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 I230 R1
|
226 |
18.8 |
1048726 |
96.7% |
1014118 |
86.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
3,273,721 |
A→G |
E49G (GAA→GGA) |
agaV → |
PTS N‑acetylgalactosamine transporter subunit IIB |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,273,721 | 0 | A | G | 100.0%
| 34.7
/ NA
| 12 | E49G (GAA→GGA) | agaV | PTS N‑acetylgalactosamine transporter subunit IIB |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (3/9); total (3/9) |
TTCAATGGGTCGGATTTGCGGGGGCAAATCTGGTGCTGGTAGCCAACGATGAGGTTGCCGAAGATCCGGTACAACAAAACCTGATGGAAATGGTACTGGCAGAAGGGATCGCCGTACGTTTCTGGACGCTGCAAAAAGTTATCGACAACATTCATCGCGCC > NZ_CP009273/3273634‑3273794
|
ttCAATGGGTCGGATTTGCGGGGGCAAATCTGGTGCTGGTAGCCAACGATGAGGTTGCCGAAGATCCGGTACAACAAAACCTGATGGgaa < 1:430061/90‑1 (MQ=255)
cAATGGGTCGGATTTGCGGGGGCAAATCTGGTGCTGGTAGCCAACGATGAGGTTGCCGAAGATCCGGTACAACAAAACCTGATGGGAATg < 2:239122/90‑1 (MQ=255)
ggTCGGATTTGCGGGGGCAAATCTGGTGCTGGTAGCCAACGATGAGGTTGCCGAAGATCCGGTACAACAAAACCTGATGGGAATGGTACt < 2:245593/90‑1 (MQ=255)
ggTCGGATTTGCGGGGGCAAATCTGGTGCTGGTAGCCAACGATGAGGTTGCCGAAGATCCGGTACAACAAAACCTGATGGGAATGGTACt < 2:35826/90‑1 (MQ=255)
tCGGATTTGCGGGGGCAAATCTAGTGCTGGTAGCCAACGATGAGGTTGCCGAAGATCCGGTACAACAAAACCTGATGGGAATGGTACTgg > 2:282896/1‑90 (MQ=255)
gaaTTGGCGGGGGCAAATCTGGTGTGGGTGGCC‑ACGATGAGGTTGCCGAAGATCCGGTACAACAAAACCTGATGGGAATGGTACTGGCAg < 2:340189/88‑1 (MQ=255)
ggggCAAAGCTGGTGCTGGTAGCCAACGATGAGGTTGCCGAAGATCCGGTACAACAAAACCTGATGGGAATGGTACTGGCAGAAGGGATc < 2:222865/90‑1 (MQ=255)
aTCTGGTGCTGGTAGCCAACGATGAGGTTGCCGAAGATCCGGTACAACAAAACCTGATGGGAATGGTACTGGCAGAAGGGATCGCCGTAc < 1:142768/90‑1 (MQ=255)
aTCTGGTGCTGGTAGCCAACGATGAGGTTGCCGAAGATCCGGTACAACAAAACCTGATGGGAATGGTACTGGCAGAAGGGATCGCCGTAc < 1:390908/90‑1 (MQ=255)
gCTGGTAGCCAACGATGAGGTTGCCGAAGATCCGGTACAACAAAACCTGATGGGAATGGTACTGGCAGAAGGGATCGCCGTACGTTTCTg < 1:84090/90‑1 (MQ=255)
aaCGATGAGGTTGCCGAAGATCCGGTACAACAAAACCTGATGGgaa < 1:448368/46‑1 (MQ=255)
ggTTGCCGAAGATCCGGTACAACAAAACCTGATGGGAATGGTACTGGCAGAAGGGATCGCCGTACGTTTCTGGACGCTGCAAAAAGTTAt > 1:125888/1‑90 (MQ=255)
gCCGAAGATCCGGTACAACAAAACCTGATGGGAATGGTACTGGCAGAAGGGATCGCCGTACGTTTCTGGACGCTGCAAAAAGTTATCGac > 1:251836/1‑90 (MQ=255)
