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 I199 R1
|
220 |
57.5 |
3163680 |
97.0% |
3068769 |
86.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,153,703 |
A→T |
I127F (ATC→TTC) |
ptsG → |
PTS glucose transporter subunit IIBC |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,153,703 | 0 | A | T | 100.0%
| 134.1
/ NA
| 35 | I127F (ATC→TTC) | ptsG | PTS glucose transporter subunit IIBC |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base T (19/16); total (19/16) |
CTGGTACTGCATTTACCTGCTGAAGAAATCGCCTCTAAACACCTGGCGGATACTGGCGTACTCGGAGGGATTATCTCCGGTGCGATCGCAGCGTACATGTTTAACCGTTTCTACCGTATTAAGCTGCCTGAGTATCTTGGCTTCTTTGCCGGTAAACGCTTTGTGCCGATC > NZ_CP009273/1153619‑1153789
|
cTGGTACTGCATTTACCTGCTGAAGAAATCGCCTCTAAACACCTGGCGGATACTGGCGTACTCGGAGGGATTATCTCCGGTGCGTTCGCa > 1:113477/1‑90 (MQ=255)
tGGTACTGCATTTACCTGCTGAAGAAATCGCCTCTAAACACCTGGCGGATACTGGCGTACTCGGAGGGATTATCTCCGGTGCGTTCGCAg < 1:1122324/90‑1 (MQ=255)
aCTGCATTTACCTGCTGAAGAAATCGCCTCTAAACACCTGGCGGATACTGGCGTACTCGGAGGGATTATCTCCGGTGCGTTCGCAGCGTa > 1:1302605/1‑90 (MQ=255)
aCTGCATTTACCTGCTGAAGAAATCGCCTCTAAACACCTGGCGGATACTGGCGTACTCGGAGGGATTATCTCCGGTGCGTTCGCAGCGTa < 2:1302605/90‑1 (MQ=255)
gCATTTACCTGCTGAAGAAATCGCCTCTAAACACCTGGCGGATACTGGCGTACTCGGAGGGATTATCTCCGGTGCGTTCGCAGCGTACAt > 2:722018/1‑90 (MQ=255)
ttACCTGCTGAAGAAATCGCCTCTAAACACCTGGCGGATACTGGCGTACTCGGAGGGATTATCTCCGGTGCGTTCGCAGCGTACATGttt > 2:295742/1‑90 (MQ=255)
gctgAAGAAATCGCCTCTAAACACCTGGCGGATACTGGCGTACTCGGAGGGATTATCTCCGGTGCGTTCGCAGCGTACATGTTTAACCGt > 2:662644/1‑90 (MQ=255)
gctgAAGAAATCGCCTCTAAACACCTGGCGGATACTGGCGTACTCGGAGGGATTATCTCCGGTGCGTTCGCAGCGTACATGTTTAACCGt > 1:259151/1‑90 (MQ=255)
gctgAAGAAATCGCCTCTAAACACCTGGCGGATACTGGCGTACTCGGAGGGATTATCTCCGGTGCGTTCGCAGCGTACATGTTTAACCGt > 1:514650/1‑90 (MQ=255)
ctgAAGAAATCGCCTCTAAACACCTGGCGGATACTGGCGTACTCGGAGGGATTATCTCCGGTGCGTTCGCAGCGTACATGTTTAACCGtt < 1:1304188/90‑1 (MQ=255)
agaaATCGCCTCTAAACACCTGGCGGATACTGGCGTACTCGGAGGGATTATCTCCGGTGCGTTCGCAGCGTACATGTTTAACCGTTTCTa > 1:41350/1‑90 (MQ=255)
gaaATCGCCTCTAAACACCTGGCGGATACTGGCGTACTCGGAGGGATTATCTCCGGTGCGTTCGCAGCGTACATGTTTAACCGTTTCTAc < 2:41350/90‑1 (MQ=255)
