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 |
3,301,576 |
+G |
intergenic (+45/‑146) |
lspA → / → dfp |
lipoprotein signal peptidase II/phosphopantothenoylcysteine synthetase/decarboxylase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260479 | 3,301,574 | 1 | . | G | 100.0%
| 46.0
/ NA
| 13 | intergenic (+43/‑148) | lspA/dfp | lipoprotein signal peptidase II/phosphopantothenoylcysteine synthetase/decarboxylase |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base G (4/9); total (4/9) |
CCGGCCTTCAACGTGGCCGACTGCGCGATCACGGTCGGCGCGGTGCTGCTGATCGTGGACGAGCTGCGCAGGGTGCGGCGCCACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCA‑GGTGAGGGGCGGTTCAGCAAGGCACCACGCCACCAGAAC > AM260479/3301445‑3301613
|
ccggccTTCAACGTGGCCGACTGCGCGATCACGGTCGGCGCGGTGCTGCTGATCGTGGACGAGCTGCGCAGGGTGCGGCGCCACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCA‑gggt < 1:979381/134‑3 (MQ=255)
ggccTTCAACGTGGCCGACTGCGCGATCACGGTCGGCGCGGTGCTGCTGATCGTGGACGAGCTGCGCAGGGTGCGGCGCCACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCA‑gggtga < 1:826422/134‑5 (MQ=255)
cgcgATCACGGTCGGCGCGGTGCTGCTGATCGTGGACGAGCTGCGCAGGGTGCGGCGCCACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCAGGGTGAGGGGCGGTTCAGCAAGGca < 2:112311/132‑1 (MQ=255)
cgcgATCACGGTCGGCGCGGTGCTGCTGATCGTGGACGAGCTGCGCAGGGTGCGGCGCCACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCAGGGTGAGGGGCGGTTCAGCAAGGca < 2:493544/132‑1 (MQ=255)
gTCGGCGCGGTGCTGCTGATCGTGGACGAGCTGCGCAGGGTGCGGCGCCACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCAGGGTGAGGGGCGGTTCAGCAAGGCACCACGCCACCAg < 1:720292/134‑1 (MQ=255)
gTCGGCGCGGTGCTGCTGATCGTGGACGAGCTGCGCAGGGTGCGGCGCCACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCAGGGTGAGGGGCGGTTCAGCAAGGCACCACGCCACCAg < 2:125881/134‑1 (MQ=255)
ggCGCGGTGCTGCTGATCGTGGACGAGCTGCGCAGGGTGCGGCGCCACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCAGGGTGAGGGGCGGTTCAGCAAGGCACCACGCCACCAGAAc < 2:407234/134‑1 (MQ=255)
gcgcGGTGCTGCTGATCGTGGACGAGCTGCGCAGGGTGCGGCGCCACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCAGGGTGAGGGGc > 1:1067866/1‑104 (MQ=255)
gcgcGGTGCTGCTGATCGTGGACGAGCTGCGCAGGGTGCGGCGCCACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCAGGGTGAGGGGc < 2:1067866/104‑1 (MQ=255)
gTGCTGCTGATCGTGGACGAGCTGCGCAGGGTGCGGCGCCACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCAGGGTGAggg > 1:452767/1‑97 (MQ=255)
gTGCTGCTGATCGTGGACGAGCTGCGCAGGGTGCGGCGCCACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCAGGGTGAggg < 2:452767/97‑1 (MQ=255)
gTGCTGCTGATCGTGGACGAGCTGCACAGGGTGCGGCGCCACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCAGGGTGAggg > 1:125783/1‑97 (MQ=255)
gTGCTGCTGATCGTGGACGAGCTGCACAGGGTGCGGCGCCACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCAGGGTGAggg < 2:125783/97‑1 (MQ=255)
ccACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCAGGGTGAGGGGCGGTTCAGCAAGGca > 1:1118487/1‑75 (MQ=255)
ccACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCAGGGTGAGGGGCGGTTCAGCAAGGca < 2:1118487/75‑1 (MQ=255)
|
CCGGCCTTCAACGTGGCCGACTGCGCGATCACGGTCGGCGCGGTGCTGCTGATCGTGGACGAGCTGCGCAGGGTGCGGCGCCACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCA‑GGTGAGGGGCGGTTCAGCAAGGCACCACGCCACCAGAAC > AM260479/3301445‑3301613
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 38 ≤ 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
