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 I209 R1
|
216 |
14.4 |
815930 |
96.1% |
784108 |
85.2 |
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%
| 51.2
/ NA
| 17 | V127G (GTC→GGC) | ascF | PTS cellobiose/arbutin/salicin transporter subunit IIBC |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base G (9/8); total (9/8) |
TTGGTGCGGGGATCCTCGATGCGCTGATCGGCACCATGTCACCGCTGATCCCGGCGATTATCGGCGGATCGATGGTCAAACTGCTGGCAATGATCCTCGAGATGAGCGGCGTGCTGACAAAAGGATCGCCGACCTTAACCATTCTGAAT > NZ_CP009273/2833187‑2833335
|
ttGGTGCGGGGATCCTCGATGCGCTGATCGGCACCATGTCACCGCTGATCCCGGCGATTATCGGCGGATCGATGGGCAAACTGCTGGCaa > 1:230597/1‑90 (MQ=255)
ggTGCGGGGATCCTCGATGCGCTGATCGGCACCATGTCACCGCTGATCCCGGCGATTATCGGCGGATCGATGGGCAAACTGCTGGCAATg < 2:138759/90‑1 (MQ=255)
ggATCCTCGATGCGCTGATCGGCACCATGTCACCGCTGATCCCGGCGATTATCGGCGGATCGATGGGCAAACTGCTGGCAATGATCCTCg < 2:230597/90‑1 (MQ=255)
tCCTCGATGCGCTGATCGGCACCATGTCACCGCTGATCCCGGCGATTATCGGCGGATCGATGGGCAAACTGCTGGCAATGATCCTCgaga > 1:40953/1‑90 (MQ=255)
gcTGATCGGCACCATGTCACCGCTGATCCCGGCGATTATCGGCGGATCGATGGGCAAACTGCTGGCAATGATCCTCGAGATGAGCGGCGt > 1:7107/1‑90 (MQ=255)
tGATCGGCACCATGTCACCGCTGATCCCGGCGATTATCGGCGGATCGATGGGCAAACTGCTGGCAATGATCCTCGAGATGAGCGGCGTGc < 2:40953/90‑1 (MQ=255)
aTCGGCACCATGTCACCGCTGATCCCGGCGATTATCGGCGGATCGATGGGCAAACTGCTGGCAATGATCCTCGAGATGAGCGGCGTGCTg > 2:1687/1‑90 (MQ=255)
aTGTCACCGCTGATCCCGGCGATTATCGGCGGATCGATGGGCAGACTGCTGGCAATGATCCTCGAGATGAGCGGCGTGCTGACAAAAGGa > 2:205256/1‑90 (MQ=255)
aTGTCACCGCTGATCCCGGCGATTATCGGCGGATCGATGGGCAAACTGCTGGCAATGATCCTCGAGATGAGCGGCGTGCTGACAAAAGGa > 2:190280/1‑90 (MQ=255)
aCCGCTGATCCCGGCGATTATCGGCGGATCGATGGGCAAACTGCTGGCAATGATCCTCGAGATGAGCGGCGTGCTGACAAAAGGATCGcc < 1:140425/90‑1 (MQ=255)
aCCGCTGATCCCGGCGATTATCGGCGGATCGATGGGCAAACTGCTGGCAATGATCCTCGAGATGAGCGGCGTGCTGACAAAAGGATCGcc < 2:326596/90‑1 (MQ=255)
aCCGCTGATCCCGGCGATTATCGGCGGATCGATGGGCAAACTGCTGGCAATGATCCTCGAGATGAGCGGCGTGCTGACAAAAGGATCGcc > 1:326596/1‑90 (MQ=255)
gATCCCGGCGATTATCGGCGGATCGATGGGCAAACTGCTGGCAATGATCCTCGAGATGAGCGGCGTGCTGACAAAAGGATCGCCGACCtt > 2:116002/1‑90 (MQ=255)
ccGGCGATTATCGGCGGATCGATGGGCAAACTGCTGGCAATGATCCTCGAGATGAGCGGCGTGCTGACAAAAGGATCGCCGACCTTAAcc < 1:145018/90‑1 (MQ=255)
