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 |
|
A0 F0 I1 R1
|
146 |
27.9 |
2327082 |
89.7% |
2087392 |
107.8 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
AM260479 |
2,594,082 |
T→C |
Q124Q (CAA→CAG) |
cR ← |
Recombinational DNA repair protein (RecF pathway) |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260479 | 2,594,082 | 0 | T | C | 100.0%
| 77.6
/ NA
| 21 | Q124Q (CAA→CAG) | cR | Recombinational DNA repair protein (RecF pathway) |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (9/12); total (9/12) |
CGCAGCGCATCGCCCAGCTTGCGCGCGCCCTCGCGGTCGTGCTGCAGCAGGTGGTAGGCCATGCGCTGGGCGGACTTGGGCCCGACGCCGGGCAGCACCCGCAGCGCTTCGACCAGTGCTTGCAGCGAGGTCGGGGACGATGCCTTCACAGTGGCGTTCAGAACGCGCAGCTTGAAGCCCGGGGGCAGCGGCAGGCCCGAGGTCATCGAGCCCATCTTTTCCTGCGAGGTGGCTTCGGCCTTGCGC > AM260479/2593963‑2594208
|
cgcagcgcaTCGCCCAGCTTGCGCGCGCCCTCGCGGTCGTGCTGCAGCAGGTGGTAGGCCATGCGCTGGGCGGACTTGGGCCCGACGCCGGGCAGCACCCGCAGCGCTTCGACCAGTGCCTGCAGCGAGGTCgg < 2:742966/134‑1 (MQ=255)
cagcgcaTCGCCCAGCTTGCGCGCGCCCTCGCGGTCGTGCTGCAGCAGGTGGTAGGCCATGCGCTGGGCGGACTTGGGCCCGACGCCGGGCAGCACCCGCAGCGCTTCGACCAGTGCCTGCAGCGAGGTCgggg < 1:1099561/134‑1 (MQ=255)
aGCTTGCGCGCGCCCTCGCGGTCGTGCTGCAGCAGGTGGTAGGCCATGCGCTGGGCGGACTTGGGCCCGACGCCGGGCAGCACCCGCAGCGCTTCGACCAGTGCCTGCAGCGAGGTCGGGGACGATGCCTTcac < 2:613338/134‑1 (MQ=255)
gcgcCCTCGCGGTCGTGCTGCAGCAGGTGGTAGGCCATGCGCTGGGCGGACTTGGGCCCGACGCCGGGCAGCACCCGCAGCGCTTCGACCAGTGCCTGc < 2:109777/99‑1 (MQ=255)
gcgcCCTCGCGGTCGTGCTGCAGCAGGTGGTAGGCCATGCGCTGGGCGGACTTGGGCCCGACGCCGGGCAGCACCCGCAGCGCTTCGACCAGTGCCTGc > 1:109777/1‑99 (MQ=255)
gtggtAGGCCATGCGCTGGGCGGACTTGGGCCCGACGCCGGGCAGCACCCGCAGCGCTTCGACCAGTGCCTGc > 1:626779/1‑73 (MQ=255)
gtggtAGGCCATGCGCTGGGCGGACTTGGGCCCGACGCCGGGCAGCACCCGCAGCGCTTCGACCAGTGCCTGc < 2:626779/73‑1 (MQ=255)
ggCCATGCGCTGGGCGGACTTGGGCCCGACGCCGGGCAGCACCCGCAGCGCTTCGACCAGTGCCTGc < 1:645019/67‑1 (MQ=255)
ggCCATGCGCTGGGCGGACTTGGGCCCGACGCCGGGCAGCACCCGCAGCGCTTCGACCAGTGCCTGc > 2:645019/1‑67 (MQ=255)