gaaATCGCCTCTAAACACCTGGCGGATACTGGCGTACTCGGAGGGATTATCTCCGGTGCGTTCGCAGCGTACATGTTTAACCGTTTCTAc < 2:259151/90‑1 (MQ=255)
tCGCCTCTAAACACCTGGCGGATACTGGCGTACTCGGAGGGATTATCTCCGGTGCGTTCGCAGCGTACATGTTTAACCGTTTCTACCGTa > 1:1570834/1‑90 (MQ=255)
ctctAAACACCTGGCGGATACTGGCGTACTCGGAGGGATTATCTCCGGTGCGTTCGCAGCGTACATGTTTAACCGTTTCTACCGTATTaa < 1:917950/90‑1 (MQ=255)
acacCTGGCGGATACTGGCGTACTCGGAGGGATTATCTCCGGTGCGTTCGCAGCGTACATGTTTAACCGTTTCTACCGTATTAAGCTGcc < 2:737283/90‑1 (MQ=255)
cTGGCGGATACTGGCGTACTCGGAGGGATTATCTCCGGTGCGTTCGCAGCGTACATGTTTAACCGTTTCTACCGTATTAAGCTGCCTGAg > 2:931634/1‑90 (MQ=255)
tGGCGGATACTGGCGTACTCGGAGGGATTATCTCCGGTGCGTTCGCAGCGTACATGTTTAACCGTTTCTACCGTATTAAGCTGCCTGAGt > 2:125888/1‑90 (MQ=255)
tGGCGGATACTGGCGTACTCGGAGGGATTATCTCCGGTGCGTTCGCAGCGTACATGTTTAACCGTTTCTACCGTATTAAGCTGCCTGAGt > 1:366764/1‑90 (MQ=255)
aTACTGGCGTACTCGGAGGGATTATCTCCGGTGCGTTCGCAGCGTACATGTTTAACCGTTTCTACCGTATTAAGCTGCCTGAGTATCTTg < 2:1103159/90‑1 (MQ=255)
ggCGTCCTCGGAGGGATTATCTCCGGTGCGTTCGCAGCGTACa < 2:1350156/43‑1 (MQ=38)
ggCGTACTCGGAGGGATTATCTCCGGTGCGTTCGCAGCGTACa > 1:1350156/1‑43 (MQ=255)
ggCGTACTCGGAGGGATTATCTCCGGTGCGTTCGCAGCGTACATGTTTAACCGTTTCTAc > 2:247412/1‑60 (MQ=255)
ggCGTACTCGGAGGGATTATCTCCGGTGCGTTCGCAGCGTACATGTTTAACCGTTTCTAc < 1:247412/60‑1 (MQ=255)
ggCGTACTCGGAGGGATTATCTCCGGTGCGTTCGCAGCGTACATGTTTAACCGTTTCTACCGTATTAAGCTGCCTGAGTATCTTGGcttc > 1:1180540/1‑90 (MQ=255)
ggCGTACTCGGAGGGATTATCTCCGGTGCGTTCGCAGCGTACATGTTTAACCGTTTCTACCGTATTAAGCTGCCTGAGTATCTTGGcttc > 2:904585/1‑90 (MQ=255)
gAGGGATTATCTCCGGTGCGTTCGCAGCGTACATGTTTAACCGTTTCTACCGTATTAAGCTGCCTGAGTATCTTGGCTTCTTTGCCGGTa > 1:994606/1‑90 (MQ=255)
gggATTATCTCCGGTGCGTTCGCAGCGTACATGTTTAACCGTTTCTACCGTATTAAGCTGCCTGAGTATCTTGGCTTCTTTGCCGGTaaa < 2:1161452/90‑1 (MQ=255)
gggATTATCTCCGGTGCGTTCGCAGCGTACATGTTTAACCGTTTCTACCGTATTAAGCTGCCTGAGTATCTTGGCTTCTTTGCCGGTaaa < 1:1284051/90‑1 (MQ=255)
gggATTATCTCCGGTGCGTTCGCAGCGTACATGTTTAACCGTTTCTACCGTATTAAGCTGCCTGAGTATCTTGGCTTCTTTGCCGGTaaa < 1:777061/90‑1 (MQ=255)
ttATCTCCGGTGCGTTCGCAGCGTACATGTTTAACCGTTTCTACCGTATTAAGCTGCCTGAGTATCTTGGCTTCTTTGCCGGTAAACGCt > 1:1550963/1‑90 (MQ=255)
