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 F2 I199 R1
|
220 |
57.5 |
3163680 |
97.0% |
3068769 |
86.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,062,210 |
T→C |
G390G (GGT→GGC) |
agp → |
bifunctional glucose‑1‑phosphatase/inositol phosphatase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,062,210 | 0 | T | C | 100.0%
| 126.7
/ NA
| 39 | G390G (GGT→GGC) | agp | bifunctional glucose‑1‑phosphatase/inositol phosphatase |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (23/16); total (23/16) |
GAGTGCGGAACAGTTACGTAATGCCGATGCGTTAACCCTGCAGGCACCTGCGCAGCGTGTGACGCTGGAATTAAGCGGTTGCCCGATAGACGCTGATGGTTTCTGCCCGATGGATAAGTTTGATAGCGTGTTGAATGAAGCGGTGAAATAACAGAA > NZ_CP009273/1062132‑1062287
|
gagTGCGGAACAGTTACGTAATGCCGATGCGTTAACCCTGCAGGCACCTGCGCAGCGTGTGACGCTGGAATTAAGCGGCTGcc < 2:51428/83‑1 (MQ=255)
gagTGCGGAACAGTTACGTAATGCCGATGCGTTAACCCTGCAGGCACCTGCGCAGCGTGTGACGCTGGAATTAAGCGGCTGcc > 1:51428/1‑83 (MQ=255)
gagTGCGGAACAGTTACGTAATGCCGATGCGTTAACCCTGCAGGCACCTGCGCAGCGTGTGACGCTGGAATTAAGCGGCTGCCCGATAGa > 1:120670/1‑90 (MQ=255)
gTGCGGAACAGTTACGTAATGCCGATGCGTTAACCCTGCAGGCACCTGCGCAGCGTGTGACGCTGGAATTAAGCGGCTGCCCGATAGACg > 2:1544077/1‑90 (MQ=255)
gTGCGGAACAGTTACGTAATGCCGATGCGTTAACCCTGCAGGCACCTGCGCAGCGTGTGACGCTGGAATTAAGCGGCTGCCCGATAGACg > 1:345948/1‑90 (MQ=255)
tGCGGAACAGTTACGTAATGCCGATGCGTTAACCCTGCAGGCACCTGCGCAGCGTGTGACGCTGGAATTAAGCGGCTGCCCGATAGACGc < 2:213823/90‑1 (MQ=255)
gCGGAACAGTTACGTAATGCCGATGCGTTAACCCTGCAGGCACCTGCGCAGCGTGTGACGCTGGAATTAAGCGGCTGCCCGATAGACGCt > 2:859080/1‑90 (MQ=255)
gCGGAACAGTTACGTAATGCCGATGCGTTAACCCTGCAGGCACCTGCGCAGCGTGTGACGCTGGAATTAAGCGGCTGCCCGATAGACGCt > 2:1416757/1‑90 (MQ=255)
gAACAGTTACGTAATGCCGATGCGTTAACCCTGCAGGCACCTGCGCAGCGTGTGACGCTGGAATTAAGCGGCTGCCCGATAGACGCTGAt < 1:609049/90‑1 (MQ=255)
gTTACGTAATGCCGATGCGTTAACCCTGCAGGCACCTGCGCAGCGTGTGACGCTGGAATTAAGCGGCTGCCCGATAGACGCTGATGGttt > 1:1331032/1‑90 (MQ=255)
aCGTAATGCCGATGCGTTAACCCTGCAGGCACCTGCGCAGCGTGTGACGCTGGAATTAAGCGGCTGCCCGATAGACGCTGATGGTTTCTg < 2:212740/90‑1 (MQ=255)
gTAATGCCGATGCGTTAACCCTGCAGGCACCTGCGCAGCGTGTGACGCTGGAATTAAGCGGCTGCCCGATAGACGCTGATGGTTTCTGcc > 1:749248/1‑90 (MQ=255)
