCCCGCGCCTGTCTCGCCCCTGGGTT < GWNJ‑0478:712:GW2002102894th:2:2213:4651:24358/46‑1 (MQ=60)
cgtgggctcggagatgtgtataagagacagggccaaccgggccaccagcccggccaacgtCCCGCCACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAG‑CCCCGCGCCTGTCTCGCCCCTGGGTTGATACC < GWNJ‑0478:712:GW2002102894th:2:2202:19443:38877/89‑1 (MQ=60)
CGCCAGGCCCCGCACCTGCGGGCCTGGCCGGCCCCGCCACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAG‑CCCCGCGCCTGTCTCGCCCCTGtctcttatacacatctccgagcccacgagacggagctac > GWNJ‑0478:712:GW2002102894th:2:2216:14896:88328/1‑111 (MQ=60)
GGCCCCGCACCTGCGGGCCTGGCCGGCCCCGCCACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAG‑CCCCGCGCCTGTCTCGCCCCTGGGTTGATACCTATCGTTGCATCACGACAGGTGCAATCGCTGCGC > GWNJ‑0478:712:GW2002102894th:2:1111:15546:41426/1‑150 (MQ=60)
CACCTGCGGGCCTGGCCGGCCCCGCCACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAG‑CCCCGCGCCTGTCTCGCCCCTGGGTTGATACCTATCGTTGCATCACGACAGGTGCAATCGCTGtctcttatac > GWNJ‑0478:712:GW2002102894th:2:2207:17988:40365/1‑140 (MQ=60)
CCTGCGGGCCTGGCCGGCCCCGCCACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAG‑CCCCGCGCCTGTCTCGCCCCTGtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgt > GWNJ‑0478:712:GW2002102894th:2:2204:2171:13389/1‑97 (MQ=60)
CCTGCGGGCCTGGCCGGCCCCGCCACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAG‑CCCCGCGCCTGTCTCGCCCCTGGGTTGATACCTATCGTTGCATCACGACAGGTGCAATCGCTGCGCCTGCAACA > GWNJ‑0478:712:GW2002102894th:2:2107:10879:55744/1‑149 (MQ=60)
GCGGGCCTGGCCGGCCCCGCCACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAG‑CCCCGCGCCTGTCTCGCCCCTGGGTTGATACCTATCGTTGCATCACGACAGGTGCAATCGCTGCGCCTGCAACAACAG < GWNJ‑0478:712:GW2002102894th:2:1207:9242:94369/150‑1 (MQ=60)
GGCCTGGCCGGCCCCGCCACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAG‑CCCCGCGCCTGTCTCGCCCCTGGGTTGATACCTATCGTTGCATCACGACAGGTGCAATCGCTGCGCCTGCAACAACAGAC > GWNJ‑0478:712:GW2002102894th:2:1212:16191:66308/1‑149 (MQ=60)
GGCCGGCCCCGCCACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAG‑CCCCGCGCCTGTCTCGCCCCTGGGTTGATACCTgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccg > GWNJ‑0478:712:GW2002102894th:2:1107:3795:77654/1‑97 (MQ=60)
ACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAG‑CCCCGCGCCTGTCTCGCCCCTGGGTTGATACCTATCctgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtcttctgc > GWNJ‑0478:712:GW2002102894th:2:2110:6914:33531/1‑87 (MQ=60)
GCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAG‑CCCCGCGCCTGTCTCGCCCCTGGGTTGATACCTATCGTTctgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtcttctg > GWNJ‑0478:712:GW2002102894th:2:1203:16094:61362/1‑88 (MQ=60)
GTCCGACATGCGATTCGGAG‑CCCCGCGCCTGTCTCGCCCCTGGGTTGATACCTATCGTTGCATCACGACAGGTGCAATCGCTGCGCCTGCAACAACAGACAGCCAACTGGCCACGCGACCGGCGCGCCCCCGCGCGGGCATGGGCC > GWNJ‑0478:712:GW2002102894th:2:2113:16433:69262/1‑146 (MQ=60)
GCGATTCGGAG‑CCCCGCGCCTGTCTCGCCCCTGGGTTGATACCTATCGTTGCATCACGACAGGTGCAATCGCTGCGCCTGCAACAACAGACAGCCAACTGGCCACGCGACCGGCGCGCCCCCGCGCGGGCATGGGCCAGATCGTCTCTG > GWNJ‑0478:712:GW2002102894th:2:1111:11629:13757/1‑149 (MQ=60)
|
ACACTGGCGGCCACCGGCCAACCGGGCCACCAGCCCGGCCAACGTCCCGCCAGGCCCCGCACCTGCGGGCCTGGCCGGCCCCGCCACGCACGCACGCGTCACCGCTTGTCGGAATTGTCCGACATGCGATTCGGAGCCCCCGCGCCTGTCTCGCCCCTGGGTTGATACCTATCGTTGCATCACGACAGGTGCAATCGCTGCGCCTGCAACAACAGACAGCCAACTGGCCACGCGACCGGCGCGCCCCCGCGCGGGCATGGGCCAGATCGTCTCTG > AM260480/2308093‑2308367
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