aTCTCCGGTGCGTTCGCAGCGTACATGTTTAACCGTTTCTACCGTATTAAGCTGCCTGAGTATCTTGGCTTCTTTGCCGGTAAACGCttt < 1:662644/90‑1 (MQ=255)
ctcCGGTGCGTTCGCAGCGTACATGTTTAACCGTTTCTACCGTATTAAGCTGcc > 2:555502/1‑54 (MQ=255)
ctcCGGTGCGTTCGCAGCGTACATGTTTAACCGTTTCTACCGTATTAAGCTGcc < 1:555502/54‑1 (MQ=255)
gCGTTCGCAGCGTACATGTTTAACCGTTTCTACCGTATTAAGCTGCCTGAGTATCTTGGCTTCTTTGCCGGTAAACGCTTTGTGCCGATc < 2:1550963/90‑1 (MQ=255)
|
CTGGTACTGCATTTACCTGCTGAAGAAATCGCCTCTAAACACCTGGCGGATACTGGCGTACTCGGAGGGATTATCTCCGGTGCGATCGCAGCGTACATGTTTAACCGTTTCTACCGTATTAAGCTGCCTGAGTATCTTGGCTTCTTTGCCGGTAAACGCTTTGTGCCGATC > NZ_CP009273/1153619‑1153789
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ 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
GGTTGCGCCACTGGTACTGCATTTACCTGCTGAAGAAATCGCCTCTAAACACCTGGCGGATACTGGCGTACTCGGAGGGATTATCTCCGGTGCGATCGCAGCGTACATGTTTAACCGTTTCTACCGTATTAAGCTGCCTGAGTATCTTGGCTTCTTTGCCGGTAAACGCTTTGTGCCGATCATTTCTGGCCTGG > NZ_CP009273/1153609‑1153802
|
GGTTGCGCCACTGGTACTGCATTTACCTGCTGAAGAAATCGCCTCTAAACACCTGGCGGATACTGGCGTACTCGGAGGGATTATCTCCGGTGCGTTCGCA > SRR3722078.114813/1‑100 (MQ=60)
CGCCACTGGTACTGCATTTACCTGCTGAAGAAATCGCCTCTAAACACCTGGCGGATACTGGCGTACTCGGAGGGATTATCTCCGGTGCGTTCGCAGCGTA > SRR3722078.1323377/1‑100 (MQ=60)
TGGTACTGCATTTACCTGCTGAAGAAATCGCCTCTAAACACCTGGCGGATACTGGCGTACTCGGAGGGATTATCTCCGGTGCGTTCGCAGCGTACATGTT < SRR3722078.1139461/100‑1 (MQ=60)
GCATTTACCTGCTGAAGAAATCGCCTCTAAACACCTGGCGGATACTGGCGTACTCGGAGGGATTATCTCCGGTGCGTTCGCAGCGTACATGTTTAACCGT > SRR3722078.520737/1‑100 (MQ=60)
GCATTTACCTGCTGAAGAAATCGCCTCTAAACACCTGGCGGATACTGGCGTACTCGGAGGGATTATCTCCGGTGCGTTCGCAGCGTACATGTTTAACCGT > SRR3722078.262319/1‑100 (MQ=60)
TACCTGCTGAAGAAATCGCCTCTAAACACCTGGCGGATACTGGCGTACTCGGAGGGATTATCTCCGGTGCGTTCGCAGCGTACATGTTTAACCGTTTCTA > SRR3722078.41842/1‑100 (MQ=60)
GCTGAAGAAATCGCCTCTAAACACCTGGCGGATACTGGCGTACTCGGAGGGATTATCTCCGGTGCGTTCGCAGCGTACATGTTTAACCGTTTCTACCGTA > SRR3722078.1596393/1‑100 (MQ=60)
CTGAAGAAATCGCCTCTAAACACCTGGCGGATACTGGCGTACTCGGAGGGATTATCTCCGGTGCGTTCGCAGCGTACATGTTTAACCGTTTCTACCGTAT < SRR3722078.1324985/100‑1 (MQ=60)
