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 F1 I1 R1
|
26 |
102.0 |
3326124 |
78.0% |
2594376 |
98.8 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
CP002094 |
1,095,659 |
(A)7→6 |
intergenic (+76/‑149) |
LLNZ_05830 → / → LLNZ_05835 |
hypothetical protein/hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | CP002094 | 1,095,653 | 0 | A | . | 94.4%
| 71.8
/ ‑0.7
| 18 | intergenic (+70/‑155) | LLNZ_05830/LLNZ_05835 | hypothetical protein/hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base A (1/0); new base . (10/7); total (11/7) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.49e-01 |
AGACATTAACTTCTGGGGAAAGAAAATAATAAAATTAAAATAAAGTCATCATTTATGATGGCTTTTTCTGTTTAATAAAATAAAAATAAATAAATAATAAAAAAATGAAAAATAAATAATAATATATATTGACAAAAATAATTTGATTTAATATAATATGAGTATAAATGAGAAAAAAATAATAAAACAAAAA > CP002094/1095555‑1095747
|
aGACATTAACTTCTGGGGAAAGAAAATAATAAAATTAAAATAAAGTCATCATTTATGATGGCTTTTTCTGTTTAATAAAATAAAAATAAATAAataata < 1:13232/99‑1 (MQ=255)
aCATTAACTTCTGGGGAAAGAAAATAATAAAATTAAAATAAAGTCATCATTTATGATGGCTTTTTCTGTTTAATAAAATAAAAATAAATAAATAATaaa < 1:1114334/99‑1 (MQ=255)
aaaTAATAAAATTAAAATAAAGTCATCATTTATGATGGCTTTTTCTGTTTAATAAAATAAAAATAAATAAATAAT‑AAAAAATGAAAAATAaataataat < 1:56005/99‑1 (MQ=255)
aataatAAAATTAAAATAAAGTCATCATTTATGATGGCTTTTTCTGTTTAATAAAATAAAAATAAATAAATAAT‑AAAAAATGAAAAATAAataataata < 2:202296/99‑1 (MQ=255)
aataaAATTAAAATAAAGTCATCATTTATGATGGCTTTTTCTGTTTAATAAAATAAAAATAAATAAATAATAAAAAAATGAAAAATAAATAATAatata > 1:1190822/1‑99 (MQ=255)
ataaAATTAAAATAAAGTCATCATTTATGATGGCTTTTTCTGTTTAATAAAATAAAAATAAATAAATAAT‑AAAAAATGAAAAATAAATAATAatatata > 1:227082/1‑99 (MQ=255)
taaaattaaaatAAAGTCATCATTTATGATGGCTTTTTCTGTTTAATAAAATAAAAATAAATAAATAAT‑AAAAAATGAAAAATAAATAATAatatatat < 2:901235/99‑1 (MQ=255)
aaattaaaatAAAGTCATCATTTATGATGGCTTTTTCTGTTTAATAAAATAAAAATAAATAAATAAT‑AAAAAATGAAAAATAAATAATAATATATATTg > 2:626110/1‑99 (MQ=255)
gTCATCATTTATGATTGCTTTTTCTGTTTAATAAAATAAAAATAAATAAATAAT‑AAAAAATGAAAAATAAAGAATAATATATAGTGACAAAAATAAttt < 2:48814/99‑1 (MQ=255)
tcatTTATGATGGCTTTTTCTGTTTAATAAAATAAAAATAAATAAATAAT‑AAAAAATGAAAAATAAATAATAATATATATTGACAAAAATAATTTGAtt > 1:1291524/1‑99 (MQ=255)
tcatTTATGATGGCTTTTTCTGTTTAATAAAATAAAAATAAATAAATAAT‑AAAAAATGAAAAATAAATAATAATATATATTGACAAAAATAATTTGAtt < 2:1218195/99‑1 (MQ=255)
gCTTTTTCTGTTTAATAAAATAAAAATAAATAAATAAT‑AAAAAATGAAAAATAAATAATAATATATATTGACAAAAATAATTTGATTTAATATAATATg > 1:1292323/1‑99 (MQ=255)
tttCTGTTTAATAAAATAAAAATAAATAAATAAT‑AAAAAATGAAAAATAAATAATAATATATATTGACAAAAATAATTTGATTTAATATAATATGAGta < 1:1125963/99‑1 (MQ=255)
ataaaataaaAATAAATAAATAAT‑AAAAAATGAAAAATAAATAATAATATATATTGACAAAAATAATTTGATTTAATATAATATGAGTATAAATGAGaa > 1:832588/1‑99 (MQ=255)
aaataaaaataaATAAATAAT‑AAAAAATGAAAAATAAATAATAATATATATTGACAAAAATAATTTGATTTAATATAATATGAGTATAAATGAGaaaaa > 1:513678/1‑99 (MQ=255)