tGCGCTGGGCGGACTTGGGCCCGACGCCGGGCAGCACCCGCAGCGCTTCGACCAGTGCCTGCAGCGAGGTCGGGGACGATGCCTTc > 1:805887/1‑86 (MQ=255)
tGCGCTGGGCGGACTTGGGCCCGACGCCGGGCAGCACCCGCAGCGCTTCGACCAGTGCCTGCAGCGAGGTCGGGGACGATGCCTTc < 2:805887/86‑1 (MQ=255)
cTGGGCGGACTTGGGCCCGACGCCGGGCAGCACCCGCAGCGCTTCGACCAGTGCCTGCAGCGAGGTCGGGGACGATGCCTTCACAGTGGCGTTCAGAACG‑GCAGc > 1:832810/1‑105 (MQ=255)
cTGGGCGGACTTGGGCCCGACGCCGGGCAGCACCCGCAGCGCTTCGACCAGTGCCTGCAGCGAGGTCGGGGACGATGCCTTCACAGTGGCGTTCAGAACG‑GCAGc < 2:832810/105‑1 (MQ=255)
gACTTGGGCCCGACGCCGGGCAGCACCCGCAGCGCTTCGACCAGTGCCTGCAGCGAGGTCGGGGACGATGCCTTcac < 1:912197/77‑1 (MQ=255)
gACTTGGGCCCGACGCCGGGCAGCACCCGCAGCGCTTCGACCAGTGCCTGCAGCGAGGTCGGGGACGATGCCTTcac > 2:912197/1‑77 (MQ=255)
gACTTGGGCCCGACGCCGGGCAGCACCCGCAGCGCTTCGACCAGTGCCTGCAGCGAGGTCGGGGACGATGCCTTCACAGTGGCGTTCAGAACG‑GCAGCTTGAAGCCCGGGGGCAGCGGCAGGCCCGAGGTCATc > 1:750678/1‑134 (MQ=255)
ccGGGCAGCACCCGCAGCGCTTCGACCAGTGCCTGCAGCGAGGTCGGGGACGATGCCTTCACAGTGGCGTTCAGAACG‑GCAGCTTGAAGCCCGGGGGCAGCGGCa < 2:593949/105‑1 (MQ=255)
ccGGGCAGCACCCGCAGCGCTTCGACCAGTGCCTGCAGCGAGGTCGGGGACGATGCCTTCACAGTGGCGTTCAGAACG‑GCAGCTTGAAGCCCGGGGGCAGCGGCa > 1:593949/1‑105 (MQ=255)
aCCAGTGCCTGCAGCGAGGTCGGGGACGATGCCTTCACAGTGGCGTTCAGAACG‑GCAGCTTGAAGCCCGGGGGCAGCGGCAGGCCCGAGGTCATCGAGCCCATCTTTTCCTGCGAGGTGGCTTCGGCCTTgcgc < 2:550271/134‑1 (MQ=255)
ccAGTGCCTGCAGCGAGGTCGGGGACGATGCCTTCACAGTGGCGTTCAGAACG‑GCAGc < 2:435005/58‑1 (MQ=38)
ccAGTGCCTGCAGCGAGGTCGGGGACGATGCCTTCACAGTGGCGTTCAGAACG‑GCAGc > 1:435005/1‑58 (MQ=38)
|
CGCAGCGCATCGCCCAGCTTGCGCGCGCCCTCGCGGTCGTGCTGCAGCAGGTGGTAGGCCATGCGCTGGGCGGACTTGGGCCCGACGCCGGGCAGCACCCGCAGCGCTTCGACCAGTGCTTGCAGCGAGGTCGGGGACGATGCCTTCACAGTGGCGTTCAGAACGCGCAGCTTGAAGCCCGGGGGCAGCGGCAGGCCCGAGGTCATCGAGCCCATCTTTTCCTGCGAGGTGGCTTCGGCCTTGCGC > AM260479/2593963‑2594208
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 36 ≤ 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
