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 |
AM260480 |
157,096 |
+G |
intergenic (‑26/+41) |
h16_B0136 ← / ← h16_B0137 |
cysteine desulfurase/conserved hypothetical membrane protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260480 | 157,094 | 1 | . | G | 100.0%
| 99.4
/ NA
| 26 | intergenic (‑24/+43) | h16_B0136/h16_B0137 | cysteine desulfurase/conserved hypothetical membrane protein |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base G (12/14); total (12/14) |
TATCGAGCACCGCGTCGGGCGGCAACGAGGCCGCGGCGGTGTCGAGATAGATGGTGGAGGCCGTCAGCGGGGTGTCGGCGCGGATCGCCTGGATGGCTTGGATATCCATGGAACGTCTCGGGTAATGACAGGC‑GGACGCGGCGACCGCGCCCCGAGGTAAGACTCAGTTGCGCACTTACTTGCGCAGCTTGGTGACGGAGCCGAAG > AM260480/156962‑157167
|
tATCGAGCACCGCGTCGGGCGGCAACGAGGCCGCGGCGGTGTCGAGATAGATGGTGGAGGCCGTCAGCGGGGTGTCGGCGCGGATCGCCTGGATGGCTTGGATATCCATGGAACGTCTCGGGTAATGACAGGC‑g > 1:1020415/1‑134 (MQ=255)
aGCACCGCGTCGGGCGGCAACGAGGCCGCGGCGGTGTCGAGATAGATGGTGGAGGCCGTCAGCGGGGTGTCGGCGCGGATCGCCTGGATGGCTTGGATATCCATGGAACGTCTCGGGTAATGACAGGC‑gggacg > 1:480294/1‑130 (MQ=255)
tCGGGCGGCAACGAGGCCGCGGCGGTGTCGAGATAGATGGTGGAGGCCGTCAGCGGGGTGTCGGCGCGGATCGCCTGGATGGCTTGGATATCCATGGAACGTCTCGGGTAATGACAGGCGGGACGCGGCGAc < 1:711739/132‑1 (MQ=255)
tCGGGCGGCAACGAGGCCGCGGCGGTGTCGAGATAGATGGTGGAGGCCGTCAGCGGGGTGTCGGCGCGGATCGCCTGGATGGCTTGGATATCCATGGAACGTCTCGGGTAATGACAGGCGGGACGCGGCGAc > 2:711739/1‑132 (MQ=255)
tCGGGCGGCAACGAGGCCGCGGCGGTGTCGAGATAGATGGTGGAGGCCGTCAGCGGGGTGTCGGCGCGGATCGCCTGGATGGCTTGGATATCCATGGAACGTCTCGGGTAATGACAGGCGGGACGCGGCGACcg > 2:738257/1‑134 (MQ=255)
gggCGGCAACGAGGCCGCGGCGGTGTCGAGATAGATGGTGGAGGCCGTCAGCGGGGTGTCGGCGCGGATCGCCTGGATGGCTTGGATATCCATGGAACGTCTCGGGTAATGACAGGCGGGACgcgg < 2:813997/126‑1 (MQ=255)
gggCGGCAACGAGGCCGCGGCGGTGTCGAGATAGATGGTGGAGGCCGTCAGCGGGGTGTCGGCGCGGATCGCCTGGATGGCTTGGATATCCATGGAACGTCTCGGGTAATGACAGGCGGGACgcgg > 1:813997/1‑126 (MQ=255)
gggCGGCAACGAGGCCGCGGCGGTGTCGAGATAGATGGTGGAGGCCGTCAGCGGGGTGTCGGCGCGGATCGCCTGGATGGCTTGGATATCCATGGAACGTCTCGGGTAATGACAGGCGGGACGCGGCGACcgcg > 1:404963/1‑134 (MQ=255)
gggCGGCAACGAGGCCGCGGCGGTGTCGAGATAGATGGTGGAGGCCGTCAGCGGGGTGTCGGCGCGGATCGCCTGGATGGCTTGGATATCCATGGAACGTCTCGGGTAATGACAGGCGGGACGCGGCGACcgc < 1:632942/133‑1 (MQ=255)
