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 |
2,833,262 |
T→G |
V127G (GTC→GGC) |
ascF → |
PTS cellobiose/arbutin/salicin transporter subunit IIBC |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,833,262 | 0 | T | G | 100.0%
| 56.4
/ NA
| 19 | V127G (GTC→GGC) | ascF | PTS cellobiose/arbutin/salicin transporter subunit IIBC |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base G (11/8); total (11/8) |
GTCGCATTGGTGCGGGGATCCTCGATGCGCTGATCGGCACCATGTCACCGCTGATCCCGGCGATTATCGGCGGATCGATGGTCAAACTGCTGGCAATGATCCTCGAGATGAGCGGCGTGCTGACAAAAGGATCGCCGACCTTAACCATTCTGAATGT > NZ_CP009273/2833181‑2833337
|
gTCGCATTGGTGCGGGGATCCTCGATGCGCTGATCGGCACCATGTCACCGCTGATCCCGGCGATTATCGGCGGATCGATGGGCAAActgc < 2:371618/90‑1 (MQ=255)
ggTGCGGGGATCCTCGATGCGCTGATCGGCACCATGTCACCGCTGATCCCGGCGATTATCGGCGGAGCGATGGGCCAAGTGCTGGCAATg > 2:442385/1‑90 (MQ=255)
tCCTCGATGCGCTGATCGGCACCATGTCACCGCTGATCCCGGCGATTATCGGCGGATCGATGGGCAAACTGCTGGCAATGATCCTCgaga > 1:354769/1‑90 (MQ=255)
ccTCGATGCGCTGATCGGCACCATGTCACCGCTGATCCCGGCGATTATCGGCGGATCGATGGGCAAACTGCTGGCAATGATTCTCGAGAt > 2:114516/1‑90 (MQ=255)
aTGCGCTGATCGGCACCATGTCACCGCTGATCCCGGCGATTATCGGCGGATCGATGGGCAAACTGCTGGCAATGATCCTCGAGATGAgcg > 1:433108/1‑90 (MQ=255)
gcgcTGATCGGCACCATGTCACCGCTGATCCCGGCGATTATCGGCGGATCGATGGGCAAACTGCTGGCAATGATCCTCGAGATGAgcggc > 2:489154/1‑90 (MQ=255)
tGATCGGCACCATGTCACCGCTGATCCCGGCGATTATCGGCGGATCGATGGGCAAACTGCTGGCAATGATCCTCGAGATGAGCGGCGTGc < 2:354769/90‑1 (MQ=255)
gCACCATGTCACCGCTGATCCCGGCGATTATCGGCGGATCGATGGGCAAACTGCTGGCAATGATCCTCGAGATGAGCGGCGGGCTGACaa > 2:133810/1‑90 (MQ=255)
ccATGTCACCGCTGATCCCGGCGATTATCGGCGGATCGATGGGCAAACTGCTGGCAATGATCCTCGAGATGAGCGGCGTGCTGACAAAAg < 1:93044/90‑1 (MQ=255)
aTGTCACCGCTGATCCCGGCGATTATCGGCGGATCGATGGGCAAACTGCTGGCAATGATCCTCGAGATGAGCGGCGTGCTGACAAAAGGa > 2:152735/1‑90 (MQ=255)
gCTGATCCCGGCGATTATCGGCGGATCGATGGGCAAACTGCTGGCAATg > 2:521030/1‑49 (MQ=255)
gCTGATCCCGGCGATTATCGGCGGATCGATGGGCAAACTGCTGGCAATg < 1:521030/49‑1 (MQ=255)
cTGATCCCGGCGATTATCGGCGGATCGATGGGCAAACTGCTGGCAATGATCCTCGAGATGAGCGGCGTGCTGACAAAAGGATCGCCGAcc < 2:31225/90‑1 (MQ=255)
gATCCCGGCGATTATCGGCGGATCGATGGGCAAACTGCTGGCAATGATCCTCGAGATGAGCGGCGTGCTGACAAAAGGATCGCCGACCtt > 2:94366/1‑90 (MQ=255)
cGGCGATTATCGGCGGATCGATGGGCAAACTGCTGGCAATGATCCTCGAGATGAGCGGCGTGCTGACAAAAGGATCGCCGACCTTAACCa > 1:22668/1‑90 (MQ=255)