ATGGCGGATATGGTCCGCCGCGCCGCGCAGCGCATCGCCCAGCTTGCGCGCGCCCTCGCGGTCGTGCTGCAGCAGGTGGTAGGCCATGCGCTGGGCGGACTTGGGCCCGACGCCGGGCAGCACCCGCAGCGCTTCGACCAGTGCTTGCAGCGAGGTCGGGGACGATGCCTTCACAGTGGCGTTCAGAACGCGCAGCTTGAAGCCCGGGGGCAGCGGCAGGCCCGAGGTCATCGAGCCCATCTTTTCCTGCGAGGTGGCTTCGGCCTTGCGCACGGCGTCATTGAAGGCGGC > AM260479/2593938‑2594228
|
ATGGCGGATATGGTCCGCCGCGCCGCGCAGCGCATCGCCCAGCTTGCGCGCGCCCTCGCGGTCGTGCTGCAGCAGGTGGTAGGCCATGCGCTGGGCGGACTTGGGCCCGACGCCGGGCAGCACCCGCAGCGCTTCGACCAGTGCCTGCAG < GWNJ‑0478:712:GW2002102894th:2:1114:8402:10356/150‑1 (MQ=60)
ATGGCGGATATGGTCCGCCGCGCCGCGCAGCGCATCGCCCAGCTTGCGCGCGCCCTCGCGGTCGTGCTGCAGCAGGTGGTAGGCCATGCGCTGGGCGGACTTGGGCCCGACGCCGGGCAGCACCCGCAGCGCTTCGACCAGTGCCTGCAG < GWNJ‑0478:712:GW2002102894th:2:1212:18340:93531/150‑1 (MQ=60)
cggagatgtgtataagagacagGCGCAGCGCATCGCCCAGCTTGCGCGCGCCCTCGCGGTCGTGCTGCAGCAGGTGGTAGGCCATGCGCTGGGCGGACTTGGGCCCGACGCCGGGCAGCACCCGCAGCGCTTCGACCAGTGCCTGCAG < GWNJ‑0478:712:GW2002102894th:2:2212:20931:3350/126‑1 (MQ=60)
gcatacgagattagcgagtgtctcgtgggctcggagatgtgtataagagacaGCTGCAGCAGGTGGTAGGCCATGCGCTGGGCGGACTTGGGCCCGACGCCGGGCAGCACCCGCAGCGCTTCGACCAGTGCCTGCAGCGAGGTCGGGGAC < GWNJ‑0478:712:GW2002102894th:2:2105:18939:91496/98‑1 (MQ=60)
GCAGCGCATCGCCCAGCTTGCGCGCGCCCTCGCGGTCGTGCTGCAGCAGGTGGTAGGCCATGCGCTGGGCGGACTTGGGCCCGACGCCGGGCAGCACCCGCAGCGCTTCGACCAGTGCCTGCAGCGAGGTCGGGGACGATGCCTTCACAG < GWNJ‑0478:712:GW2002102894th:2:2213:1685:97735/150‑1 (MQ=60)
TCGCCCAGCTTGCGCGCGCCCTCGCGGTCGTGCTGCAGCAGGTGGTAGGCCATGCGCTGGGCGGACTTGGGCCCGACGCCGGGCAGCACCCGCAGCGCTTCGACCAGTGCCTGCAGCGAGGTCGGGGACctgtctcttatacacatctcc > GWNJ‑0478:712:GW2002102894th:2:1106:17038:68293/1‑129 (MQ=60)
tagcgagtgtctcgtgggctcggagatgtgtataagagacAGGCCATGCGCTGGGCGGACTTGGGCCCGACGCCGGGCAGCACCCGCAGCGCTTCGACCAGTGCCTGCAGCGAGGTCGGGGACGATGCCTTCACAGTGGCGTTCAGAAC < GWNJ‑0478:712:GW2002102894th:2:2202:6607:67406/109‑1 (MQ=60)
GTCGTGCTGCAGCAGGTGGTAGGCCATGCGCTGGGCGGACTTGGGCCCGACGCCGGGCAGCACCCGCAGCGCTTCGACCAGTGCCTGCAGCGAGGTCGGGGACctgtctcttatacacatctccgagcccacgagacactcgctaatctc > GWNJ‑0478:712:GW2002102894th:2:2102:15723:82146/1‑103 (MQ=60)