ggcAACGAGGCCGCGGCGGTGTCGAGATAGATGGTGGAGGCCGTCAGCGGGGTGTCGGCGCGGATCGCCTGGATGGCTTGGATATCCATGGAACGTCTCGGGTAATGACAGGCGGGACGCGGCGACCGCGcccc < 1:132022/134‑1 (MQ=255)
aGGCCGCGGCGGTGTCGAGATAGATGGTGGAGGCCGTCAGCGGGGTGTCGGCGCGGATCGCCTGGATGGCTTGGATATCCATGGAACGTCTCGGGTAATGACAGGCGGGACGCGGCGACCGCGCCCCGAGGTaa < 2:1020415/134‑1 (MQ=255)
cggTGTCGAGATAGATGGTGGAGGCCGTCAGCGGGGTGTCGGCGCGGATCGCCTGGATGGCTTGGATATCCATGGAACGTCTCGGGTAATGACAGGCGGGACGCGGCGACCGCGCCCCGAGGTAAGACTCAGtt > 1:550459/1‑134 (MQ=255)
ggTGTCGAGATAGATGGTGGAGGCCGTCAGCGGGGTGTCGGCGCGGATCGCCTGGATGGCTTGGATATCCATGGAACGTCTCGGGTAATGACAGGCGGGACGCGGCGACCGCGCCCCGAGGTAAGACTCAGTTg < 2:933336/134‑1 (MQ=255)
tCGAGATAGATGGTGGAGGCCGTCAGCGGGGTGTCGGCGCGGATCGCCTGGATGGCTTGGATATCCATGGAACGTCTCGGGTAATGACAGGCGGGACGCGGCGACCGCGCCCCGAGGTAAGACTCAGTTgcgc < 2:404963/133‑1 (MQ=255)
tagatGGTGGAGGCCGTCAGCGGGGTGTCGGCGCGGATCGCCTGGATGGCTTGGATATCCATGGAACGTCTCGGGTAATGACAGGCGGGACGCGGCGACCGCGCCCCGAGGTAAGACTCAGTTGCGCacttact < 1:591095/134‑1 (MQ=255)
ggAGGCCGTCAGCGGGGTGTCGGCGCGGATCGCCTGGATGGCTTGGATATCCATGGAACGTCTCGGGTAATGACAGGCGGGACGCGGCGACCGCGCCCCGAGGTAAGACTCAGTTGCGCACTTACTTGCGCAGc > 2:821421/1‑134 (MQ=255)
ggAGGCCGTCAGCGGGGTGTCGGCGCGGATCGCCTGGATGGCTTGGATATCCATGGAACGTCTCGGGTAATGACAGGC‑ggggc < 1:790173/83‑4 (MQ=255)
ggAGGCCGTCAGCGGGGTGTCGGCGCGGATCGCCTGGATGGCTTGGATATCCATGGAACGTCTCGGGTAATGACAGGC‑ggggc > 2:790173/1‑80 (MQ=255)
ccGTCAGCGGGGTGTCGGCGCGGATCGCCTGGATGGCTTGGATATCCATGGAACGTCTCGGGTAATGACAGGCGGGACGCGGCGACCGCGCCCCGAGGTAAGACTCAGTTGCGCACTTACTTGCGCAGCTTGGt > 1:655718/1‑134 (MQ=255)
tCAGCGGGGTGTCGGCGCGGATCGCCTGGATGGCTTGGATATCCATGGAACGTCTCGGGTAATGACAGGCGGGACGCGGCGACCGCGCCCCGAGGTAAGACTCAGTTGCGCACTTACTTGCGCAGCTTgg > 2:532826/1‑130 (MQ=255)
tCAGCGGGGTGTCGGCGCGGATCGCCTGGATGGCTTGGATATCCATGGAACGTCTCGGGTAATGACAGGCGGGACGCGGCGACCGCGCCCCGAGGTAAGACTCAGTTGCGCACTTACTTGCGCAGCTTgg < 1:532826/130‑1 (MQ=255)
aGCGGGGTGTCGGCGCGGATCGCCTGGATGGCTTGGATATCCATGGAACGTCTCGGGTAATGACAGGCGGGACGCGGCGACCGCGCCCCGAGGTAAGACTCAGTTGCGCACTTACTTGCGCAGCTTGGTGACg > 2:949600/1‑133 (MQ=255)
cGGGGTGTCGGCGCGGATCGCCTGGATGGCTTGGATATCCATGGAACGTCTCGGGTAATGACAGGCGGGACGCGGCGACCGCGCCCCGAGGTAAGACTCAGTTGCGCACTTACTTGCGCAGCTTGGTGACGGAg < 2:550459/134‑1 (MQ=255)