cGATTATCGGCGGATCGATGGGCAAACTGCTGGCAATGATCCTCGAGATGAGCGGCGTGCTGACAAAAGGATCGCCGACCTTAACCATTc < 2:242253/90‑1 (MQ=255)
cggcggATCGATGGGCAAACTGCTGGCAATGATCCTCGAGATGAGCGGCGTGCTGACAAAAGGATCGCCGACCTTAACCATTc < 2:360946/83‑1 (MQ=255)
cggcggATCGATGGGCAAACTGCTGGCAATGATCCTCGAGATGAGCGGCGTGCTGACAAAAGGATCGCCGACCTTAACCATTc > 1:360946/1‑83 (MQ=255)
cggcggATCGATGGGCAAACTGCTGGCAATGATCCTCGAGATGAGCGGCGTGCTGACAAAAGGATCGCCGACCTTAACCATTCTGAAtgt < 2:479457/90‑1 (MQ=255)
|
GTCGCATTGGTGCGGGGATCCTCGATGCGCTGATCGGCACCATGTCACCGCTGATCCCGGCGATTATCGGCGGATCGATGGTCAAACTGCTGGCAATGATCCTCGAGATGAGCGGCGTGCTGACAAAAGGATCGCCGACCTTAACCATTCTGAATGT > NZ_CP009273/2833181‑2833337
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
ACCCAAACTCACGCTACGTCGCATTGGTGCGGGGATCCTCGATGCGCTGATCGGCACCATGTCACCGCTGATCCCGGCGATTATCGGCGGATCGATGGTCAAACTGCTGGCAATGATCCTCGAGATGAGCGGCGTGCTGACAAAAGGATCGCCGACCTTAACCATTCTGAATGT > NZ_CP009273/2833164‑2833337
|
ACCCAAACTCACGCTACGTCGCATTGGTGCGGGGATCCTCGATGCGCTGATCGGCACCATGTCACCGCTGATCCCGGCGATTATCGGCGGATCGATGGGC > SRR3722114.16252/1‑100 (MQ=60)
tcgtgggctcggagatgtgtataagagacagCCATGTCACCGCTGATCCCGGCGATTATCGGCGGATCGATGGGCAAACTGCTGGCAATGATCCTCGAGA < SRR3722114.527561/69‑1 (MQ=60)
GGTGCGGGGATCCTCGATGCGCTGATCGGCACCATGTCACCGCTGATCCCGGCGATTATCGGCGGATCGATGGGCAAACTGCTGGCAATGATCCTCGAGA > SRR3722114.358895/1‑100 (MQ=60)
aagacggcatacgagatctagtacggtctcgtgggctcggagatgtgtataagagacaGGATCGATGGGCAAACTGCTGGCAATGATCCTCGAGATGAGC < SRR3722114.404742/42‑1 (MQ=60)
GGGATCCTCGATGCGCTGATCGGCACCATGTCACCGCTGATCCCGGCGATTATCGGCGGATCGATGGGCAAACTGCTGGCAATGATCCTCGAGATGAGCG > SRR3722114.438440/1‑100 (MQ=60)
CCATGTCACCGCTGATCCCGGCGATTATCGGCGGATCGATGGGCAAACTGCTGGCAATGATCCTCGAGATGAGCGGCGTGCTGACAAAAGGATCGCCGAC < SRR3722114.94022/100‑1 (MQ=60)
CCGCTGATCCCGGCGATTATCGGCGGATCGATGGGCAAACTGCTGGCAATGATCCTCGAGATGAGCGGCGTGCTGACAAAAGGATCGCCGACCTTAACCA > SRR3722114.22891/1‑100 (MQ=60)
CGGCGATTATCGGCGGATCGATGGGCAAACTGCTGGCAATGATCCTCGAGATGAGCGGCGTGCTGACAAAAGGATCGCCGACCTTAACCATTCTGAATGT > SRR3722114.365177/1‑100 (MQ=60)
|
ACCCAAACTCACGCTACGTCGCATTGGTGCGGGGATCCTCGATGCGCTGATCGGCACCATGTCACCGCTGATCCCGGCGATTATCGGCGGATCGATGGTCAAACTGCTGGCAATGATCCTCGAGATGAGCGGCGTGCTGACAAAAGGATCGCCGACCTTAACCATTCTGAATGT > NZ_CP009273/2833164‑2833337
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
