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 |
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%
| 74.2
/ NA
| 20 | 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 (11/9); total (11/9) |
TCCGGCCGCGTTCCCTTGGTTCGGCACGGCGCGCTACTGGCAGGATCGCATCCTCGAACTGCGCGAACAGGTGGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACC‑GTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCTTTTCCGGCGCCTTGACCAGCAGCACCGGGCACTCTGCCTGCGCCAGCACGCGGCCTGCGACTGAACCGATCACCG > AM260479/560889‑561129
|
tCCGGCCGCGTTCCCTTGGTTCGGCACGGCGCGCTACTGGCAGGATCGCATCCTCGAACTGCGCGAACAGGTGGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAgg < 2:938902/133‑1 (MQ=255)
gCCGCGTTCCCTTGGTTCGGCACGGCGCGCTACTGGCAGGATCGCATCCTCGAACTGCGCGAACAGGTGGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAGGGCGcc < 1:846922/134‑1 (MQ=255)
gTTCCCTTGGTTCGGCACGGCGCGCTACTGGCAGGATCGCATCCTCGAACTGCGCGAACAGGTGGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGttt < 1:493374/134‑1 (MQ=255)
gTTCGGCACGGCGCGCTACTGGCAGGATCGCATCCTCGAACTGCGCGAACAGGTGGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTaa < 2:309607/133‑1 (MQ=255)
cTACTGGCAGGATCGCATCCTCGAACTGCGCGAACAGGTGGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCa < 2:730150/98‑1 (MQ=255)
cTACTGGCAGGATCGCATCCTCGAACTGCGCGAACAGGTGGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCa > 1:730150/1‑98 (MQ=255)
ggCAGGATCGCATCCTCGAACTGCGCGAACAGGTGGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCTTTTcc > 2:195806/1‑134 (MQ=255)
cATCCTCGAACTGCGCGAACAGGTGGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCAc < 2:627838/100‑1 (MQ=255)
cATCCTCGAACTGCGCGAACAGGTGGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCAc > 1:627838/1‑100 (MQ=255)
aaCAGGTGGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCTTTTCCGGCGCCTTGACCAGCAGCACCGGGCAc > 2:372273/1‑134 (MQ=255)
cAGGTGGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCTTTTCCGGCGCCTTGACCAGCAGCACCGGGCActc > 1:674640/1‑134 (MQ=255)
gACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCTTTTCCGGCGCCTTGACCAGCAGCACCGGGCACTctgcctg > 2:1004057/1‑125 (MQ=255)
gACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCTTTTCCGGCGCCTTGACCAGCAGCACCGGGCACTctgcctg < 1:1004057/125‑1 (MQ=255)
aCGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCt > 2:333988/1‑74 (MQ=255)
aCGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCt < 1:333988/74‑1 (MQ=255)
cGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCTTTTCCGGCGCCTTGACCAGCAGCACCGGGCACTCTGCCTGCGCCAGCAcgc > 1:283851/1‑134 (MQ=255)
ccTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCTTTTCCGGCGCCTTGACCAGCAGCACCGGGCACTCTGCCTGCGCCAGCACGCGGCCTGCGa > 2:811304/1‑134 (MQ=255)
cTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCTTTTCCGGCGCCTTGACCAGCAGCACCGGGCACTCTGCCTGCGCCAGCACGCGGCCTGCGAc < 1:195806/134‑1 (MQ=255)
gcgcCTGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCTTTTCCGGCGCCTTGACCAGCAGCACCGGGCACTCTGCCTGCGCCAGCACGCGGCCTGCGACTGAAcc > 1:586170/1‑133 (MQ=255)
aGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCTTTTCCGGCGCCTTGACCAGCAGCACCGGGCACTCTGCCTGCGCCAGCACGCGGCCTGCGACTGAACCGATCACCg > 2:917223/1‑134 (MQ=255)
|
TCCGGCCGCGTTCCCTTGGTTCGGCACGGCGCGCTACTGGCAGGATCGCATCCTCGAACTGCGCGAACAGGTGGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACC‑GTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCTTTTCCGGCGCCTTGACCAGCAGCACCGGGCACTCTGCCTGCGCCAGCACGCGGCCTGCGACTGAACCGATCACCG > AM260479/560889‑561129
|
| 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‑GTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCTTTTCCGGCGCCTTGACCAGCAGCACCGGGCACTCTGCCTGCGCCAGCACGCGGCCTGCGACTGAACCGATCACCGCATCGAAGAACGAACC > AM260479/560858‑561145
