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 I227 R1
|
223 |
21.3 |
1167702 |
97.0% |
1132670 |
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 | 94.1%
| 44.3
/ ‑6.0
| 18 | V127G (GTC→GGC) | ascF | PTS cellobiose/arbutin/salicin transporter subunit IIBC |
| Reads supporting (aligned to +/- strand): ref base T (1/0); major base G (8/8); minor base A (0/1); total (9/9) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GGTGCGGGGATCCTCGATGCGCTGATCGGCACCATGTCACCGCTGATCCCGGCGATTATCGGCGGATCGATGGTCAAACTGCTGGCAATGATCCTCGAGATGAGCGGCGTGCTGACAAAAGGATCGCCGACCTTAACCATTC > NZ_CP009273/2833189‑2833330
|
ggTGCGGGGATCCTCGATGCGCTGATCGGCACCATGTCACCGCTGATCCCGGCGATTATCGGCGGATCGATGGGCAAACTGCTGGCAATg > 1:203344/1‑90 (MQ=255)
ggTGCGGGGATCCTCGATGCGCTGATCGGCACCATGTCACCGCTGATCCCGGCGATTATCGGCGGATCGATGGGCAAACTGCTGGCAATg < 2:574537/90‑1 (MQ=255)
ggTGCGGGGATCCTCGATGCGCTGATCGGCACCATGTCACCGCTGATCCCGGCGATTATCGGCGGATCGATGGGCAAACTGCTGGCAATg < 2:428272/90‑1 (MQ=255)
tGCGGGGATCCTCGATGCGCTTATCGGCACCATGTCACCGCTGATCCCGGCGATTATCGGCGGATCGATGGGCAAACTGCTGGCAATGAt < 1:350308/90‑1 (MQ=255)
gCGGGGATCCTCGATGCGCTGATCGGCACCATGTCACCGCTGATCCCGGCGATTATCGGCGGATCGGTGGGGAA‑‑‑GCTGGCAAGGATCCTc > 2:580298/1‑90 (MQ=255)
gCGGGGATCCTCGATGCGCTGATCGGCACCATGTCACCGCTGATCCCGGCGATTAACGGCGGATCGATGGGCAAACTGCTGGCCATGATc > 2:451537/1‑90 (MQ=255)
ggggATCCTCGATGCGCTGATCGGCACCATGTCACCGCTGATCCCGGCGATTATCGGCGGATCGATGGGCAAACTGCTGGCAAAGATCCt > 1:53608/1‑90 (MQ=255)
cgcTGATCGGCACCATGTCACCGCTGATCCCGGCGATTATCGGCGGATCGATGGGCAAACTGCTGGCAATGATCCTCGAGATGAgcggcg < 1:503916/90‑1 (MQ=255)
gATCGGCACCATGTCACCGCTGATCCCGGCGATTATCGGCGGATCGATGGGCAAACTGCTGGCAATGATCCTCGAGATGAGCGGCGTGCt > 1:201161/1‑90 (MQ=255)
aTCGGCACCATGTCACCGCTGATCCCGGCGATTATCGGCGGATCGATGGGCAAACTGCTGGCAATGATCCTCGAGATGAGCGGCGTGCTg < 2:6962/90‑1 (MQ=255)
aTGTCACCGCTGATCCCGGCGATTATCGGCGGATCGATGGGCAAACTGCTGGCAATGATCCTCGGGATGAGCGGCGTGCTGACAAAAGGa > 2:280609/1‑90 (MQ=255)
aTGTCACCGCTGATCCCGGCGATTATCGGCGGATCGATGGGCAAACTGCTGGCAATGATCCCCGAGATGAGCGGCGTGCTGACAAAAAGa > 1:357517/1‑90 (MQ=255)
aCCGCTGATCCCGGCGATTATCGGCGGATCGATGGGCAAACTGCTGGCAATGATCCTCGAGATGAGCGGCGTGCTGACAAAAGGATCGcc < 1:353486/90‑1 (MQ=255)
aCCGCTGATCCCGGCGATTATCGGCGGATCGATGGGCAAACTGCTGGCAATGATCCTCGAGATGAGCGGCGTGCTGACAAAAGGATCGcc < 1:328050/90‑1 (MQ=255)
ccGCTGATCCCGGCGCTTATCGGCGGATCGATGGACAAACTGCTGGCAATGATCCCCCAGATGAGCGGCGTCCTGACAAAAGGATCCCCg < 1:388601/90‑1 (MQ=255)
gATCCCGGCGATTATCGGCGGATCGATGGTCAAACTGCTGGCAATGATCCTCGAGATGAGCGGCGTGCTGACAAAAGGATCGCCGACCtt > 2:23614/1‑90 (MQ=255)