cagatgtgtataagagacagGGCGGATACTGGCGTACTCGGAGGGATTATCTCCGGTGCGTTCGCAGCGTACATGTTTAACCGTTTCTACCGTATTAAGC < SRR3722078.250432/80‑1 (MQ=60)
CTCTAAACACCTGGCGGATACTGGCGTACTCGGAGGGATTATCTCCGGTGCGTTCGCAGCGTACATGTTTAACCGTTTCTACCGTATTAAGCTGCCTGAG < SRR3722078.930452/100‑1 (MQ=60)
TCTAAACACCTGGCGGATACTGGCGTACTCGGAGGGATTATCTCCGGTGCGTTCGCAGCGTACATGTTTAACCGTTTCTACCGTATTAAGCTGCCTGAGT > SRR3722078.371243/1‑100 (MQ=60)
cagcgtcagatgtgtataagagacaGGAGGGATTATCTCCGGTGCGTTCGCAGCGTACATGTTTAACCGTTTCTACCGTATTAAGCTGCCTGAGTATCTT < SRR3722078.562055/75‑1 (MQ=60)
GGCGGATACTGGCGTACTCGGAGGGATTATCTCCGGTGCGTTCGCAGCGTACATGTTTAACCGctgtctcttatacacatctgacgctgccgacgaaggc > SRR3722078.1371834/1‑63 (MQ=60)
GGCGGATACTGGCGTACTCGGAGGGATTATCTCCGGTGCGTTCGCAGCGTACATGTTTAACCGTTTCTACCGTATTAAGCTGCCTGAGTATCTTGGCTTC > SRR3722078.1198976/1‑100 (MQ=60)
GGCGTACTCGGAGGGATTATCTCCGGTGCGTTCGCAGCGTACATGTTTAACCGTTTCTACCGTATTAAGCTGCCTGAGTATCTTGGCTTCTTTGCCGGTA > SRR3722078.1009075/1‑100 (MQ=60)
CTCGGAGGGATTATCTCCGGTGCGTTCGCAGCGTACATGTTTAACCGTTTCTACCGTATTAAGCTGCCTGAGTATCTTGGCTTCTTTGCCGGTAAACGCT > SRR3722078.1576228/1‑100 (MQ=60)
GGGATTATCTCCGGTGCGTTCGCAGCGTACATGTTTAACCGTTTCTACCGTATTAAGCTGCCTGAGTATCTTGGCTTCTTTGCCGGTAAACGCTTTGTGC < SRR3722078.1304472/100‑1 (MQ=60)
GGGATTATCTCCGGTGCGTTCGCAGCGTACATGTTTAACCGTTTCTACCGTATTAAGCTGCCTGAGTATCTTGGCTTCTTTGCCGGTAAACGCTTTGTGC < SRR3722078.787132/100‑1 (MQ=60)
ATCTCCGGTGCGTTCGCAGCGTACATGTTTAACCGTTTCTACCGTATTAAGCTGCCTGAGTATCTTGGCTTCTTTGCCGGTAAACGCTTTGTGCCGATCA < SRR3722078.670234/100‑1 (MQ=60)
TTCGCAGCGTACATGTTTAACCGTTTCTACCGTATTAAGCctgtctcttatacacatctgacgctgccgacgatggcggtcgtgtagatctcggtggtcg > SRR3722078.252685/1‑40 (MQ=60)
TTCGCAGCGTACATGTTTAACCGTTTCTACCGTATTAAGCTGCCTGAGTATCTTGGCTTCTTTGCCGGTAAACGCTTTGTGCCGATCATTTCTGGCCTGG > SRR3722078.1192795/1‑100 (MQ=60)
|
GGTTGCGCCACTGGTACTGCATTTACCTGCTGAAGAAATCGCCTCTAAACACCTGGCGGATACTGGCGTACTCGGAGGGATTATCTCCGGTGCGATCGCAGCGTACATGTTTAACCGTTTCTACCGTATTAAGCTGCCTGAGTATCTTGGCTTCTTTGCCGGTAAACGCTTTGTGCCGATCATTTCTGGCCTGG > NZ_CP009273/1153609‑1153802
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