ccGGCGATTATCGGCGGATCGATGGGCAAACTGCTGGCAATGATCCTCGAGATGAGCGGCGTGCTGACAAAAGGATCGCCGACCTTAAcc < 1:106450/90‑1 (MQ=255)
cGGCGATTATCGGCGGATCGATGGGCAAAATGCTGGCAATGATCCTCGAGATGAGGGGGGTGCTGACAAAAGGGTCGCCGGCCTTAACCa > 1:55600/1‑90 (MQ=255)
aTCGGCGGATCGATGGGCAAACTGCTGGCAATGATCCTCGAGATGAGCGGCGTGCTGACAAAAGGATCGCCGACCTTAACCATTCTGAAt < 2:382164/90‑1 (MQ=255)
|
TTGGTGCGGGGATCCTCGATGCGCTGATCGGCACCATGTCACCGCTGATCCCGGCGATTATCGGCGGATCGATGGTCAAACTGCTGGCAATGATCCTCGAGATGAGCGGCGTGCTGACAAAAGGATCGCCGACCTTAACCATTCTGAAT > NZ_CP009273/2833187‑2833335
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
ACTCACGCTACGTCGCATTGGTGCGGGGATCCTCGATGCGCTGATCGGCACCATGTCACCGCTGATCCCGGCGATTATCGGCGGATCGATGGTCAAACTGCTGGCAATGATCCTCGAGATGAGCGGCGTGCTGACAAAAGGATCGCCGACCTTAACCATTCTGAATG > NZ_CP009273/2833170‑2833336
|
ACTCACGCTACGTCGCATTGGTGCGGGGATCCTCGATGCGCTGATCGGCACCATGTCACCGCTGATCCCGGCGATTATAGGCGGATCGATGGGCAAACTG < SRR3722091.141044/100‑1 (MQ=60)
CTACGTCGCATTGGTGCGGGGATCCTCGATGCGCTGATCGGCACCATGTCACCGCTGATCCCGGCGATTATCGGCGGATCGATGGGCAAACTGCTGGCAA > SRR3722091.234167/1‑100 (MQ=60)
GGTGCGGGGATCCTCGATGCGCTGATCGGCACCATGTCACCGCTGATCCCGGCGATTATCGGCGGATCGATGGGCAAACTGCTGGCAATGATCCTCGAGA > SRR3722091.41538/1‑100 (MQ=60)
TCCTCGATGCGCTGATCGGCACCATGTCACCGCTGATCCCGGCGATTATCGGCGGATCGATGGGCAAACTGCTGGCAATGATCCTCGAGATGAGCGGCGT > SRR3722091.7210/1‑100 (MQ=60)
GCACCATGTCACCGCTGATCCCGGCGATTATCGGCGGATCGATGGGCAAACTGCTGGCAATGATCCTCGAGATGAGCGGCGTGCTGACAAAAAGAACGCC > SRR3722091.332252/1‑100 (MQ=60)
ACCGCTGATCCCGGCGATTATCGGCGGATCGATGGGCAAACTGCTGGCAATGATCCTCGAGATGAGCGGCGTGCTGACAAAAGGATCGCCGACCTTAACC < SRR3722091.142518/100‑1 (MQ=60)
CCGCTGATCCCGGCGATTATCGGCGGATCGATGGGCAAAATGCTGGCAATGATCCTCGAGATGAGGGGGGTGCTGACAAAAGGGTCGCCGGCCTTAACCA > SRR3722091.56428/1‑100 (MQ=60)
CCGGCGATTATCGGCGGATCGATGGGCAAACTGCTGGCAATGATCCTCGAGATGAGCGGCGTGCTGACAAAAGGATCGCCGACCTTAACCATTCTGAATG < SRR3722091.108080/100‑1 (MQ=60)
CCGGCGATTATCGGCGGATCGATGGGCAAACTGCTGGCAATGATCCTCGAGATGAGCGGCGTGCTGACAAAAGGATCGCCGACCTTAACCATTCTGAATG < SRR3722091.147162/100‑1 (MQ=60)
|
ACTCACGCTACGTCGCATTGGTGCGGGGATCCTCGATGCGCTGATCGGCACCATGTCACCGCTGATCCCGGCGATTATCGGCGGATCGATGGTCAAACTGCTGGCAATGATCCTCGAGATGAGCGGCGTGCTGACAAAAGGATCGCCGACCTTAACCATTCTGAATG > NZ_CP009273/2833170‑2833336
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
