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 I228 R1
|
214 |
26.5 |
1448192 |
97.1% |
1406194 |
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%
| 55.0
/ NA
| 14 | 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 . (2/12); total (2/12) |
TTTTAGTTGTTTTTCTTGATGAGAAGCTGATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAGTTTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTAGCGTTACCAACGCTACGCTCAAACATAATGATTC > NZ_CP009273/2283785‑2283955
|
ttttAGTTGTTTTTCTTGATGAGAAGCTGATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAGtttc < 2:76569/90‑2 (MQ=255)
ttttCTTGATGAGAAGCTGATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAG‑TTTCACTACATGTc > 1:190132/1‑90 (MQ=255)
ttCTTGATGAGAAGCTGATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAG‑TTTCACTACATGTCca < 2:178595/90‑1 (MQ=255)
tgaGAAGCTGATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAG‑TTTCACTACATGTCCATACATaa < 1:168625/90‑1 (MQ=255)
gATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAG‑TTTCACTACATGTCCATACATAAAATGGGGTa < 1:689724/90‑1 (MQ=255)
aaTTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAG‑TTTCACTACATGTCCATACATAAAATGGGGTAACATTCa < 2:684263/90‑1 (MQ=255)
ttCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAG‑TTTCACTACATGTCCATACATAAAATGGGGTAACATTCAcg < 2:290814/90‑1 (MQ=255)
ttATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAG‑TTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGt < 1:494207/90‑1 (MQ=255)
tataATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAG‑TTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTa < 1:585915/90‑1 (MQ=255)
aaaTGATGCCAAAGCGAACGACAAGGTTGTAG‑TTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTAGCGTTAcc < 1:614783/90‑1 (MQ=255)
aaTGATGCCAAAGCGAACGACAAGGTTGTAG‑TTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTAGCGTTACCa < 2:90863/90‑1 (MQ=255)
aGCGAACGACAAGGTTGTAG‑TTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTAGCGTTACCAACGCTACGCTc < 1:118511/90‑1 (MQ=255)
aaGGTTGTAG‑TTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTAGCGTTACCAACGCTACGCTCAAACATAATg < 1:84067/90‑1 (MQ=255)
aGGTTGTAG‑TTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTAGCGTTACCAACGCTACGCTCAAACATAATGa > 2:74940/1‑90 (MQ=255)
ttGTAG‑TTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTAGCGTTACCAACGCTACGCTCAAACATAATGATTc < 1:376438/90‑1 (MQ=255)
|
TTTTAGTTGTTTTTCTTGATGAGAAGCTGATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAGTTTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTAGCGTTACCAACGCTACGCTCAAACATAATGATTC > NZ_CP009273/2283785‑2283955
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ 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
TTGATTTTTTAGTTGTTTTTCTTGATGAGAAGCTGATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAGTTTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTAGCGTTACCAACGCTACGCTCAAACATAATGATTCTAATAAAACC > NZ_CP009273/2283779‑2283965
|
TTGATTTTTTAGTTGTTTTTCTTGATGAGAAGCTGATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAG‑TTTCACTA < SRR3722112.22309/100‑1 (MQ=60)
TTTTAGTTGTTTTTCTTGATGAGAAGCTGATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAG‑TTTCACTACATGTC > SRR3722112.192463/1‑100 (MQ=60)
TGAGAAGCTGATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAG‑TTTCACTACATGTCCATACATAAAATGGGGTAA < SRR3722112.170690/100‑1 (MQ=60)
GATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAG‑TTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGC < SRR3722112.700502/100‑1 (MQ=60)
TTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAG‑TTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTAGCGTTACCA < SRR3722112.501356/100‑1 (MQ=60)
TATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAG‑TTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTAGCGTTACCAA < SRR3722112.594866/100‑1 (MQ=60)
AAATGATGCCAAAGCGAACGACAAGGTTGTAG‑TTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTAGCGTTACCAACGCTACGC < SRR3722112.624237/100‑1 (MQ=60)
AGCGAACGACAAGGTTGTAG‑TTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTAGCGTTACCAACGCTACGCTCAAACATAATG < SRR3722112.119984/100‑1 (MQ=60)
CGACAAGGTTGTAG‑TTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTAGCGTTACCctgtctcttatacacatctgacgctgcc > SRR3722112.354249/1‑72 (MQ=60)
AAGGTTGTAG‑TTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTAGCGTTACCAACGCTACGCTCAAACATAATGATTCTAATAA < SRR3722112.85107/100‑1 (MQ=60)
GGTTGTAG‑TTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTAGCGTTACCAACGCTACGCTCAAACATAATGATTCTAATAAAA > SRR3722112.596170/1‑100 (MQ=60)
GTTGTAG‑TTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTAGCGTTACCAACGCTACGCTCAAACATAATGATTCTAATAAAAC > SRR3722112.715986/1‑100 (MQ=60)
TTGTAG‑TTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTAGCGTTACCAACGCTACGCTCAAACATAATGATTCTAATAAAACC < SRR3722112.381320/100‑1 (MQ=60)
|
TTGATTTTTTAGTTGTTTTTCTTGATGAGAAGCTGATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAGTTTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTAGCGTTACCAACGCTACGCTCAAACATAATGATTCTAATAAAACC > NZ_CP009273/2283779‑2283965
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