ataaaaataaaTAAATAAT‑AAAAAATGAAAAATAAATAATAATATATATTGACAAAAATAATTTGATTTAATATAATATGAGTATAAATGAGaaaaaaa > 2:1205132/1‑99 (MQ=255)
taaaaataaaTAAATAAT‑AAAAAATGAAAAATAAATAATAATATATATTGACAAAAATAATTTGATTTAATATAATATGAGTATAAATGAGAAAAAaat < 2:832588/99‑1 (MQ=255)
aaaataaaTAAATAAT‑AAAAAATGAAAAATAAATAATAATATATATTGACAAAAATAATTTGATTTAATATAATATGAGTATAAATGAGAAAAAaataa > 1:1108001/1‑99 (MQ=255)
aaataaataaT‑AAAAAATGAAAAATAAATAATAATATATATTGACAAAAATAATTTGATTTAATATAATATGAGTATAAATGAGAAAAAAATAATaaaa > 2:363388/1‑99 (MQ=255)
ataaataaT‑AAAAAATGAAAAATAAATAATAATATATATTGACAAAAATAATTTGATTTAATATAATATGAGTATAAATGAGAAAAAAATAATAAAACa > 1:721777/1‑99 (MQ=255)
taataaAAAAATGAAAAATAAATAATAATATATATTGACAAAAATAATTTGATTTAATATAATATGAGTATAAATGAGAAAAAAATAATAAAACaaaaa < 2:1190822/99‑1 (MQ=255)
|
AGACATTAACTTCTGGGGAAAGAAAATAATAAAATTAAAATAAAGTCATCATTTATGATGGCTTTTTCTGTTTAATAAAATAAAAATAAATAAATAATAAAAAAATGAAAAATAAATAATAATATATATTGACAAAAATAATTTGATTTAATATAATATGAGTATAAATGAGAAAAAAATAATAAAACAAAAA > CP002094/1095555‑1095747
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
AAATAATAAAATTAAAATAAAGTCATCATTTATGATGGCTTTTTCTGTTTAATAAAATAAAAATAAATAAATAATAAAAAAATGAAAAATAAATAATAATATATATTGACAAAAATAATTTGATTTAATATAATATGAGTATAAATGAGAAAAAAATAATAAAACA > CP002094/1095578‑1095743
|
AAATAATAAAATTAAAATAAAGTCATCATTTATGATGGCTTTTTCTGTTTAATAAAATAAAAATAAATAAATAAT‑AAAAAATGAAAAATAAATAATAATA < SRR7892090.56520/100‑1 (MQ=60)
TAATAAAATTAAAATAAAGTCATCATTTATGATGGCTTTTTCTGTTTAATAAAATAAAAATAAATAAATAATAAAAAAATGAAAAATAAATAATAATATA > SRR7892090.1198501/1‑100 (MQ=60)
AATAAAATTAAAATAAAGTCATCATTTATGATGGCTTTTTCTGTTTAATAAAATAAAAATAAATAAATAAT‑AAAAAATGAAAAATAAATAATAATATATA > SRR7892090.229227/1‑100 (MQ=60)
ATCATTTATGATGGCTTTTTCTGTTTAATAAAATAAAAATAAATAAATAAT‑AAAAAATGAAAAATAAATAATAATATATATTGACAAAAATAATTTGATT > SRR7892090.1299409/1‑100 (MQ=60)
GGCTTTTTCTGTTTAATAAAATAAAAATAAATAAATAAT‑AAAAAATGAAAAATAAATAATAATATATATTGACAAAAATAATTTGATTTAATATAATATG > SRR7892090.1300208/1‑100 (MQ=60)
TTTCTGTTTAATAAAATAAAAATAAATAAATAAT‑AAAAAATGAAAAATAAATAATAATATATATTGACAAAAATAATTTGATTTAATATAATATGAGTAT < SRR7892090.1133465/100‑1 (MQ=60)
AATAAAATAAAAATAAATAAATAAT‑AAAAAATGAAAAATAAATAATAATATATATTGACAAAAATAATTTGATTTAATATAATATGAGTATAAATGAGAA > SRR7892090.839124/1‑100 (MQ=60)
AAAATAAAAATAAATAAATAAT‑AAAAAATGAAAAATAAATAATAATATATATTGACAAAAATAATTTGATTTAATATAATATGAGTATAAATGAGAAAAA > SRR7892090.518333/1‑100 (MQ=60)
AAAAATAAATAAATAAT‑AAAAAATGAAAAATAAATAATAATATATATTGACAAAAATAATTTGATTTAATATAATATGAGTATAAATGAGAAAAAAATAA > SRR7892090.1115477/1‑100 (MQ=60)
AATAAATAAT‑AAAAAATGAAAAATAAATAATAATATATATTGACAAAAATAATTTGATTTAATATAATATGAGTATAAATGAGAAAAAAATAATAAAACA > SRR7892090.727797/1‑100 (MQ=60)
|
AAATAATAAAATTAAAATAAAGTCATCATTTATGATGGCTTTTTCTGTTTAATAAAATAAAAATAAATAAATAATAAAAAAATGAAAAATAAATAATAATATATATTGACAAAAATAATTTGATTTAATATAATATGAGTATAAATGAGAAAAAAATAATAAAACA > CP002094/1095578‑1095743
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
