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 |
1,717,498 |
G→C |
G374A (GGC→GCC) |
ydhK → |
FUSC family protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,717,498 | 0 | G | C | 100.0%
| 72.9
/ NA
| 23 | G374A (GGC→GCC) | ydhK | FUSC family protein |
| Reads supporting (aligned to +/- strand): ref base G (0/0); new base C (12/11); total (12/11) |
CACGGACATCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGGCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGCTGCGTACTCTACTCCGCCGT > NZ_CP009273/1717411‑1717582
|
cACGGACATCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGccg < 1:292375/90‑1 (MQ=255)
aCGGACATCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGccgc > 2:537758/1‑90 (MQ=255)
ggACATCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGCCGCAt < 1:108142/90‑1 (MQ=255)
ggACATCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGCCGCAt < 1:537758/90‑1 (MQ=255)
aCATCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGCCGCATgg > 1:551653/1‑90 (MQ=255)
tCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGCCGCATGGAGt > 2:291606/1‑90 (MQ=255)
tCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGCCGCATGGAGt > 1:261393/1‑90 (MQ=255)
cTGGCTCGTCATACCGATAACGCCGAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGCCGCAt > 1:246291/1‑79 (MQ=255)
cTGGCTCGTCATACCGATAACGCCGAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGCCGCAt < 2:246291/79‑1 (MQ=255)
tCGTCATACCGATAATGCCGAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCa < 2:553734/90‑1 (MQ=255)
tAACGCCGAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCgg > 1:78304/1‑90 (MQ=255)
aCGCCGAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTg > 1:407017/1‑90 (MQ=255)
cGAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCaa > 2:520028/1‑90 (MQ=255)
cGAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCaa < 1:520028/90‑1 (MQ=255)
gAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAAt < 2:164674/90‑1 (MQ=255)
gAAGCCATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAAt > 2:101721/1‑90 (MQ=255)
gAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCt > 2:121566/1‑90 (MQ=255)
ggCTGCGTACATTTTGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCg < 1:533428/66‑1 (MQ=255)
ggCTGCGTACATTTTGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCg > 2:533428/1‑66 (MQ=255)
aTTTTGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGCTg < 1:211523/90‑1 (MQ=255)
ttGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGCTGCGt < 1:477901/90‑1 (MQ=255)
tACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGCTGCGtact > 1:153454/1‑90 (MQ=255)
atgatTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGCTGCGTACTCTACTccgcc < 2:99210/90‑1 (MQ=255)
gatTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGCTGCGTACTCTACTCCGCCGt > 2:266089/1‑90 (MQ=255)
ttGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCACTAACGCTGGCAGCAATTAGCTGCGtac < 2:170927/75‑1 (MQ=255)
|
CACGGACATCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGGCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGCTGCGTACTCTACTCCGCCGT > NZ_CP009273/1717411‑1717582
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
ATACCAGACTCCCACGGACATCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGGCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGCTGCGTACTCTACTCCGCC‑GTCGCAGCAC > NZ_CP009273/1717399‑1717590
|
ATACCAGACTCCCACGGACATCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGC > SRR3722111.226948/1‑100 (MQ=60)
TACCAGACTCCCACGGACATCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGCC > SRR3722111.145199/1‑100 (MQ=60)
ACTCCCACGGACATCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGCCGCATGG > SRR3722111.560318/1‑100 (MQ=60)
CCCACGGACATCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGCCGCATGGAGT > SRR3722111.264471/1‑100 (MQ=60)
CACGGACATCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGCCGCATGGAGTAT < SRR3722111.296115/100‑1 (MQ=60)
GGACATCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGCCGCATGGAGTATTGC < SRR3722111.109501/100‑1 (MQ=60)
GGACATCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGCCGCATGGAGTATTGC < SRR3722111.546205/100‑1 (MQ=60)
GACATCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGCCGCATGGAGTATTGCC > SRR3722111.249199/1‑100 (MQ=60)
GTCATACCGATAACGCCGAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGG > SRR3722111.79258/1‑100 (MQ=60)
CATACCGATAACGCCGAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTG > SRR3722111.412957/1‑100 (MQ=60)
tgtataagagacagATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGC < SRR3722111.541790/86‑1 (MQ=60)
CGAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACG < SRR3722111.528154/100‑1 (MQ=60)
GTACATTTTGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGCTGCGTACT > SRR3722111.155392/1‑100 (MQ=60)
ATTTTGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGCTGCGTACTCTAC < SRR3722111.214108/100‑1 (MQ=60)
TTGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGCTGCGTACTCTACTCC < SRR3722111.485226/100‑1 (MQ=60)
TTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCACTAACGCTGGCAGCAATTAGCTGCGTACTCTACTCCGCCTGTC > SRR3722111.173062/1‑100 (MQ=60)
ATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGCTGCGTACTCTACTCCGCC‑GTCGCAGCAC < SRR3722111.129132/100‑1 (MQ=60)
|
ATACCAGACTCCCACGGACATCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGGCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGCTGCGTACTCTACTCCGCC‑GTCGCAGCAC > NZ_CP009273/1717399‑1717590
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
