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 I227 R1
|
223 |
21.3 |
1167702 |
97.0% |
1132670 |
86.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,283,874 |
Δ1 bp |
intergenic (‑350/‑105) |
BW25113_RS11435 ← / → narP |
IS5‑like element IS5 family transposase/nitrate/nitrite response regulator protein NarP |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,283,871 | 0 | T | . | 100.0%
| 49.6
/ NA
| 13 | intergenic (‑347/‑108) | BW25113_RS11435/narP | IS5‑like element IS5 family transposase/nitrate/nitrite response regulator protein NarP |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base . (2/11); total (2/11) |
TTTTAGTTGTTTTTCTTGATGAGAAGCTGATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAGTTTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTAGCGTTACCAACGCTACGC > NZ_CP009273/2283785‑2283939
|
ttttAGTTGTTTTTCTTGATGAGAAGCTGATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAGtttc < 2:358475/90‑2 (MQ=255)
gttgttTTTCTTGATGAGAAGCTGATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAG‑TTTCACTAc < 2:161772/90‑1 (MQ=255)
gttgttTTTCTTGATGAGAAGCTGATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAG‑TTTCACTAc < 2:247830/90‑1 (MQ=255)
ttgttTTTCTTGATGAGAAGCTGATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAG‑TTTCACTACa < 1:498651/90‑1 (MQ=255)
tCTTGATGAGAAGCTGATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAG‑TTTCACTACATGTCcat < 1:160429/90‑1 (MQ=255)
tCTTGATGAGAAGCTGATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAG‑TTTCACTACATGTCcat < 2:242056/90‑1 (MQ=255)
tCTTGATGAGAAGCTGATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAG‑TTTCACTACATGTCcat < 2:386323/90‑1 (MQ=255)
gatgaGAAGCTGATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAG‑TTTCACTACATGTCcatacat < 1:550565/90‑1 (MQ=255)
gATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAG‑TTTCACTACATGTCCATACATAAAATGGGGTa < 1:293503/90‑1 (MQ=255)
aaaTTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAG‑TTTCACTACATGTCCATACATAAAATGGGGTAACATTc > 1:110189/1‑90 (MQ=255)
cTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAG‑TTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTg < 1:51089/90‑1 (MQ=255)
aaaGCGAACGACAAGGTTGTAG‑TTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTAGCGTTACCAacgctacgc < 2:396234/90‑1 (MQ=255)
aCGACAAGGTTGTAG‑TTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTa < 1:486352/65‑1 (MQ=255)
aCGACAAGGTTGTAG‑TTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTa > 2:486352/1‑65 (MQ=255)
|
TTTTAGTTGTTTTTCTTGATGAGAAGCTGATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAGTTTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTAGCGTTACCAACGCTACGC > NZ_CP009273/2283785‑2283939
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
TTGTTTTTCTTGATGAGAAGCTGATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAGTTTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTAGCGTTACCAACGCTACGCTCAAACATAATGATTCTAATAAAACCTCAGGAGA > NZ_CP009273/2283791‑2283973
|
TTGTTTTTCTTGATGAGAAGCTGATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAG‑TTTCACTACATGTCCATACA < SRR3722111.506326/100‑1 (MQ=60)
TCTTGATGAGAAGCTGATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAG‑TTTCACTACATGTCCATACATAAAATG < SRR3722111.162452/100‑1 (MQ=60)
GATGAGAAGCTGATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAG‑TTTCACTACATGTCCATACATAAAATGGGGT < SRR3722111.559212/100‑1 (MQ=60)
AGCTGATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAG‑TTTCACTACATGTCCATACATAAAATGGGGTAACATTC > SRR3722111.111574/1‑100 (MQ=60)
GATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAG‑TTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGC < SRR3722111.297262/100‑1 (MQ=60)
CTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAG‑TTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTAGCGTTAC < SRR3722111.51707/100‑1 (MQ=60)
gtgtataagagacagcCCAAAGCGAACGACAAGGTTGTAG‑TTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTAGCGTTACCAA < SRR3722111.493823/84‑1 (MQ=60)
CGACAAGGTTGTAG‑TTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTAGCGTTACCAACGCTACGCTCAAACATAATGATTCTA > SRR3722111.141869/1‑100 (MQ=60)
CGACAAGGTTGTAG‑TTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTAGCGTTACCAACGCTACGCTCAAACATAATGATTCTA > SRR3722111.292474/1‑100 (MQ=60)
CGACAAGGTTGTAG‑TTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTAGCGTTACCAACGCTACGCTCAAACATAATGATTCTA > SRR3722111.306238/1‑100 (MQ=60)
AGGTTGTAG‑TTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTAGCGTTACCAACGCTACGCTCAAACATAATGATTCTAATAAA > SRR3722111.569878/1‑100 (MQ=60)
TTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTAGCGTTACCAACGCTACGCTCAAACATAATGATTCTAATAAAACCTCAGGAG < SRR3722111.407563/100‑1 (MQ=60)
TCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTAGCGTTACCAACGCTACGCTCAAACATAATGATTCTAATAAAACCTCAGGAGC < SRR3722111.211646/100‑1 (MQ=60)
|
TTGTTTTTCTTGATGAGAAGCTGATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAGTTTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTAGCGTTACCAACGCTACGCTCAAACATAATGATTCTAATAAAACCTCAGGAGA > NZ_CP009273/2283791‑2283973
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
