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 |
561,006 |
+G |
intergenic (+9/+38) |
h16_A0532 → / ← h16_A0533 |
conserved hypothetical protein/universal stress protein, UspA family |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260479 | 561,005 | 1 | . | G | 100.0%
| 113.0
/ NA
| 30 | intergenic (+8/+39) | h16_A0532/h16_A0533 | conserved hypothetical protein/universal stress protein, UspA family |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base G (14/16); total (14/16) |
GGCCTTTCCGGCCGCGTTCCCTTGGTTCGGCACGGCGCGCTACTGGCAGGATCGCATCCTCGAACTGCGCGAACAGGTGGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACC‑GTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCTTTTCCGGCGCCTTGACCAGCAGCACCGGGCACTCTGCCTGCGCCAGCACGCGGCCTGCGACTGAACCGATCAC > AM260479/560883‑561127
|
ggCCTTTCCGGCCGCGTTCCCTTGGTTCGGCACGGCGCGCTACTGGCAGGATCGCATCCTCGAACTGCGCGAACAGGTGGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACCGGTCGGcgccg > 1:724168/1‑134 (MQ=255)
ttCCGGCCGCGTTCCCTTGGTTCGGCACGGCGCGCTACTGGCAGGATCGCATCCTCGAACTGCGCGAACAGGTGGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAgg > 1:254861/1‑134 (MQ=255)
tCCGGCCGCGTTCCCTTGGTTCGGCACGGCGCGCTACTGGCAGGATCGCATCCTCGAACTGCGCGAACAGGTGGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAgg < 1:553558/133‑1 (MQ=255)
tCCGGCCGCGTTCCCTTGGTTCGGCACGGCGCGCTACTGGCAGGATCGCATCCTCGAACTGCGCGAACAGGTGGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAgg < 1:560362/133‑1 (MQ=255)
cTTGGTTCGGCACGGCGCGCTACTGGCAGGATCGCATCCTCGAACTGCGCGAACAGGTGGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCAc < 2:577683/134‑1 (MQ=255)
cTTGGTTCGGCACGGCGCGCTACTGGCAGGATCGCATCCTCGAACTGCGCGAACAGGTGGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCAc < 1:475539/134‑1 (MQ=255)
aCGGCGCGCTACTGGCAGGATCGCATCCTCGAACTGCGCGAACAGGTGGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTc > 2:527510/1‑133 (MQ=255)
cTGGCAGGATCGCATCCTCGAACTGCGCGAACAGGTGGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCttt < 1:80649/133‑1 (MQ=255)
gATCGCATCCTCGAACTGCGCGAACAGGTGGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCTTTTCCGgcgc < 2:724168/134‑1 (MQ=255)
gATCGCATCCTCGAACTGCGCGAACAGGTGGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCTTTTCCGgcgc < 2:254861/134‑1 (MQ=255)
gATCGCATCCTCGAACTGCGCGAACAGGTGGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCTTTTCCGgcgc < 2:1020121/134‑1 (MQ=255)
tCCTCGAACTGCGCGAACAGGTGGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCTTTTCCGGCGCCTTGAc > 1:1000119/1‑133 (MQ=255)
gAACTGCGCGAACAGGTGGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCTTTTCCGGCGCCTTGAcc > 1:274259/1‑129 (MQ=255)
gAACTGCGCGAACAGGTGGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCTTTTCCGGCGCCTTGAcc < 2:274259/129‑1 (MQ=255)
gAACTGCGCGAACAGGTGGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCTTTTCCGGCGCCTTGACcagc < 2:1000119/132‑1 (MQ=255)
aaCAGGTGGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCTTTTCCGgcgc < 2:145970/112‑1 (MQ=255)
aaCAGGTGGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCTTTTCCGgcgc > 1:145970/1‑112 (MQ=255)
aaCAGGTGGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCTTTTCCGGCGCCTTGACCAGCAGCACCGGGCAc > 1:936924/1‑134 (MQ=255)
aaCAGGTGGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCTTTTCCGGCGCCTTGACCAGCAGCACCGGGCAc > 1:695096/1‑134 (MQ=255)
cAGGTGGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCTTTTCCGGCGCCTTGACCAGCAGCACCGGGCActc > 2:522774/1‑134 (MQ=255)
gTGGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCTTTTCCGGCGCCTTGACCAGCAGCACCGGGCACTctgc > 2:1008632/1‑134 (MQ=255)
aTGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCTTTTCCGGCGCCTTGACCAGCAGCACCGGGCACTCTGCCTGCGCCAg < 1:1008632/134‑1 (MQ=255)
cGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCTTTTCCGGCGCCTTGACCAGCAGCACCGGGCACTCTGCCTGCGCCAGCAcgc < 2:695096/134‑1 (MQ=255)
cTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCTTTTCCGGCGCCTTGACCAGCAGCACCGGGCACTCTGCCTGCGCCAGCACGCGGCCTGCGAc < 1:522774/134‑1 (MQ=255)
tgGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCTTTTCCGGCGCCTTGACCAGCAGCACCGGGCACTCTGCCTGCGCCAGCACGCGGCCTGCGACt < 1:493946/132‑1 (MQ=255)
cTGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCTTTTCCGGCGCCTTGACCAGCAGCACCGGGCACTCTGCCTGCGCCAGCACGCGGCCTGCGACTGAACCGATCa > 2:259782/1‑134 (MQ=255)
tGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCTTTTCCGGCGCCTTGACCAGCAGCACCGGGCACTCTGCCTGCGCCAGCACGCGGCCTGCGACTGAACCGATCAc > 2:242840/1‑134 (MQ=255)
tGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCACAACCCTTCGTTTCCGGCGCCTTGACCAGCAGCACCGGGCACTCTGCCTGCGCCAGCACGCGGCCTGCGACTGAACCGATCAc > 2:482530/1‑134 (MQ=255)
aGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCTTTTCCGGCGCCTTGACCAGCAGCACCGGGCACTCTGCCTGCGCCAGCACGCGGCCTGCGACTg > 1:620728/1‑122 (MQ=255)
aGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCTTTTCCGGCGCCTTGACCAGCAGCACCGGGCACTCTGCCTGCGCCAGCACGCGGCCTGCGACTg < 2:620728/122‑1 (MQ=255)
|
GGCCTTTCCGGCCGCGTTCCCTTGGTTCGGCACGGCGCGCTACTGGCAGGATCGCATCCTCGAACTGCGCGAACAGGTGGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACC‑GTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCTTTTCCGGCGCCTTGACCAGCAGCACCGGGCACTCTGCCTGCGCCAGCACGCGGCCTGCGACTGAACCGATCAC > AM260479/560883‑561127
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ 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
GGCTCGCCAGCCGCTGGGCCGACCCGGCCTTTCCGGCCGCGTTCCCTTGGTTCGGCACGGCGCGCTACTGGCAGGATCGCATCCTCGAACTGCGCGAACAGGTGGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACC‑GTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCTTTTCCGGCGCCTTGACCAGCAGCACCGGGCACTCTGCCTGCGCCAGCACGCGGCCTGCGACTGAACCGATCACCGCATCGAAGAACGAACCGCGGC > AM260479/560858‑561150
|
GGCTCGCCAGCCGCTGGGCCGACCCGGCCTTTCCGGCCGCGTTCCCTTGGTTCGGCACGGCGCGCTACTGGCAGGATCGCATCCTCGAACTGCGCGAACAGGTGGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACC‑GG < GWNJ‑0478:712:GW2002102894th:2:2102:21140:6384/150‑1 (MQ=60)
CCGCTGGGCCGACCCGGCCTTTCCGGCCGCGTTCCCTTGGTTCGGCACGGCGCGCTACTGGCAGGATCGCATCCTCGAACTGCGCGAACAGGTGGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGC > GWNJ‑0478:712:GW2002102894th:2:2115:14172:23397/1‑150 (MQ=60)
GGGCCGACCCGGCCTTTCCGGCCGCGTTCCCTTGGTTCGGCACGGCGCGCTACTGGCAGGATCGCATCCTCGAACTGCGCGAACAGGTGGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAGGG > GWNJ‑0478:712:GW2002102894th:2:1116:19001:97001/1‑150 (MQ=60)
TTCCGGCCGCGTTCCCTTGGTTCGGCACGGCGCGCTACTGGCAGGATCGCATCCTCGAACTGCGCGAACAGGTGGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCAC < GWNJ‑0478:712:GW2002102894th:2:2105:12273:2151/149‑1 (MQ=60)