|
agcagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacaGCTACTGGCAGGATCGCATCCTCGAACTGCGCGAACAGGTGGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACC‑GG < GWNJ‑0478:712:GW2002102894th:2:1211:16666:62311/87‑1 (MQ=60)
CGCCAGCCGCTGGGCCGACCCGGCCTTTCCGGCCGCGTTCCCTTGGTTCGGCACGGCGCGCTACTGGCAGGATCGCATCCTCGAACTGCGCGAACAGGTGGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACC‑Ggtc < GWNJ‑0478:712:GW2002102894th:2:1102:9515:34646/148‑4 (MQ=60)
GGCCGCGTTCCCTTGGTTCGGCACGGCGCGCTACTGGCAGGATCGCATCCTCGAACTGCGCGAACAGGTGGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATT < GWNJ‑0478:712:GW2002102894th:2:2209:17174:36900/150‑1 (MQ=60)
CGTTCCCTTGGTTCGGCACGGCGCGCTACTGGCAGGATCGCATCCTCGAACTGCGCGAACAGGTGGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTC < GWNJ‑0478:712:GW2002102894th:2:1214:12297:76553/150‑1 (MQ=60)
GTTCGGCACGGCGCGCTACTGGCAGGATCGCATCCTCGAACTGCGCGAACAGGTGGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCctgtctcttatacacatctccg > GWNJ‑0478:712:GW2002102894th:2:2115:11457:82165/1‑128 (MQ=60)
agatgtagctccgtctcgtgggctcggagatgtgtataagagacagAGGTGGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCTTTTCC < GWNJ‑0478:712:GW2002102894th:2:1207:20160:47611/104‑1 (MQ=60)
CTACTGGCAGGATCGCATCCTCGAACTGCGCGAACAGGTGGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCtgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtc > GWNJ‑0478:712:GW2002102894th:2:2212:18282:56980/1‑94 (MQ=60)
CTACTGGCAGGATCGCATCCTCGAACTGCGCGAACAGGTGGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCctgtctcttatacacatctc > GWNJ‑0478:712:GW2002102894th:2:2108:18943:69553/1‑130 (MQ=60)
CTCGAACTGCGCGAACAGGTGGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCTTTTCCGGCGCCTTGACCAGCAGCACCGGGCACTCT > GWNJ‑0478:712:GW2002102894th:2:2110:18030:53500/1‑150 (MQ=60)
GGTGGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCTTTTCCGGCGCCTTGACCAGCAGCACCGGGCACTCTGCCTGCGCCAGCACGCG > GWNJ‑0478:712:GW2002102894th:2:1202:19191:20357/1‑150 (MQ=60)
GGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCTTTTCCGGCGCCTTGACCAGCAGCACCGGGCACTCTGCCTGCGCCAGCACGCGGCC < GWNJ‑0478:712:GW2002102894th:2:2215:10262:67880/150‑1 (MQ=60)
AAGCGCCCCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCTTTTCCGGCGCCTTGACCAGCAGCACCGGGCACTCTGCCTGCGCCAGCACGCGGCCTGCGACTGAACCG > GWNJ‑0478:712:GW2002102894th:2:2104:16850:98781/1‑149 (MQ=60)
CCTGTGGGGCGCCTGAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCTTTTCCGGCGCCTTGACCAGCAGCACCGGGCACTCTGCCTGCGCCAGCACGCGGCCTGCGACTGAACCGATCACCGC < GWNJ‑0478:712:GW2002102894th:2:1112:10874:55636/150‑1 (MQ=60)
GAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCTTTTCCGGCGCCTTGACCAGCAGCACCGGGCACTCTGCCTGCGCCAGCACctgtctcttatacacatctccgagcccacgagacggagct > GWNJ‑0478:712:GW2002102894th:2:2212:16790:64345/1‑109 (MQ=60)
GAGGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCTTTTCCGGCGCCTTGACCAGCAGCACCGGGCACTCTGCCTGCGCCAGCACGCGGCCTGCGACTGAACCGATCACCGCATCGAAGAACGAAC > GWNJ‑0478:712:GW2002102894th:2:1115:15319:88517/1‑150 (MQ=60)
GGTCTACCGGTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCTTTTCCGGCGCCTTGACCAGCctgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtcttctgcttgaaaaa > GWNJ‑0478:712:GW2002102894th:2:1112:18870:40996/1‑78 (MQ=60)
|
GGCTCGCCAGCCGCTGGGCCGACCCGGCCTTTCCGGCCGCGTTCCCTTGGTTCGGCACGGCGCGCTACTGGCAGGATCGCATCCTCGAACTGCGCGAACAGGTGGCGCTGATGGACGAAGCGCCCCTGTGGGGCGCCTGAGGTCTACC‑GTCGGCGCCGCCAGGGCGCCGGTTTTCCACTAATTTGCTCAACCCTTCTTTTCCGGCGCCTTGACCAGCAGCACCGGGCACTCTGCCTGCGCCAGCACGCGGCCTGCGACTGAACCGATCACCGCATCGAAGAACGAACC > AM260479/560858‑561145
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