gggTGTCGGCGCGGATCGCCTGGATGGCTTGGATATCCATGGAACGTCTCGGGTAATGACAGGCGGGACGCGGCGACCGCGCCCCGAGGTAAGACTCAGTTGCGCACTTACTTGCGCAGCTTGGTGACGGAGcc < 1:871282/134‑1 (MQ=255)
tgtCGGCGCGGATCGCCTGGATGGCTTGGATATCCATGGAACGTCTCGGGTAATGACAGGCGGGACGCGGCGACCGCGCCCCGAGGTAAGACTCAGTTGCGCACTTACTTGCGCAGCTTGGTGACGGAGCCgaa < 1:821421/134‑1 (MQ=255)
cGGCGCGGATCGCCTGGATGGCTTGGATATCCATGGAACGTCTCGGGTAATGACAGGCGGGACGCGGCGACCGCGCCCCGAGGTAAGACTCAGTTGCGCACTTACTTGCGCAGCTTGGTGACGGAGCCgaag > 2:403998/1‑132 (MQ=255)
tcGGGTAATGACAGGCGGGACGCGGCGACCGCGCCCCGAGGt > 2:995111/1‑42 (MQ=37)
tcGGGTAATGACAGGCGGGACGCGGCGACCGCGCCCCGAGGt < 1:995111/42‑1 (MQ=37)
tcGGGTAATGACAGGCGGGACGCGGCGACCGCGCCCCGAGGTAAGACTCAGTTg < 2:498078/54‑1 (MQ=39)
tcGGGTAATGACAGGCGGGACGCGGCGACCGCGCCCCGAGGTAAGACTCAGTTg > 1:498078/1‑54 (MQ=39)
|
TATCGAGCACCGCGTCGGGCGGCAACGAGGCCGCGGCGGTGTCGAGATAGATGGTGGAGGCCGTCAGCGGGGTGTCGGCGCGGATCGCCTGGATGGCTTGGATATCCATGGAACGTCTCGGGTAATGACAGGC‑GGACGCGGCGACCGCGCCCCGAGGTAAGACTCAGTTGCGCACTTACTTGCGCAGCTTGGTGACGGAGCCGAAG > AM260480/156962‑157167
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 37 ≤ 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
GGTAGCTGCGCACGGTATCGAGCACCGCGTCGGGCGGCAACGAGGCCGCGGCGGTGTCGAGATAGATGGTGGAGGCCGTCAGCGGGGTGTCGGCGCGGATCGCCTGGATGGCTTGGATATCCATGGAACGTCTCGGGTAATGACAGGC‑GGACGCGGCGACCGCGCCCCGAGGTAAGACTCAGTTGCGCACTTACTTGCGCAGCTTGGTGACGGAGCCGAAGAAGCTGAACAGGGCGTCGCCGGCAATCACGCCGCCGGCGAAGGCGCTCATCTCGGCCACGTGCTTGTCGCCGCGC > AM260480/156947‑157242
|
GGTAGCTGCGCACGGTATCGAGCACCGCGTCGGGCGGCAACGAGGCCGCGGCGGTGTCGAGATAGATGGTGGAGGCCGTCAGCGGGGTGTCGGCGCGGATCGCCTGGATGGCTTGGATATCCATGGAACGTCTCGGGTAATGACAGGC‑GG > GWNJ‑0478:712:GW2002102894th:2:2216:13189:23325/1‑150 (MQ=60)
CTGCGCACGGTATCGAGCACCGCGTCGGGCGGCAACGAGGCCGCGGCGGTGTCGAGATAGATGGTGGAGGCCGTCAGCGGGGTGTCGGCGCGGATCGCCTGGATGGCTTGGATATCCATGGAACGTCTCGGGTAATGACAGGCGGGACGC > GWNJ‑0478:712:GW2002102894th:2:1215:14600:87428/1‑150 (MQ=60)
ATCGAGCACCGCGTCGGGCGGCAACGAGGCCGCGGCGGTGTCGAGATAGATGGTGGAGGCCGTCAGCGGGGTGTCGGCGCGGATCGCCTGGATGGCTTGGATATCCATGGAACGTCTCGGGTAATGACAGGCGGGACGCGGCGACCGCGC > GWNJ‑0478:712:GW2002102894th:2:1211:10938:69876/1‑150 (MQ=60)