aTGCCGATGCGTTAACCCTGCAGGCACCTGCGCAGCGTGTGACGCTGGAATTAAGCGGCTGCCCGATAGACGCTGACGGTTTCTGCCCGa > 2:683134/1‑90 (MQ=255)
gATGCGTTAACCCTGCAGGCACCTGCGCAGCGTGTGACGCTGGAATTAAGCGGCTGCCCGATAGACGCTGATGGTTTCTGCCCGATGGAt > 1:752044/1‑90 (MQ=255)
gATGCGTTAACCCTGCAGGCACCTGCGCAGCGTGTGACGCTGGAATTAAGCGGCTGCCCGATAGACGCTGATGGTTTCTGCCCGATGGAt > 1:8158/1‑90 (MQ=255)
gATGCGTTAACCCTGCAGGCACCTGCCCAGCGTGTGACGCTGGAATTAAGCGGCTGCCCGATAGACGCTGATGGTTTCTGCCCGATGGAt > 1:755351/1‑90 (MQ=255)
aTGCGTTAACCCTGCAGGCACCTGCGCAGCGTGTGACGCTGGAATTAAGCGGCTGCCCGATAGACGCTGATGGTTTCTGCCCGATGGATa < 2:1046198/90‑1 (MQ=255)
aTGCGTTAACCCTGCAGGCACCTGCGCAGCGTGTGACGCTGGAATTAAGCGGCTGCCCGATAGACGCTGATGGTTTCTGCCCGATGGATa < 1:1267095/90‑1 (MQ=255)
aTGCGTTAACCCTGCAGGCACCTGCGCAGCGTGTGACGCTGGAATTAAGCGGCTGCCCGATAGACGCTGATGGTTTCTGCCCGATGGATa < 2:252838/90‑1 (MQ=255)
aTGCGTTAACCCTGCAGGCACCTGCGCAGCGTGTGACGCTGGAATTAAGCGGCTGCCCGATAGACGCTGATGGTTTCTGCCCGATGGATa < 2:752044/90‑1 (MQ=255)
aTGCGTTAACCCTGCAGGCACCTGCCCAGCGTGTGACGCTGGAATTAAGCGGCTGCCCGATAGACGCTGATGGTTTCTGCCCGATGGATa < 2:755351/90‑1 (MQ=255)
gTTAACCCTGCAGGCACCTGCGCAGCGTGTGACGCTGGAATTAAGCGGCTGCCCGATAGACGCTGATGGTTTCTGCCCGATGGATAAGtt > 2:1428155/1‑90 (MQ=255)
ccTGCAGGCACCTGCGCAGCGTGTGACGCTGGAATTAAGCGGCTGCCCGATAGACGCTGATGGTTTCTGCCCGATGGATAAGTTTGATAg < 2:78576/90‑1 (MQ=255)
tGCAGGCACCTGGGCAGCGTGGGACGCTGGAATTAAGCGGCTGCCCGATAGACGCGGAAGGGGTCTGCCCGATGGATAAGGTTGATAGCg > 1:702525/1‑90 (MQ=255)
tGCAGGCACCTGCGCAGCGTGTGACGCTGGAATTAAGCGGCTGCCCGATAGACGCTGAt > 1:669046/1‑59 (MQ=255)
tGCAGGCACCTGCGCAGCGTGTGACGCTGGAATTAAGCGGCTGCCCGATAGACGCTGAt < 2:669046/59‑1 (MQ=255)
gCAGGCACCTGCGCAGCGTGTGACGCTGGAATTAAGCGGCTGCCCGATAGACGCTGATGGTTTCTGCCCGATGGATAAGTTTGATAGCgt > 2:1392885/1‑90 (MQ=255)
gCAGGCACCTGCGCAGCGTGTGACGCTGGAATTAAGCGGCTGCCCGATAGACGCTGATGGTTTCTGCCCGATGGATAAGTTTGATAGCgt > 2:1446857/1‑90 (MQ=255)
gCAGGCACCTGCGCAGCGTGTGACGCTGGAATTAAGCGGCTGCCCGATAGACGCTGATGGTTTCTGCCCGATGGATAAGTTTGATAGCgt > 1:1542034/1‑90 (MQ=255)
cACCTGCGCAGCGTGTGACGCTGGAATTAAGCGGCTGCCCGATAGACGCTGATGGTTTCTGCCCGATGGATAAGTTTGATAGCGTGTtga > 1:910079/1‑90 (MQ=255)
gcgcAGCGTGTGACGCTGGAATTAAGCGGCTGCCCGATAGACGCTGATGGTTTCTGCCCGATGGATAAGTTTGATAGCGTGTtgaatgaa > 1:1576110/1‑90 (MQ=255)