GCGCAACTACCACTGGCCGGCCTTCAACGTGGCCGACTGCGCGATCACGGTCGGCGCGGTGCTGCTGATCGTGGACGAGCTGCGCAGGGTGCGGCGCCACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCA‑GGTGAGGGGCGGTTCAGCAAGGCACCACGCCACCAGAACCGCCCGCCCTCACCCCCGGCCCCACTCCCGCCGTGCGGGAGTGGGGAGCCAACCCTCAGCCGGCTTCCCCGGTATCATTTCCCTTTCTCCCCAG > AM260479/3301429‑3301707
|
GCGCAACTACCACTGGCCGGCCTTCAACGTGGCCGACTGCGCGATCACGGTCGGCGCGGTGCTGCTGATCGTGGACGAGCTGCGCAGGGTGCGGCGCCACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCA‑GGG < GWNJ‑0478:712:GW2002102894th:2:1206:10708:25583/149‑1 (MQ=60)
gatgtgtataagagacaGGCCTTCAACGTGGCCGACTGCGCGATCACGGTCGGCGCGGTGCTGCTGATCGTGGACGAGCTGCGCAGGGTGCGGCGCCACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCA‑GGgtg < GWNJ‑0478:712:GW2002102894th:2:1104:9573:23425/133‑4 (MQ=60)
GCCGGCCTTCAACGTGGCCGACTGCGCGATCACGGTCGGCGCGGTGCTGCTGATCGTGGACGAGCTGCGCAGGGTGCGGCGCCACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCAGGGTGAGGGGCGGTTCAGC < GWNJ‑0478:712:GW2002102894th:2:2206:10329:59284/150‑1 (MQ=60)
aaatgattatcatattgttcttgttctagcatttttttttttttttcaagcagaagacggcatacgagattagcgagtgtctcgtgggctcggagatgtgtataagagacagCTCACGGGGAGAGGCCAGGGTGAGGGGCGGTTCAGCAA < GWNJ‑0478:712:GW2002102894th:2:2214:6346:83705/38‑1 (MQ=56)
CGGCCTTCAACGTGGCCGACTGCGCGATCACGGTCGGCGCGGTGCTGCTGATCGTGGACGAGCTGCGCAGGGTGCGGCGCCACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCAGGGTGAGGGGCGGTTCAGCAA < GWNJ‑0478:712:GW2002102894th:2:2115:11954:84034/150‑1 (MQ=60)
GCGCGATCACGGTCGGCGCGGTGCTGCTGATCGTGGACGAGCTGCGCAGGGTGCGGCGCCACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCAGGGTGAGGGGCGGTTCAGCAAGGCACCtgtctcttatacac > GWNJ‑0478:712:GW2002102894th:2:2212:15354:40657/1‑135 (MQ=60)
ATCACGGTCGGCGCGGTGCTGCTGATCGTGGACGAGCTGCGCAGGGTGCGGCGCCACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCAGGGTGAGGGGCGGTTCAGCAAGGCctgtctcttatacacatctccg > GWNJ‑0478:712:GW2002102894th:2:1211:2112:65411/1‑127 (MQ=60)
ATCACGGTCGGCGCGGTGCTGCTGATCGTGGACGAGCTGCACAGGGTGCGGCGCCACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCAGGGTGAGGGGCGGTTCAGCAAGGCctgtctcttatacacatctccg > GWNJ‑0478:712:GW2002102894th:2:1108:5117:59046/1‑127 (MQ=60)
GGTCGGCGCGGTGCTGCTGATCGTGGACGAGCTGCGCAGGGTGCGGCGCCACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCAGGGTGAGGGGCGGTTCAGCAAGGCACCACGCCACCAGAACCGC‑‑‑CCCTCACCC < GWNJ‑0478:712:GW2002102894th:2:2109:20269:32206/150‑1 (MQ=60)
GCGCAGGGTGCGGCGCCACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCAGGGTGAGGGGCctgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgtcttctgcttgaaaaaaa > GWNJ‑0478:712:GW2002102894th:2:2109:20193:94705/1‑76 (MQ=60)
GCGCAGGGTGCGGCGCCACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCAGGGTGAGGGGCGGTTCAGCAAGGCACCACGCCACCAGAACCtgtctcttatacacatctccgagcccacgagacactcgctaatc > GWNJ‑0478:712:GW2002102894th:2:2214:8260:89964/1‑106 (MQ=60)
CACGGGGAGAGGCCAGGGTGAGGGGCGGTTCAGCAAGGCACCACGCCtgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgtcttctgcttgaaaaaaaaaaaaacaaaataagacagatgcacaaaca > GWNJ‑0478:712:GW2002102894th:2:1215:17268:89391/1‑47 (MQ=60)
|
GCGCAACTACCACTGGCCGGCCTTCAACGTGGCCGACTGCGCGATCACGGTCGGCGCGGTGCTGCTGATCGTGGACGAGCTGCGCAGGGTGCGGCGCCACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCA‑GGTGAGGGGCGGTTCAGCAAGGCACCACGCCACCAGAACCGCCCGCCCTCACCCCCGGCCCCACTCCCGCCGTGCGGGAGTGGGGAGCCAACCCTCAGCCGGCTTCCCCGGTATCATTTCCCTTTCTCCCCAG > AM260479/3301429‑3301707
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