GCAGGTGGTAGGCCATGCGCTGGGCGGACTTGGGCCCGACGCCGGGCAGCACCCGCAGCGCTTCGACCAGTGCCTGCAGCGAGGTCGGGGACGATGCCTTCACAGTGGCGTTCAGActgtctcttatacacatctccgagcccacgagac > GWNJ‑0478:712:GW2002102894th:2:2112:19176:83261/1‑116 (MQ=60)
GTGGTAGGCCATGCGCTGGGCGGACTTGGGCCCGACGCCGGGCAGCACCCGCAGCGCTTCGACCAGTGCCTGCAGCGAGGTCGGGGACGATGCCTTCACAGTGGCGTTCAGAACG‑GCAGCTTGAAGCCCGGGGGCctgtctcttatacac > GWNJ‑0478:712:GW2002102894th:2:2114:9697:15952/1‑135 (MQ=60)
GCCATGCGCTGGGCGGACTTGGGCCCGACGCCGGGCAGCACCCGCAGCGCTTCGACCAGTGCCTGCAGCGAGGTCGGGGACGATGCCTTCACAGTGGCGTTCAGAACG‑GCAGCTTGAAGCCCGGGGGCAGCGGCAGGCCCGAGGTCATCG > GWNJ‑0478:712:GW2002102894th:2:2111:14572:95163/1‑150 (MQ=60)
GACTTGGGCCCGACGCCGGGCAGCACCCGCAGCGCTTCGACCAGTGCCTGCAGCGAGGTCGGGGACGATGCCTTCACAGTGGCGTTCAGAACG‑GCAGCTTGAAGCCCGGGGGCAGCGGCAGGCCCGAGGTCATCGctgtctcttatacac > GWNJ‑0478:712:GW2002102894th:2:2101:7138:71383/1‑135 (MQ=60)
CCCGCAGCGCTTCGACCAGTGCCTGCAGCGAGGTCGGGGACGATGCCTTCACAGTGGCGTTCAGAACG‑GCAGCTTGAAGCCCGGGGGCctgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgtcttctg > GWNJ‑0478:712:GW2002102894th:2:1209:16607:72325/1‑88 (MQ=60)
GACCAGTGCCTGCAGCGAGGTCGGGGACGATGCCTTCACAGTGGCGTTCAGAACG‑GCAGCTTGAAGCCCGGGGGCAGCGGCAGGCCCGAGGTCATCGAGCCCATCTTTTCCTGCGAGGTGGCTTCGGCCTTGCGCACGGCGTCATTGAAC > GWNJ‑0478:712:GW2002102894th:2:2102:4665:2809/1‑150 (MQ=60)
GTGCCTGCAGCGAGGTCGGGGACGATGCCTTCACAGTGGCGTTCAGAACG‑GCAGCTTGAAGCCCGGGGGCAGCGGCAGGCCCGAGGTCATCGAGCCCATCTTTTCCTGCGAGGTGGCTTCGGCCTTGCGCACGGCGTCATTGAAGGCGGC > GWNJ‑0478:712:GW2002102894th:2:2109:16727:93130/1‑150 (MQ=60)
|
ATGGCGGATATGGTCCGCCGCGCCGCGCAGCGCATCGCCCAGCTTGCGCGCGCCCTCGCGGTCGTGCTGCAGCAGGTGGTAGGCCATGCGCTGGGCGGACTTGGGCCCGACGCCGGGCAGCACCCGCAGCGCTTCGACCAGTGCTTGCAGCGAGGTCGGGGACGATGCCTTCACAGTGGCGTTCAGAACGCGCAGCTTGAAGCCCGGGGGCAGCGGCAGGCCCGAGGTCATCGAGCCCATCTTTTCCTGCGAGGTGGCTTCGGCCTTGCGCACGGCGTCATTGAAGGCGGC > AM260479/2593938‑2594228
|
| 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: ‑ |