ATCGAGCACCGCGTCGGGCGGCAACGAGGCCGCGGCGGTGTCGAGATAGATGGTGGAGGCCGTCAGCGGGGTGTCGGCGCGGATCGCCTGGATGGCTTGGATATCCATGGAACGTCTCGGGTAATGACAGGCGGGACGCGGCGACCGCGC > GWNJ‑0478:712:GW2002102894th:2:2202:3520:84037/1‑150 (MQ=60)
ccgtctcgtgggctcggagatgtgtataagagacagGTCGAGATAGATGGTGGAGGCCGTCAGCGGGGTGTCGGCGCGGATCGCCTGGATGGCTTGGATATCCATGGAACGTCTCGGGTAATGACAGGC‑GGggcgcggtcgccgcgtcc < GWNJ‑0478:712:GW2002102894th:2:2203:17020:20906/113‑19 (MQ=60)
GCGTCGGGCGGCAACGAGGCCGCGGCGGTGTCGAGATAGATGGTGGAGGCCGTCAGCGGGGTGTCGGCGCGGATCGCCTGGATGGCTTGGATATCCATGGAACGTCTCGGGTAATGACAGGCGGGACGCGGCGACCGCGCCCCGAGGTAA < GWNJ‑0478:712:GW2002102894th:2:2112:4877:51133/150‑1 (MQ=60)
CGGGCGGCAACGAGGCCGCGGCGGTGTCGAGATAGATGGTGGAGGCCGTCAGCGGGGTGTCGGCGCGGATCGCCTGGATGGCTTGGATATCCATGGAACGTCTCGGGTAATGACAGGCGGGACGCGGCGACCGCGCCCCGAGGTAAGAC < GWNJ‑0478:712:GW2002102894th:2:2108:3195:81454/149‑1 (MQ=60)
CGGCAACGAGGCCGCGGCGGTGTCGAGATAGATGGTGGAGGCCGTCAGCGGGGTGTCGGCGCGGATCGCCTGGATGGCTTGGATATCCATGGAACGTCTCGGGTAATGACAGGCGGGACGCGGCGACCGCGCCCCGAGGTAAGACTCAGT < GWNJ‑0478:712:GW2002102894th:2:1109:20581:78438/150‑1 (MQ=60)
GCAACGAGGCCGCGGCGGTGTCGAGATAGATGGTGGAGGCCGTCAGCGGGGTGTCGGCGCGGATCGCCTGGATGGCTTGGATATCCATGGAACGTCTCGGGTAATGACAGGCGGGACGCGGCGACCGCGCCCCGAGGTAAGACTCAGTTG > GWNJ‑0478:712:GW2002102894th:2:2102:13518:25251/1‑150 (MQ=60)
tttttttttttcaagcagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacagTATCCATGGAACGTCTCGGGTAATGACAGGCGGGACGCGGCGACCGCGCCCCGAGGTAAGACTCAGTTGCGC < GWNJ‑0478:712:GW2002102894th:2:2214:12804:84633/72‑1 (MQ=60)
GATAGATGGTGGAGGCCGTCAGCGGGGTGTCGGCGCGGATCGCCTGGATGGCTTGGATATCCATGGAACGTCTCGGGTAATGACAGGCGGGACGCGGCGACCGCGCCCCGAGGTAAGACTCAGTTGCGCACTTACTTGCGCAGCTTGGTG > GWNJ‑0478:712:GW2002102894th:2:2111:13033:21961/1‑150 (MQ=60)
ATAGATGGTGGAGGCCGTCAGCGGGGTGTCGGCGCGGATCGCCTGGATGGCTTGGATATCCATGGAACGTCTCGGGTAATGACAGGCGGGACGCGGCGACCGCGCCCCGAGGTAAGACTCAGTTGCGCACTTACTTGCGCAGCTTGGTGA < GWNJ‑0478:712:GW2002102894th:2:2107:20877:10931/150‑1 (MQ=60)
GGCCGTCAGCGGGGTGTCGGCGCGGATCGCCTGGATGGCTTGGATATCCATGGAACGTCTCGGGTAATGACAGGCGGGACGCGGCGACCGCGCCCCGAGGTAAGACTCAGTTGCGCACTTACTTGCGCAGCTTGGTGACGGAGCCGAAGA < GWNJ‑0478:712:GW2002102894th:2:2101:18990:100468/150‑1 (MQ=60)
