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 I211 R1
|
223 |
18.0 |
1007644 |
96.3% |
970361 |
85.7 |
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%
| 46.3
/ 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 . (0/12); total (0/12) |
ATTTTTTAGTTGTTTTTCTTGATGAGAAGCTGATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAGTTTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTAGCGTTACCAACGCTACGCTCAAACATAATGATTCT > NZ_CP009273/2283782‑2283956
|
attTTTTAGTTGTTTTTCTTGATGAGAAGCTGATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAGt < 1:76727/90‑1 (MQ=255)
ttttttAGTTGTTTTTCTTGATGAGAAGCTGATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAGtt < 2:273567/90‑1 (MQ=255)
gttgttTTTCTTGATGAGAAGCTGATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAG‑TTTCACTAc < 1:41585/90‑1 (MQ=255)
gttgttTTTCTTGATGAGAAGCTGATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAG‑TTTCACTAc < 2:280724/90‑1 (MQ=255)
ttgcTTGATGAGAAGCTGATGCAAAATTCCGTCTTTATAATG‑AAATGATGCCAAAGCGAACGACAAGGTTGTAG‑TTTCACTACATGTCca < 1:96650/87‑1 (MQ=255)
ttCTTGATGAGAAGCTGATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAG‑TTTCACTACATGTCca < 2:231300/90‑1 (MQ=255)
tCTTGATGAGAAGCTGATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAG‑TTTCACTACATGTCcat < 2:39736/90‑1 (MQ=255)
tgCCAAAGCGAACGACAAGGTTGTAG‑TTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTAGCGTTACCAacgct < 1:203148/90‑1 (MQ=255)
ccAAAGCGAACGACAAGGTTGTAG‑TTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTAGCGTTACCAacgctac < 1:40899/90‑1 (MQ=255)
ccAAAGCGAACGACAAGGTTGTAG‑TTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTAGCGTTACCAacgctac < 2:486611/90‑1 (MQ=255)
aaaGCGAACGACAAGGTTGTAG‑TTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTAGCGTTACCAacgctacgc < 2:203005/90‑1 (MQ=255)
aGCGAACGACAAGGTTGTAG‑TTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTAGCGTTACCAACGCTACGCTc < 2:51265/90‑1 (MQ=255)
aaCGACAAGGTTGTAG‑TTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTAGCGTTACCAACGCTACGCTCAAAc < 2:252589/90‑1 (MQ=255)
tGTAG‑TTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCAGGTAGCGTTACCAACGCTACGCTCAAACATAATGATTCt < 2:460197/90‑1 (MQ=255)
|
ATTTTTTAGTTGTTTTTCTTGATGAGAAGCTGATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAGTTTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTAGCGTTACCAACGCTACGCTCAAACATAATGATTCT > NZ_CP009273/2283782‑2283956
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
ATTTTTTAGTTGTTTTTCTTGATGAGAAGCTGATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAGTTTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTAGCGTTACCAACGCTACGCTCAAACATAATGATTCTAATAAAACCTCAGGA > NZ_CP009273/2283782‑2283971
|
ATTTTTTAGTTGTTTTTCTTGATGAGAAGCTGATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAG‑TTTCACTACAT < SRR3722094.77827/100‑1 (MQ=60)
GTTGTTTTTCTTGATGAGAAGCTGATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAG‑TTTCACTACATGTCCATAC < SRR3722094.42171/100‑1 (MQ=60)
TTGCTTGATGAGAAGCTGATGCAAAATTCCGTCTTTATAATG‑AAATGATGCCAAAGCGAACGACAAGGTTGTAG‑TTTCACTACATGTCCATACATAAAAT < SRR3722094.98050/100‑1 (MQ=60)
nnnnnnnnnnnnnnnnantnATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAG‑TTTCACTACATGTCCATACATAAAATGGGGTAACATTCACG < SRR3722094.466612/80‑1 (MQ=60)
TGCCAAAGCGAACGACAAGGTTGTAG‑TTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTAGCGTTACCAACGCTACGCTCAAAC < SRR3722094.205908/100‑1 (MQ=60)
CCAAAGCGAACGACAAGGTTGTAG‑TTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTAGCGTTACCAACGCTACGCTCAAACAT < SRR3722094.41476/100‑1 (MQ=60)
GTTGTAG‑TTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTAGCGTTACCAACGCTACGCTCAAACATAATGATTCTAATAAAAC > SRR3722094.303078/1‑100 (MQ=60)
GTTGTAG‑TTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTAGCGTTACCAACGCTACGCTCAAACATAATGATTCTAATAAAAC > SRR3722094.318038/1‑100 (MQ=60)
TTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTAGCGTTACCAACGCTACGCTCAAACATAATGATTCTAATAAAACCTCAGGA > SRR3722094.461863/1‑100 (MQ=60)
|
ATTTTTTAGTTGTTTTTCTTGATGAGAAGCTGATGCAAAATTCCGTCTTTATAATGAAAATGATGCCAAAGCGAACGACAAGGTTGTAGTTTTCACTACATGTCCATACATAAAATGGGGTAACATTCACGCGCCTGGTAGCGTTACCAACGCTACGCTCAAACATAATGATTCTAATAAAACCTCAGGA > NZ_CP009273/2283782‑2283971
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