cAGCGTGTGACGCTGGAATTAAGCGGCTGCCCGATAGACGCTGATGGTTTCTGCCCGATGGATAAGTTTGATAGCGTGTTGAATGAAGCg < 1:1416757/90‑1 (MQ=255)
cAGCGTGTGACGCTGGAATTAAGCGGCTGCCCGATAGACGCTGATGGTTTCTGCCCGATGGATAAGTTTGATAGCGTGTTGAATGAAGCg < 2:1572826/90‑1 (MQ=255)
gCGTGTGACGCTGGAATTAAGCGGCTGCCCGATAGACGCTGATGGTTTCTGCCCGATGGATAAGTTTGATAGCGTGTTGAATGAAGCGGt > 1:628336/1‑90 (MQ=255)
gCGTGTGACGCTGGAATTAAGCGGCTGCCCGATAGACGCTGATGGTTTCTGCCCGATGGATAAGTTTGATAGCGTGTTGAATGAAGCGGt < 1:1429012/90‑1 (MQ=255)
gtgtGACGCTGGAATTAAGCGGCTGCCCGATAGACGCTGATGGTTTCTGCCCGATGGATAAGTTTGATAGCGTGTTGAATGAAGCGGTGa > 2:847062/1‑90 (MQ=255)
tgACGCTGGAATTAAGCGGCTGCCCGATAGACGCTGATGGTTTCTGCCCGATGGATAAGTTTGATAGCGTGTTGAATGAAGCGGTGAAAt < 1:822579/90‑1 (MQ=255)
cTGGAATTAAGCGGCTGCCCGATAGACGCTGATGGTTTCTGCCCGATGGATAAGTTTGATAGCGTGTTGAATGAAGCGGTGAAATAACAg < 2:307817/90‑1 (MQ=255)
ggAATTAAGCGGCTGCCCGATAGACGCTGATGGTTTCTGCCCGATGGATAAGTTTGATAGCGTGTTGAATGAAGCGGTGAAATAACAGaa > 1:656725/1‑90 (MQ=255)
|
GAGTGCGGAACAGTTACGTAATGCCGATGCGTTAACCCTGCAGGCACCTGCGCAGCGTGTGACGCTGGAATTAAGCGGTTGCCCGATAGACGCTGATGGTTTCTGCCCGATGGATAAGTTTGATAGCGTGTTGAATGAAGCGGTGAAATAACAGAA > NZ_CP009273/1062132‑1062287
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
ATGTGTATCAGAGTGCGGAACAGTTACGTAATGCCGATGCGTTAACCCTGCAGGCACCTGCGCAGCGTGTGACGCTGGAATTAAGCGGTTGCCCGATAGACGCTGATGGTTTCTGCCCGATGGATAAGTTTGATAGCGTGTTGAATGAAGCGGTGAAATAACAGAAAAC > NZ_CP009273/1062122‑1062290
|
ATGTGTATCAGAGTGCGGAACAGTTACGTAATGCCGATGCGTTAACCCTGCAGGCACCTGCGCAGCGTGTGACGCTGGAATTAAGCGGCTGCCCGATAGA > SRR3722078.122078/1‑100 (MQ=60)
ATGTGTATCAGAGTGCGGAACAGTTACGTAATGCCGATGCGTTAACCCTGCAGGCACCTGCGCAGCGTGTGACGCTGGAATTAAGCGGCTGCCCGATAGA > SRR3722078.52030/1‑100 (MQ=60)
GTGTATCAGAGTGCGGAACAGTTACGTAATGCCGATGCGTTAACCCTGCAGGCACCTGCGCAGCGTGTGACGCTGGAATTAAGCGGCTGCCCGATAGACG > SRR3722078.350184/1‑100 (MQ=60)
GTGCGGAACAGTTACGTAATGCCGATGCGTTAACCCTGCAGGCACCTGCGCAGCGTGTGACGCTGGAATTAAGCGGCTGCCCGATAGACGCTGATGGTTT > SRR3722078.1352343/1‑100 (MQ=60)
GAACAGTTACGTAATGCCGATGCGTTAACCCTGCAGGCACCTGCGCAGCGTGTGACGCTGGAATTAAGCGGCTGCCCGATAGACGCTGATGGTTTCTGCC < SRR3722078.616085/100‑1 (MQ=60)
GAACAGTTACGTAATGCCGATGCGTTAACCCTGCAGGCACCTGCGCAGCGTGTGACGCTGGAATTAAGCGGCTGCCCGATAGACGCTGATGGTTTCTGCC > SRR3722078.758796/1‑100 (MQ=60)