gCGATTATCGGCGGATCGATGGGCAAACTGCTGGCAATGATCCTCGAGATGAGCGGCGTGCTGACAAAAGGATCGCCGACCTTAACCAtt > 1:201011/1‑90 (MQ=255)
cGATTATCGGCGGATCGATGGGCAAACTGCTGGCAATGATCCTCGAGATGAGCGGCGTGCTGACAAAAGGATCGCCGACCTTAACCATTc < 1:434272/90‑1 (MQ=255)
|
GGTGCGGGGATCCTCGATGCGCTGATCGGCACCATGTCACCGCTGATCCCGGCGATTATCGGCGGATCGATGGTCAAACTGCTGGCAATGATCCTCGAGATGAGCGGCGTGCTGACAAAAGGATCGCCGACCTTAACCATTC > NZ_CP009273/2833189‑2833330
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
ACGTCGCATTGGTGCGGGGATCCTCGATGCGCTGATCGGCACCATGTCACCGCTGATCCCGGCGATTATCGGCGGATCGATGGTCAAACTGCTGGCAATGATCCTCGAGATGAGCGGCGTGCTGACAAAAGGATCGCCGACCTTAACCATTCTGAATGTGAT > NZ_CP009273/2833179‑2833340
|
ACGTCGCATTGGTGCGGGGATCCTCGATGCGCTGATCGGCACCATGTCACCGCTGATCCCGGCGATTATCGGCGGATCGATGGGCAAACTGCTGGCAATG > SRR3722111.205858/1‑100 (MQ=60)
TCGCATTGGTGCGGGGATCCTCGATGCGCTGATCGGCACCATGTCACCGCTGATCCCGGCGATTATCGGCGGATCGATGGGCAAACTGCTGtctcttata > SRR3722111.591713/1‑91 (MQ=60)
GCATTGGTGCGGGGATCCTCGATGCGCTGATCGGCACCATGTCACCGCTGATCCCGGCGATTATCGGCGGATCGATGGGCAAACTGCTGGCAAAGATCCT > SRR3722111.54256/1‑100 (MQ=60)
TGCGGGGATCCTCGATGCGCTTATCGGCACCATGTCACCGCTGATCCCGGCGATTATCGGCGGATCGATGGGCAAACTGCTGGCAATGATCCTCGAGATG < SRR3722111.355061/100‑1 (MQ=60)
TCGATGCGCTGATCGGCACCATGTCACCGCTGATCCCGGCGATTATCGGCGGATCGATGGGCAAACTGCTGGCAATGATCCTCGAGATGAGCGGCGTGCT > SRR3722111.203661/1‑100 (MQ=60)
CGCTGATCGGCACCATGTCACCGCTGATCCCGGCGATTATCGGCGGATCGATGGGCAAACTGCTGGCAATGATCCTCGAGATGAGCGGCGTGCTGACAAA < SRR3722111.511695/100‑1 (MQ=60)
GATCGGCACCATGTCACCGCTGATCCCGGCGATTATCGGCGGATCGATGGGCAAACTGCTGGCAATGATCCCCGAGATGAGCGGCGTGCTGACAAAAAGA > SRR3722111.362450/1‑100 (MQ=60)
ACCGCTGATCCCGGCGATTATCGGCGGATCGATGGGCAAACTGCTGGCAATGATCCTCGAGATGAGCGGCGTGCTGACAAAAGGATCGCCGACCTTAACC < SRR3722111.332443/100‑1 (MQ=60)
ACCGCTGATCCCGGCGATTATCGGCGGATCGATGGGCAAACTGCTGGCAATGATCCTCGAGATGAGCGGCGTGCTGACAAAAGGATCGCCGACCTTAACC < SRR3722111.358321/100‑1 (MQ=60)
CCGCTGATCCCGGCGCTTATCGGCGGATCGATGGACAAACTGCTGGCAATGATCCCCCAGATGAGCGGCGTCCTGACAAAAGGATCCCCGCCCTTAACCC < SRR3722111.394224/100‑1 (MQ=60)
GCTGATCCCGGCGATTATCGGCGGATCGATGGGCAAACTGCTGGCAATGATCCTCGAGATGAGCGGCGTGCTGACAAAAGGATCGCCGACCTTAACCATT > SRR3722111.203509/1‑100 (MQ=60)
CGATTATCGGCGGATCGATGGGCAAACTGCTGGCAATGATCCTCGAGATGAGCGGCGTGCTGACAAAAGGATCGCCGACCTTAACCATTCTGAATGTGAT < SRR3722111.440763/100‑1 (MQ=60)
|
ACGTCGCATTGGTGCGGGGATCCTCGATGCGCTGATCGGCACCATGTCACCGCTGATCCCGGCGATTATCGGCGGATCGATGGTCAAACTGCTGGCAATGATCCTCGAGATGAGCGGCGTGCTGACAAAAGGATCGCCGACCTTAACCATTCTGAATGTGAT > NZ_CP009273/2833179‑2833340
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
