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 I206 R1
|
206 |
23.7 |
1314362 |
96.8% |
1272302 |
86.2 |
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%
| 45.9
/ NA
| 12 | 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 . (2/10); total (2/10) |
TTTTTTAGTTGTTTTTCTTGATGAGAAGCTGATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAGTTTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTAGCGTTACCAACGCTACGCTCAAAC > NZ_CP009273/2283783‑2283945
|
ttttttAGTTGTTTTTCTTGATGAGAAGCTGATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAGtt < 1:70272/90‑1 (MQ=255)
ttttttAGTTGTTTTTCTTGATGAGAAGCTGATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAGtt < 2:96508/90‑1 (MQ=255)
ttttAGTTGTTTTTCTTGATGAGAAGCTGATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAGtttc < 2:41789/90‑2 (MQ=255)
ttCTTGATGAGAAGCTGATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAG‑TTTCACTACATGTCca < 1:397753/90‑1 (MQ=255)
ttCTTGATGAGAAGCTGATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAG‑TTTCACTACATGTCca < 1:588411/90‑1 (MQ=255)
cTTGATGAGAAGCTGATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAG‑TTTCACTACATGTCcata < 1:472398/90‑1 (MQ=255)
atgaGAAGCTGATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAG‑TTTCACTACATGTCcatacata > 2:184587/1‑90 (MQ=255)
tGATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAG‑TTTCACTACATGTCCATACATAAAATGTGGt < 1:577790/90‑1 (MQ=255)
gATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAG‑TTTCACTACATGTCCATACATAAAATGGGGTa < 2:149809/90‑1 (MQ=255)
ccGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAG‑TTTCACTACATGTCCATACATAAAATGGGGTAACATTCAcgcg < 2:61059/90‑1 (MQ=255)
tataATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAG‑TTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTa > 2:644455/1‑90 (MQ=255)
gCCAAAGCGAACGACAAGGTTGTAG‑TTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTAGCGTTACCAacgcta < 1:242734/90‑1 (MQ=255)
aGCGAACGACAAGGTTGTAG‑TTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTAGCGTTACCAACGCTACGCTc < 1:381322/90‑1 (MQ=255)
cGAACGACAAGGTTGTAG‑TTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTAGCGTTACCAACGCTACGCTCaa < 2:257129/90‑1 (MQ=255)
aaCGACAAGGTTGTAG‑TTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTAGCGTTACCAACGCTACGCTCAAAc < 1:276524/90‑1 (MQ=255)
|
TTTTTTAGTTGTTTTTCTTGATGAGAAGCTGATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAGTTTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTAGCGTTACCAACGCTACGCTCAAAC > NZ_CP009273/2283783‑2283945
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ 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
TGATTTTTTAGTTGTTTTTCTTGATGAGAAGCTGATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAGTTTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTAGCGTTACCAACGCTACGCTCAAACATAATGATTCTAATAAAAC > NZ_CP009273/2283780‑2283964
|
TGATTTTTTAGTTGTTTTTCTTGATGAGAAGCTGATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAG‑TTTCACTAC < SRR3722088.405613/100‑1 (MQ=60)
TTTTTTAGTTGTTTTTCTTGATGAGAAGCTGATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAG‑TTTCACTACATG < SRR3722088.71002/100‑1 (MQ=60)
TTCTTGATGAGAAGCTGATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAG‑TTTCACTACATGTCCATACATAAAAT < SRR3722088.402056/100‑1 (MQ=60)
TTCTTGATGAGAAGCTGATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAG‑TTTCACTACATGTCCATACATAAAAT < SRR3722088.595632/100‑1 (MQ=60)
CTTGATGAGAAGCTGATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAG‑TTTCACTACATGTCCATACATAAAATGG < SRR3722088.477984/100‑1 (MQ=60)
TGATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAG‑TTTCACTACATGTCCATACATAAAATGTGGTAACATTCACG < SRR3722088.584874/100‑1 (MQ=60)
GCCAAAGCGAACGACAAGGTTGTAG‑TTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTAGCGTTACCAACGCTACGCTCAAACA < SRR3722088.245120/100‑1 (MQ=60)
AGCGAACGACAAGGTTGTAG‑TTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTAGCGTTACCAACGCTACGCTCAAACATAATG < SRR3722088.385366/100‑1 (MQ=60)
AACGACAAGGTTGTAG‑TTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTAGCGTTACCAACGCTACGCTCAAACATAATGATTC < SRR3722088.279192/100‑1 (MQ=60)
GTTGTAG‑TTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTAGCGTTACCAACGCTACGCTCAAACATAATGATTCTAATAAAAC > SRR3722088.398855/1‑100 (MQ=60)
|
TGATTTTTTAGTTGTTTTTCTTGATGAGAAGCTGATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAGTTTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTAGCGTTACCAACGCTACGCTCAAACATAATGATTCTAATAAAAC > NZ_CP009273/2283780‑2283964
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