caacaaAACCTGATGGGAATGGTACTGGCAGAAGGGATCGCCGTACGTTTCTGGACGCTGCAAAAAGTTATCGACAACATTCATCGcgcc < 1:265086/90‑1 (MQ=255)
|
TTCAATGGGTCGGATTTGCGGGGGCAAATCTGGTGCTGGTAGCCAACGATGAGGTTGCCGAAGATCCGGTACAACAAAACCTGATGGAAATGGTACTGGCAGAAGGGATCGCCGTACGTTTCTGGACGCTGCAAAAAGTTATCGACAACATTCATCGCGCC > NZ_CP009273/3273634‑3273794
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 29 ≤ 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
TTCAATGGGTCGGATTTGCGGGGGCAAATCTGGTGCTGGTAGCCAACGATGAGGTTGCCGAAGATCCGGTACAACAAAACCTGATGGAAATGGTACTGGCAGAAGGGATCGCCGTACGTTTCTGGACGCTGCAAAAAGTTATCGACAACATTCATCGCGCCGCCGATCGAC > NZ_CP009273/3273634‑3273804
|
gtctcgtgggctcggagatgtgtataagagacagGCTGGTAGCCAACGATGAGGTTGCCGAAGATCCGGTACAACAAAACCTGATGGGAATGGTACTGGC < SRR3722114.453936/66‑1 (MQ=60)
TTCAATGGGTCGGATTTGCGGGGGCAAATCTGGTGCTGGTAGCCAACGATGAGGTTGCCGAAGATCCGGTACAACAAAACCTGATGGGAATGGTACTGGC < SRR3722114.435356/100‑1 (MQ=60)
agatctagtacggtctcgtgggctcggagatgtgtataagagacagACAAAACCTGATGGGAATGGTACTGGCAGAAGGGATCGCCGTACGTTTCTGGAC < SRR3722114.400217/54‑1 (MQ=60)
ATCTGGTGCTGGTAGCCAACGATGAGGTTGCCGAAGATCCGGTACAACAAAACCTGATGGGAATGGTACTGGCAGAAGGGATCGCCGTACGTTTCTGGAC < SRR3722114.144236/100‑1 (MQ=60)
ATCTGGTGCTGGTAGCCAACGATGAGGTTGCCGAAGATCCGGTACAACAAAACCTGATGGGAATGGTACTGGCAGAAGGGATCGCCGTACGTTTCTGGAC < SRR3722114.395648/100‑1 (MQ=60)
GCTGGTAGCCAACGATGAGGTTGCCGAAGATCCGGTACAACAAAACCTGATGGGAATGGTACTGGCAGAAGGGATCGCCGTACGTTTCTGGACGCTGCAA < SRR3722114.84984/100‑1 (MQ=60)
CCAACGATGAGGTTGCCGAAGATCCGGTACAACAAAACCTGATGGGAATGGTACTGGCAGAAGGGATCGCCGTACGTTTCTGGACGCTGCAAAAAGTTAT > SRR3722114.127206/1‑100 (MQ=60)
CGATGAGGTTGCCGAAGATCCGGTACAACAAAACCTGATGGGAATGGTACTGGCAGAAGGGATCGCCGTACGTTTCTGGACGCTGCAAAAAGTTATCGAC > SRR3722114.254318/1‑100 (MQ=60)
CAACAAAACCTGATGGGAATGGTACTGGCAGAAGGGATCGCCGTACGTTTCTGGACGCTGCAAAAAGTTATCGACAACATTCATCGCGCCGCCGATCGAC < SRR3722114.267792/100‑1 (MQ=60)
|
TTCAATGGGTCGGATTTGCGGGGGCAAATCTGGTGCTGGTAGCCAACGATGAGGTTGCCGAAGATCCGGTACAACAAAACCTGATGGAAATGGTACTGGCAGAAGGGATCGCCGTACGTTTCTGGACGCTGCAAAAAGTTATCGACAACATTCATCGCGCCGCCGATCGAC > NZ_CP009273/3273634‑3273804
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