GGGGTGTCGGCGCGGATCGCCTGGATGGCTTGGATATCCATGGAACGTCTCGGGTAATGACAGGCGGGACGCGGCGACCGCGCCCCGAGGTAAGACTCAGTTGCGCACTTACTTGCGCAGCTTGGTGACGGAGCCGAAGAAGCTGAACAG < GWNJ‑0478:712:GW2002102894th:2:2206:16515:53602/150‑1 (MQ=60)
GTGTCGGCGCGGATCGCCTGGATGGCTTGGATATCCATGGAACGTCTCGGGTAATGACAGGCGGGACGCGGCGACCGCGCCCCGAGGTAAGACTCAGTTGCGCACTTACTTGCGCAGCTTGGTGACGGAGCCGAAGAAGCTGAACAGGGC < GWNJ‑0478:712:GW2002102894th:2:2204:14038:35460/150‑1 (MQ=60)
gagatgtgtataagagacaGGGTAATGACAGGCGGGACGCGGCGACCGCGCCCCGAGGTAAGACTCAGTTGCGCACTTACTTGCGCAGCTTGGTGACGGAGCCGAAGAAGCTGAACAGGGCGTCGCCGGCAATCACGCCGCCGGCGAAGG < GWNJ‑0478:712:GW2002102894th:2:1106:11982:99430/131‑1 (MQ=60)
TATCCATGGAACGTCTCGGGTAATGACAGGCGGGACGCGGCGACCGCGCCCCGAGGTAAGACTCAGTTGCGCACTTACTTGCGCctgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtcttctgcttg > GWNJ‑0478:712:GW2002102894th:2:1214:17606:83460/1‑84 (MQ=60)
ATGACAGGCGGGACGCGGCGACCGCGCCCCGAGGTAAGACTCAGTTGCGCACTTACTTGCGCAGCTTGGTGACGGAGCCGAAGAAGCTGAACAGGGCctgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgc > GWNJ‑0478:712:GW2002102894th:2:2216:2704:8726/1‑97 (MQ=60)
TGACAGGCGGGACGCGGCGACCGCGCCCCGAGGTAAGACTCAGTTGCGCACTTACTTGCGCAGCTTGGTGACGGAGCCGAAGAAGCTGAACAGGGCGTCGCCtgtctcttatacacatctccgagcccacgagacggagctacatctcgt > GWNJ‑0478:712:GW2002102894th:2:1205:8317:52347/1‑102 (MQ=60)
GACAGGCGGGACGCGGCGACCGCGCCCCGAGGTAAGACTCAGTTGCtgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtcttctgcttgaaaaaaaaaatcagctgggtgcgccagatgcccgggaa > GWNJ‑0478:712:GW2002102894th:2:1109:18082:77269/1‑46 (MQ=60)
cgGGACGCGGCGACCGCGCCCCGAGGTAAGACTCAGTTGCGCACTTACTTGCGCAGCTTGGTGACGGAGCCGAAGAAGCTGAACAGGGCGTCGCCGGCAATCACGCCGCCGGCGAAGGCGCTCATCTCGGCCACGTGCTTGTCGCCGCGC < GWNJ‑0478:712:GW2002102894th:2:2212:16507:30268/148‑1 (MQ=60)
|
GGTAGCTGCGCACGGTATCGAGCACCGCGTCGGGCGGCAACGAGGCCGCGGCGGTGTCGAGATAGATGGTGGAGGCCGTCAGCGGGGTGTCGGCGCGGATCGCCTGGATGGCTTGGATATCCATGGAACGTCTCGGGTAATGACAGGC‑GGACGCGGCGACCGCGCCCCGAGGTAAGACTCAGTTGCGCACTTACTTGCGCAGCTTGGTGACGGAGCCGAAGAAGCTGAACAGGGCGTCGCCGGCAATCACGCCGCCGGCGAAGGCGCTCATCTCGGCCACGTGCTTGTCGCCGCGC > AM260480/156947‑157242
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