ACGTAATGCCGATGCGTTAACCCTGCAGGCACCTGCGCAGCGTGTGACGCTGGAATTAAGCGGCTGCCCGATAGACGCTGATGGTTTCTGCCCGATGGAT > SRR3722078.8242/1‑100 (MQ=60)
ACGTAATGCCGATGCGTTAACCCTGCAGGCACCTGCGCAGCGTGTGACGCTGGAATTAAGCGGCTGCCCGATAGACGCTGATGGTTTCTGCCCGATGGAT > SRR3722078.761661/1‑100 (MQ=60)
ACGTAATGCCGATGCGTTAACCCTGCAGGCACCTGCCCAGCGTGTGACGCTGGAATTAAGCGGCTGCCCGATAGACGCTGATGGTTTCTGCCCGATGGAT > SRR3722078.765020/1‑100 (MQ=60)
ATGCGTTAACCCTGCAGGCACCTGCGCAGCGTGTGACGCTGGAATTAAGCGGCTGCCCGATAGACGCTGATGGTTTCTGCCCGATGGATAAGTTTGATAG < SRR3722078.1287204/100‑1 (MQ=60)
GCGTTAACCCTGCAGGCACCTGGGCAGCGTGGGACGCTGGAATTAAGCGGCTGCCCGATAGACGCGGAAGGGGTCTGCCCGATGGATAAGGTTGATAGCG > SRR3722078.710995/1‑100 (MQ=60)
GCGTTAACCCTGCAGGCACCTGCGCAGCGTGTGACGCTGGAATTAAGCGGCTGCCCGATAGACGCTGATGGTTTCTGCCCtgtctcttatacacatctga > SRR3722078.676693/1‑80 (MQ=60)
CGTTAACCCTGCAGGCACCTGCGCAGCGTGTGACGCTGGAATTAAGCGGCTGCCCGATAGACGCTGATGGTTTCTGCCCGATGGATAAGTTTGATAGCGT > SRR3722078.1567174/1‑100 (MQ=60)
ACCCTGCAGGCACCTGCGCAGCGTGTGACGCTGGAATTAAGCGGCTGCCCGATAGACGCTGATGGTTTCTGCCCGATGGATAAGTTTGATAGCGTGTTGA > SRR3722078.922360/1‑100 (MQ=60)
GCAGGCACCTGCGCAGCGTGTGACGCTGGAATTAAGCGGCTGCCCGATAGACGCTGATGGTTTCTGCCCGATGGATAAGTTTGATAGCGTGTTGAATGAA > SRR3722078.1601764/1‑100 (MQ=60)
CACCTGCGCAGCGTGTGACGCTGGAATTAAGCGGCTGCCCGATAGACGCTGATGGTTTCTGCCCGATGGATAAGTTTGATAGCGTGTTGAATGAAGCGGT > SRR3722078.635565/1‑100 (MQ=60)
CAGCGTGTGACGCTGGAATTAAGCGGCTGCCCGATAGACGCTGATGGTTTCTGCCCGATGGATAAGTTTGATAGCGTGTTGAATGAAGCGGTGAAATAAC < SRR3722078.1439769/100‑1 (MQ=60)
GCGTGTGACGCTGGAATTAAGCGGCTGCCCGATAGACGCTGATGGTTTCTGCCCGATGGATAAGTTTGATAGCGTGTTGAATGAAGCGGTGAAATAACAG < SRR3722078.1452247/100‑1 (MQ=60)
GTGTGACGCTGGAATTAAGCGGCTGCCCGATAGACGCTGATGGTTTCTGCCCGATGGATAAGTTTGATAGCGTGTTGAATGAAGCGGTGAAATAACAGAA > SRR3722078.664251/1‑100 (MQ=60)
TGACGCTGGAATTAAGCGGCTGCCCGATAGACGCTGATGGTTTCTGCCCGATGGATAAGTTTGATAGCGTGTTGAATGAAGCGGTGAAATAACAGAAAAC < SRR3722078.833470/100‑1 (MQ=60)
|
ATGTGTATCAGAGTGCGGAACAGTTACGTAATGCCGATGCGTTAACCCTGCAGGCACCTGCGCAGCGTGTGACGCTGGAATTAAGCGGTTGCCCGATAGACGCTGATGGTTTCTGCCCGATGGATAAGTTTGATAGCGTGTTGAATGAAGCGGTGAAATAACAGAAAAC > NZ_CP009273/1062122‑1062290
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