TTCCGGCCGCGTTCCCTTGGTTCGGCACGGCGCGCTACTGGCAGGATCGCATCCTCGAACTGCGCGAACAGGTGGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCAC < GWNJ‑0478:712:GW2002102894th:2:2102:12951:50346/149‑1 (MQ=60)
CCTTGGTTCGGCACGGCGCGCTACTGGCAGGATCGCATCCTCGAACTGCGCGAACAGGTGGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCC < GWNJ‑0478:712:GW2002102894th:2:1215:5357:62582/150‑1 (MQ=60)
ACTGGCAGGATCGCATCCTCGAACTGCGCGAACAGGTGGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCTTTTCCGGCGCCTTGACC < GWNJ‑0478:712:GW2002102894th:2:1107:15387:52568/149‑1 (MQ=60)
ACTGGCAGGATCGCATCCTCGAACTGCGCGAACAGGTGGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCTTTTCCGGCGCCTTGACC > GWNJ‑0478:712:GW2002102894th:2:2215:11090:11622/1‑149 (MQ=60)
CAGGATCGCATCCTCGAACTGCGCGAACAGGTGGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCTTTTCCGGCGCCTTGACCAGCAGC > GWNJ‑0478:712:GW2002102894th:2:1203:4305:38834/1‑150 (MQ=60)
TCCTCGAACTGCGCGAACAGGTGGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCTTTTCCGGCGCCTTGACCAGCAGCACCtgtctct > GWNJ‑0478:712:GW2002102894th:2:1111:18191:61988/1‑143 (MQ=60)
TCCTCGAACTGCGCGAACAGGTGGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCTTTTCCGGCGCCTTGACCAGCAGCACCGGGCACT > GWNJ‑0478:712:GW2002102894th:2:2113:8467:52361/1‑150 (MQ=60)
TCCTCGAACTGCGCGAACAGGTGGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCTTTTCCGGCGCCTTGACCAGCAGCACCGGGCACT > GWNJ‑0478:712:GW2002102894th:2:2210:17594:55002/1‑150 (MQ=60)
cgtgggctcggagatgtgtataagagacaGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCTTTTCCGGCGCCTTGACCAGCAGCACCGGGCACTCTGCCTGCGCCAGCACGCGGCCTGCGAC < GWNJ‑0478:712:GW2002102894th:2:2208:15431:97268/121‑1 (MQ=60)
GATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCTTTTCCGGCGCCTTGACCAGCAGCACCGGGCACTCTGCCTGCGCCAGCACGCGGCCTGCGAC < GWNJ‑0478:712:GW2002102894th:2:2215:15919:57219/150‑1 (MQ=60)
CCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCTTTTCCGGCGCCTTGACCAGCAGCACCGGGCACTCTGCCTGCGCCAGCACGCGGCCTGCGACTGAACCGATCACCGC < GWNJ‑0478:712:GW2002102894th:2:2101:20304:30193/150‑1 (MQ=60)
CCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCTTTTCCGGCGCCTTGACCAGCAGCACCGGGCACTCTGCCTGCGCCAGCACGCGGCCTGCGACTGAACCGATCACCGC > GWNJ‑0478:712:GW2002102894th:2:2108:5695:5495/1‑150 (MQ=60)
GTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCTTTTCCGGCGCCTTGACCAGCAGCACCGGGCACTCTGCCTGCGCCAGCACGCGGCCTGCGACTGAACCGATCACCGCA < GWNJ‑0478:712:GW2002102894th:2:1214:14076:59992/148‑1 (MQ=60)
CCTGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCTTTTCCGGCGCCTTGACCAGCAGCACCGGGCACTCTGCCTGCGCCAGCACGCGGCCTGCGACTGAACCGATCACCGCATCGAAGAACG > GWNJ‑0478:712:GW2002102894th:2:2209:13895:66805/1‑150 (MQ=60)
ACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCTTTTCCGGCGCCTTGACCAGCAGCACCGGGCACTCTGCCTGCGCCAGCACGCGGCCTGCGACTGAACCGATCACCGCATCGAAGAACGAACCGCGGC < GWNJ‑0478:712:GW2002102894th:2:1201:8545:32404/149‑1 (MQ=60)
|
GGCTCGCCAGCCGCTGGGCCGACCCGGCCTTTCCGGCCGCGTTCCCTTGGTTCGGCACGGCGCGCTACTGGCAGGATCGCATCCTCGAACTGCGCGAACAGGTGGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACC‑GTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCTTTTCCGGCGCCTTGACCAGCAGCACCGGGCACTCTGCCTGCGCCAGCACGCGGCCTGCGACTGAACCGATCACCGCATCGAAGAACGAACCGCGGC > AM260479/560858‑561150
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
