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 F3 I96 R1
|
172 |
34.7 |
2005794 |
96.2% |
1929573 |
85.4 |
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%
| 90.8
/ NA
| 27 | G374A (GGC→GCC) | ydhK | FUSC family protein |
| Reads supporting (aligned to +/- strand): ref base G (0/0); new base C (11/16); total (11/16) |
TCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGGCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGCTGCGTACTCTACTCCGCC > NZ_CP009273/1717419‑1717580
|
tCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGCCGCATgg < 1:1001974/87‑1 (MQ=255)
tCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGCCGCATgg > 2:1001974/1‑87 (MQ=255)
tCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGCCGCATGGAGt > 1:869947/1‑90 (MQ=255)
ggCTCGTCATACCGATAACGCCGAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTc > 2:166841/1‑90 (MQ=255)
tCGTCATACCGATAACGCCGAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCa < 2:655919/90‑1 (MQ=255)
aCCGATAACGCCGAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGAt > 1:861537/1‑90 (MQ=255)
cGATAACGCCGAAGCTATGTGGGGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGc < 1:707740/90‑1 (MQ=255)
gATAACGCCGAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGcc < 2:782107/90‑1 (MQ=255)
aCGCCGAAGCTATGTGGAGCGGGCTGCGTCCATTTTGTTCGTTGATGATGATTGCCGCATGGAGTATTGCTCCGCAATGGGATGCCGGTg < 1:540089/90‑1 (MQ=255)
gCCGAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGcc > 2:139490/1‑90 (MQ=255)
cGAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCaa < 1:325363/90‑1 (MQ=255)
gAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAAt < 2:429586/90‑1 (MQ=255)
gCGGGCTGCGTACATTTTGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTgg > 2:683781/1‑90 (MQ=255)
gCGGGCTGCGTACATTTTGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTgg > 2:108656/1‑90 (MQ=255)
gCGGGCTGCGTACATTTTGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTgg > 2:392071/1‑90 (MQ=255)
ggCTGCGTACATTTTGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGgcag > 1:835514/1‑90 (MQ=255)
aCATTTTGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGc < 2:541057/90‑1 (MQ=255)
aTTTTGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGCTg < 1:459324/90‑1 (MQ=255)
aTTTTGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGCTg < 1:16341/90‑1 (MQ=255)
ttGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGCTGCGt < 1:79299/90‑1 (MQ=255)
ttGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGCTGCGt < 1:232247/90‑1 (MQ=255)
tGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGCTGCGta > 2:386164/1‑90 (MQ=255)
gatgatTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTa > 1:761082/1‑55 (MQ=255)
gatgatTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTa < 2:761082/55‑1 (MQ=255)
atgatTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGCTGCGTACTCTACTccgcc < 1:837594/90‑1 (MQ=255)
atgatTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGCTGCGTACTCTACTccgcc < 1:683781/90‑1 (MQ=255)
atgatTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGCTGCGTACTCTACTccgcc < 1:139490/90‑1 (MQ=255)
|
TCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGGCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGCTGCGTACTCTACTCCGCC > NZ_CP009273/1717419‑1717580
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ 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: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CCCACGGACATCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGGCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGCTGCGTACTCTACTCCGCCGTCGCAGCAC > NZ_CP009273/1717409‑1717590
|
CCCACGGACATCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGCCGCATGGAGT > SRR3722236.885214/1‑100 (MQ=60)
ACATCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGCCGCATGGAGTATTGCTT < SRR3722236.1019605/100‑1 (MQ=60)
GGCTCGTCATACCGATAACGCCGAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGAT > SRR3722236.876648/1‑100 (MQ=60)
CGATAACGCCGAAGCTATGTGGGGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAAT < SRR3722236.719727/100‑1 (MQ=60)
ACGCCGAAGCTATGTGGAGCGGGCTGCGTCCATTTTGTTCGTTGATGATGATTGCCGCATGGAGTATTGCTCCGCAATGGGATGCCGGTGCCAATGCATT < SRR3722236.548394/100‑1 (MQ=60)
CGAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACG < SRR3722236.330009/100‑1 (MQ=60)
ATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAG > SRR3722236.850107/1‑100 (MQ=60)
ATTTTGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGCTGCGTACTCTAC < SRR3722236.16570/100‑1 (MQ=60)
ATTTTGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGCTGCGTACTCTAC < SRR3722236.466034/100‑1 (MQ=60)
TTGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGCTGCGTACTCTACTCC < SRR3722236.235701/100‑1 (MQ=60)
TTGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGCTGCGTACTCTACTCC < SRR3722236.80420/100‑1 (MQ=60)
GTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCtgtctcttatacacatctgacgct > SRR3722236.774171/1‑76 (MQ=60)
ATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGCTGCGTACTCTACTCCGCCGTCGCAGCAC < SRR3722236.141501/100‑1 (MQ=60)
ATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGCTGCGTACTCTACTCCGCCGTCGCAGCAC < SRR3722236.695230/100‑1 (MQ=60)
ATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGCTGCGTACTCTACTCCGCCGTCGCAGCAC < SRR3722236.852242/100‑1 (MQ=60)
|
CCCACGGACATCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGGCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGCTGCGTACTCTACTCCGCCGTCGCAGCAC > NZ_CP009273/1717409‑1717590
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
